From 852298bd53796037d2f302ffb179347e8362089c Mon Sep 17 00:00:00 2001 From: yelenacox Date: Wed, 3 Jun 2026 10:58:48 -0500 Subject: [PATCH 1/7] test signing From 287fabef3e166bbb81a5b42cb374a8395188b940 Mon Sep 17 00:00:00 2001 From: yelenacox Date: Thu, 4 Jun 2026 14:03:15 -0500 Subject: [PATCH 2/7] Script running dragon_search --- .gitignore | 2 +- pyproject.toml | 3 +- scripts/__init__.py | 0 scripts/expand_enums.py | 110 ++++++++++++++++++++++++++++++++++++++++ 4 files changed, 113 insertions(+), 2 deletions(-) create mode 100644 scripts/__init__.py create mode 100644 scripts/expand_enums.py diff --git a/.gitignore b/.gitignore index 131c4bd..d6fcca5 100644 --- a/.gitignore +++ b/.gitignore @@ -9,7 +9,7 @@ __pycache__/ .direnv # Temp place for script to turn the design into MD -scripts +#scripts # C extensions *.so diff --git a/pyproject.toml b/pyproject.toml index 206fa97..e3df151 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,8 @@ dependencies = [ "requests", "linkml", "PyYAML", - "jinja2"] + "jinja2", + "search-dragon@git+https://github.com/NIH-NCPI/search-dragon.git@yc/fd-3693"] dynamic = ["version"] [project.optional-dependencies] diff --git a/scripts/__init__.py b/scripts/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/scripts/expand_enums.py b/scripts/expand_enums.py new file mode 100644 index 0000000..9b9bc14 --- /dev/null +++ b/scripts/expand_enums.py @@ -0,0 +1,110 @@ +import argparse +import logging +import subprocess +from pathlib import Path + +import yaml + + +class IndentedDumper(yaml.Dumper): + def increase_indent(self, flow=False, indentless=False): + return super().increase_indent(flow=flow, indentless=False) + + +def expand( + local_filepath: Path | None = None, + output_filepath: Path | None = None, + iri: str | None = None, +): + """Extract Enums from a monolithic LinkML model into individual YAML files + Args: + local_filepath: The file containing the monolithic linkml model + model_filepath: The file containing master LinkML model, used to get the id property to reuse for enums + output_filepath: The directory where the enum YAMLs are to be written + Returns: + list of enum names + """ + if output_filepath is None: + output_filepath = Path("output") + + output_filepath.mkdir(parents=True, exist_ok=True) + enum_count = 0 + expanded_count = 0 + for enum_file in local_filepath.glob("Enum*.yaml"): + raw_enum = enum_file.read_text() + parsed = yaml.safe_load(raw_enum) + + enums = parsed.get("enums", {}) + for name, enum in enums.items(): + expanded_enum = output_filepath / f"{name}.yaml" + + if "permissible_values" in (enum) and enum["permissible_values"]: + expanded_enum.write_text(raw_enum) + logging.info(f"Copied {name} (permissible_values already exists)") + enum_count += 1 + expanded_count += 1 + continue + + reachable = enum.get("reachable_from") or {} + source_onto = reachable.get("source_ontology") + if not source_onto: + continue + ontology = source_onto.split(":")[1] + + result = subprocess.run( + [ + "dragon_search", + "-o", + str(ontology), + "-i", + str(iri), + "-f", + str(expanded_enum), + "-d", + ], + capture_output=True, + text=True, + ) + enum_count += 1 + if result.returncode != 0: + logging.error(f"Failed for {name}: {result.stdout}") + logging.error(f"Failed for {name}: {result.stderr}") + else: + expanded_count += 1 + logging.info(f"Expanded enumeration: {name}") + + if expanded_count != enum_count: + logging.error(f"{enum_count - expanded_count} failed to be expanded.") + + +if __name__ == "__main__": + logging.basicConfig(level=logging.INFO) + parser = argparse.ArgumentParser( + description="Expand enums from a monolithic LinkML model" + ) + parser.add_argument( + "-s", + "--source", + required=True, + type=Path, + help="The source file containing the enumerations to be expanded", + ) + parser.add_argument( + "-o", + "--output", + required=False, + type=Path, + help="The directory where expanded output YAML files will be written", + ) + parser.add_argument( + "-i", + "--iri", + required=True, + help="A string value containing the iri for the code", + ) + + args = parser.parse_args() + + enums = expand( + local_filepath=args.source, output_filepath=args.output, iri=args.iri + ) From 109c86ff3f5d097e0d117b7ac7ccccf0738599de Mon Sep 17 00:00:00 2001 From: yelenacox Date: Tue, 9 Jun 2026 14:03:54 -0500 Subject: [PATCH 3/7] Expanding enumerations with dragon-search script --- scripts/expand_enums.py | 101 +++++++++++++++++++++++++++------------- 1 file changed, 69 insertions(+), 32 deletions(-) diff --git a/scripts/expand_enums.py b/scripts/expand_enums.py index 9b9bc14..7e47a87 100644 --- a/scripts/expand_enums.py +++ b/scripts/expand_enums.py @@ -1,4 +1,6 @@ import argparse +import csv +import io import logging import subprocess from pathlib import Path @@ -6,6 +8,25 @@ import yaml +def parsed_csv(csv_text: str) -> dict: + """Parse dragon_search CSV output into permissible_values object for enum yaml file.""" + reader = csv.DictReader(io.StringIO(csv_text)) + permissible_values = {} + for row in reader: + code = row["descendant_code"] + if code.lower() == "no results": + continue + description = row.get("description", "") + if description.startswith("['") and description.endswith("']"): + description = description[2:-2] + permissible_values[code] = { + "text": code, + "description": description, + "title": row.get("display", ""), + } + return permissible_values + + class IndentedDumper(yaml.Dumper): def increase_indent(self, flow=False, indentless=False): return super().increase_indent(flow=flow, indentless=False) @@ -45,33 +66,57 @@ def expand( expanded_count += 1 continue - reachable = enum.get("reachable_from") or {} - source_onto = reachable.get("source_ontology") + reachable_from = enum.get("reachable_from") or {} + source_onto = reachable_from.get("source_ontology") + source_nodes = reachable_from.get("source_nodes") if not source_onto: continue ontology = source_onto.split(":")[1] + if not source_nodes: + continue - result = subprocess.run( - [ - "dragon_search", - "-o", - str(ontology), - "-i", - str(iri), - "-f", - str(expanded_enum), - "-d", - ], - capture_output=True, - text=True, - ) - enum_count += 1 - if result.returncode != 0: - logging.error(f"Failed for {name}: {result.stdout}") - logging.error(f"Failed for {name}: {result.stderr}") - else: - expanded_count += 1 - logging.info(f"Expanded enumeration: {name}") + all_permissible_values = {} + node_failed = False + for node in source_nodes: + result = subprocess.run( + [ + "dragon_search", + "-ak", + str(node), + "-o", + str(ontology), + "-f", + str(expanded_enum), + "-d", + "-s", + "0", + ], + capture_output=True, + text=True, + ) + enum_count += 1 + if result.returncode != 0: + logging.error(f"Failed for {name}: {result.stdout}") + logging.error(f"Failed for {name}: {result.stderr}") + node_failed = True + else: + parsed_nodes = parsed_csv(expanded_enum.read_text()) + all_permissible_values.update(parsed_nodes) + logging.info(f"Expanded enumeration: {name}") + + if all_permissible_values: + parsed["enums"][name]["permissible_values"] = all_permissible_values + expanded_enum.write_text( + yaml.dump( + parsed, + Dumper=IndentedDumper, + default_flow_style=False, + sort_keys=False, + allow_unicode=True, + ) + ) + if not node_failed: + expanded_count += 1 if expanded_count != enum_count: logging.error(f"{enum_count - expanded_count} failed to be expanded.") @@ -96,15 +141,7 @@ def expand( type=Path, help="The directory where expanded output YAML files will be written", ) - parser.add_argument( - "-i", - "--iri", - required=True, - help="A string value containing the iri for the code", - ) args = parser.parse_args() - enums = expand( - local_filepath=args.source, output_filepath=args.output, iri=args.iri - ) + enums = expand(local_filepath=args.source, output_filepath=args.output) From 71b80eaa33fe711cbed6191b5a34b8a9cd5bae19 Mon Sep 17 00:00:00 2001 From: yelenacox Date: Tue, 9 Jun 2026 15:33:21 -0500 Subject: [PATCH 4/7] Removing log statements --- scripts/expand_enums.py | 40 +++++++++++++++++++++++++++------------- 1 file changed, 27 insertions(+), 13 deletions(-) diff --git a/scripts/expand_enums.py b/scripts/expand_enums.py index 7e47a87..323bfb4 100644 --- a/scripts/expand_enums.py +++ b/scripts/expand_enums.py @@ -15,6 +15,7 @@ def parsed_csv(csv_text: str) -> dict: for row in reader: code = row["descendant_code"] if code.lower() == "no results": + print(f"No descendants found for {row['parent_code']}") continue description = row.get("description", "") if description.startswith("['") and description.endswith("']"): @@ -78,19 +79,23 @@ def expand( all_permissible_values = {} node_failed = False for node in source_nodes: + cmd = [ + "dragon_search", + "-ak", + str(node), + "-o", + str(ontology), + "-f", + str(expanded_enum), + "-d", + "-s", + "0", + ] + if iri: + cmd.extend(["-i", str(iri)]) + result = subprocess.run( - [ - "dragon_search", - "-ak", - str(node), - "-o", - str(ontology), - "-f", - str(expanded_enum), - "-d", - "-s", - "0", - ], + cmd, capture_output=True, text=True, ) @@ -141,7 +146,16 @@ def expand( type=Path, help="The directory where expanded output YAML files will be written", ) + parser.add_argument( + "-i", + "--iri", + required=False, + default=None, + help="Optional iri for the parent code to pull descendants.", + ) args = parser.parse_args() - enums = expand(local_filepath=args.source, output_filepath=args.output) + enums = expand( + local_filepath=args.source, output_filepath=args.output, iri=args.iri + ) From 25d4b179601d915a7428866bfb119bd9592ceba5 Mon Sep 17 00:00:00 2001 From: yelenacox Date: Wed, 10 Jun 2026 10:37:29 -0500 Subject: [PATCH 5/7] Initialise git with minimal project --- .copier-answers.yml | 17 + .editorconfig | 18 + .github/dependabot.yml | 13 + .github/workflows/deploy-docs.yaml | 62 + .github/workflows/main.yaml | 55 + .gitignore | 128 +- .pre-commit-config.yaml | 50 + .yamllint.yaml | 19 + CODE_OF_CONDUCT.md | 76 + CONTRIBUTING.md | 121 + LICENSE | 21 + config.public.mk | 29 + config.yaml | 63 + docs/about.md | 3 + docs/elements/.gitkeep | 0 docs/index.md | 5 + docs/js/extra-loader.js | 2 + docs/templates-linkml/README.md | 7 + examples/README.md | 9 + input/cam_imports_model.yaml | 54 + input/common_access_model.yaml | 1332 ++++++ justfile | 295 ++ mkdocs.yml | 78 + output/EnumAssertionProvenance.yaml | 21 + output/EnumAvailabilityStatus.yaml | 15 + output/EnumClinicalDataSourceType.yaml | 23 + output/EnumConsanguinityAssertion.yaml | 23 + output/EnumDataCategory.yaml | 38 + output/EnumDataUseModifier.yaml | 86 + output/EnumDataUsePermission.yaml | 34 + output/EnumEDAMDataTypes.yaml | 3806 +++++++++++++++++ output/EnumEDAMFormats.yaml | 2513 +++++++++++ output/EnumEthnicity.yaml | 19 + output/EnumFamilyType.yaml | 23 + output/EnumFileHashType.yaml | 13 + output/EnumNull.yaml | 10 + output/EnumParticipantLifespanStage.yaml | 20 + output/EnumProgram.yaml | 14 + output/EnumRace.yaml | 50 + output/EnumResearchDomain.yaml | 34 + output/EnumSex.yaml | 19 + output/EnumSpatialQualifiers.yaml | 23 + output/EnumStudyDesign.yaml | 29 + output/EnumSubjectType.yaml | 20 + output/EnumVitalStatus.yaml | 14 + project.justfile | 5 + pyproject.toml | 99 +- source | 1 + src/README.md | 4 + .../EnumAvailabilityStatus.yaml | 16 + .../EnumClinicalDataSourceType.yaml | 29 + .../EnumConsanguinityAssertion.yaml | 26 + src/cam-expanded-enums/EnumDataCategory.yaml | 52 + .../EnumDataUseModifier.yaml | 127 + .../EnumDataUsePermission.yaml | 45 + src/cam-expanded-enums/EnumEDAMDataTypes.yaml | 14 + src/cam-expanded-enums/EnumEDAMFormats.yaml | 14 + src/cam-expanded-enums/EnumEthnicity.yaml | 22 + src/cam-expanded-enums/EnumFamilyType.yaml | 27 + src/cam-expanded-enums/EnumFileHashType.yaml | 15 + src/cam-expanded-enums/EnumLaterality.yaml | 6 + src/cam-expanded-enums/EnumNull.yaml | 10 + .../EnumParticipantLifespanStage.yaml | 23 + src/cam-expanded-enums/EnumProgram.yaml | 16 + src/cam-expanded-enums/EnumRace.yaml | 62 + .../EnumResearchDomain.yaml | 42 + .../EnumSampleCollectionMethod.yaml | 7 + src/cam-expanded-enums/EnumSex.yaml | 22 + src/cam-expanded-enums/EnumSite.yaml | 7 + src/cam-expanded-enums/EnumStudyDesign.yaml | 38 + src/cam-expanded-enums/EnumSubjectType.yaml | 26 + src/cam-expanded-enums/EnumVitalStatus.yaml | 15 + src/cam_expanded_enums/__init__.py | 10 + src/cam_expanded_enums/_version.py | 8 + src/cam_expanded_enums/datamodel/__init__.py | 9 + .../schema/EnumAssertionProvenance.yaml | 21 + .../schema/EnumAvailabilityStatus.yaml | 15 + .../schema/EnumClinicalDataSourceType.yaml | 23 + .../schema/EnumConsanguinityAssertion.yaml | 23 + .../schema/EnumDataCategory.yaml | 38 + .../schema/EnumDataUseModifier.yaml | 86 + .../schema/EnumDataUsePermission.yaml | 34 + .../schema/EnumEDAMDataTypes.yaml | 3806 +++++++++++++++++ .../schema/EnumEDAMFormats.yaml | 2513 +++++++++++ .../schema/EnumEthnicity.yaml | 19 + .../schema/EnumFamilyType.yaml | 23 + .../schema/EnumFileHashType.yaml | 13 + src/cam_expanded_enums/schema/EnumNull.yaml | 10 + .../schema/EnumParticipantLifespanStage.yaml | 20 + .../schema/EnumProgram.yaml | 14 + src/cam_expanded_enums/schema/EnumRace.yaml | 50 + .../schema/EnumResearchDomain.yaml | 34 + src/cam_expanded_enums/schema/EnumSex.yaml | 19 + .../schema/EnumSpatialQualifiers.yaml | 3123 ++++++++++++++ .../schema/EnumStudyDesign.yaml | 29 + .../schema/EnumSubjectType.yaml | 20 + .../schema/EnumVitalStatus.yaml | 14 + src/cam_expanded_enums/schema/README.md | 3 + .../schema/cam-expanded-enums.yaml | 74 + src/tweaver/_version.py | 6 +- tests/__init__.py | 1 + tests/data/README.md | 14 + tests/data/invalid/.gitkeep | 0 tests/data/problem/invalid/.gitkeep | 0 tests/data/problem/valid/.gitkeep | 0 tests/data/valid/.gitkeep | 0 uv.lock | 2927 +++++++++++++ 107 files changed, 22951 insertions(+), 122 deletions(-) create mode 100644 .copier-answers.yml create mode 100644 .editorconfig create mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/deploy-docs.yaml create mode 100644 .github/workflows/main.yaml create mode 100644 .pre-commit-config.yaml create mode 100644 .yamllint.yaml create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.md create mode 100644 LICENSE create mode 100644 config.public.mk create mode 100644 config.yaml create mode 100644 docs/about.md create mode 100644 docs/elements/.gitkeep create mode 100644 docs/index.md create mode 100644 docs/js/extra-loader.js create mode 100644 docs/templates-linkml/README.md create mode 100644 examples/README.md create mode 100644 input/cam_imports_model.yaml create mode 100644 input/common_access_model.yaml create mode 100644 justfile create mode 100644 mkdocs.yml create mode 100644 output/EnumAssertionProvenance.yaml create mode 100644 output/EnumAvailabilityStatus.yaml create mode 100644 output/EnumClinicalDataSourceType.yaml create mode 100644 output/EnumConsanguinityAssertion.yaml create mode 100644 output/EnumDataCategory.yaml create mode 100644 output/EnumDataUseModifier.yaml create mode 100644 output/EnumDataUsePermission.yaml create mode 100644 output/EnumEDAMDataTypes.yaml create mode 100644 output/EnumEDAMFormats.yaml create mode 100644 output/EnumEthnicity.yaml create mode 100644 output/EnumFamilyType.yaml create mode 100644 output/EnumFileHashType.yaml create mode 100644 output/EnumNull.yaml create mode 100644 output/EnumParticipantLifespanStage.yaml create mode 100644 output/EnumProgram.yaml create mode 100644 output/EnumRace.yaml create mode 100644 output/EnumResearchDomain.yaml create mode 100644 output/EnumSex.yaml create mode 100644 output/EnumSpatialQualifiers.yaml create mode 100644 output/EnumStudyDesign.yaml create mode 100644 output/EnumSubjectType.yaml create mode 100644 output/EnumVitalStatus.yaml create mode 100644 project.justfile create mode 120000 source create mode 100644 src/README.md create mode 100644 src/cam-expanded-enums/EnumAvailabilityStatus.yaml create mode 100644 src/cam-expanded-enums/EnumClinicalDataSourceType.yaml create mode 100644 src/cam-expanded-enums/EnumConsanguinityAssertion.yaml create mode 100644 src/cam-expanded-enums/EnumDataCategory.yaml create mode 100644 src/cam-expanded-enums/EnumDataUseModifier.yaml create mode 100644 src/cam-expanded-enums/EnumDataUsePermission.yaml create mode 100644 src/cam-expanded-enums/EnumEDAMDataTypes.yaml create mode 100644 src/cam-expanded-enums/EnumEDAMFormats.yaml create mode 100644 src/cam-expanded-enums/EnumEthnicity.yaml create mode 100644 src/cam-expanded-enums/EnumFamilyType.yaml create mode 100644 src/cam-expanded-enums/EnumFileHashType.yaml create mode 100644 src/cam-expanded-enums/EnumLaterality.yaml create mode 100644 src/cam-expanded-enums/EnumNull.yaml create mode 100644 src/cam-expanded-enums/EnumParticipantLifespanStage.yaml create mode 100644 src/cam-expanded-enums/EnumProgram.yaml create mode 100644 src/cam-expanded-enums/EnumRace.yaml create mode 100644 src/cam-expanded-enums/EnumResearchDomain.yaml create mode 100644 src/cam-expanded-enums/EnumSampleCollectionMethod.yaml create mode 100644 src/cam-expanded-enums/EnumSex.yaml create mode 100644 src/cam-expanded-enums/EnumSite.yaml create mode 100644 src/cam-expanded-enums/EnumStudyDesign.yaml create mode 100644 src/cam-expanded-enums/EnumSubjectType.yaml create mode 100644 src/cam-expanded-enums/EnumVitalStatus.yaml create mode 100644 src/cam_expanded_enums/__init__.py create mode 100644 src/cam_expanded_enums/_version.py create mode 100644 src/cam_expanded_enums/datamodel/__init__.py create mode 100644 src/cam_expanded_enums/schema/EnumAssertionProvenance.yaml create mode 100644 src/cam_expanded_enums/schema/EnumAvailabilityStatus.yaml create mode 100644 src/cam_expanded_enums/schema/EnumClinicalDataSourceType.yaml create mode 100644 src/cam_expanded_enums/schema/EnumConsanguinityAssertion.yaml create mode 100644 src/cam_expanded_enums/schema/EnumDataCategory.yaml create mode 100644 src/cam_expanded_enums/schema/EnumDataUseModifier.yaml create mode 100644 src/cam_expanded_enums/schema/EnumDataUsePermission.yaml create mode 100644 src/cam_expanded_enums/schema/EnumEDAMDataTypes.yaml create mode 100644 src/cam_expanded_enums/schema/EnumEDAMFormats.yaml create mode 100644 src/cam_expanded_enums/schema/EnumEthnicity.yaml create mode 100644 src/cam_expanded_enums/schema/EnumFamilyType.yaml create mode 100644 src/cam_expanded_enums/schema/EnumFileHashType.yaml create mode 100644 src/cam_expanded_enums/schema/EnumNull.yaml create mode 100644 src/cam_expanded_enums/schema/EnumParticipantLifespanStage.yaml create mode 100644 src/cam_expanded_enums/schema/EnumProgram.yaml create mode 100644 src/cam_expanded_enums/schema/EnumRace.yaml create mode 100644 src/cam_expanded_enums/schema/EnumResearchDomain.yaml create mode 100644 src/cam_expanded_enums/schema/EnumSex.yaml create mode 100644 src/cam_expanded_enums/schema/EnumSpatialQualifiers.yaml create mode 100644 src/cam_expanded_enums/schema/EnumStudyDesign.yaml create mode 100644 src/cam_expanded_enums/schema/EnumSubjectType.yaml create mode 100644 src/cam_expanded_enums/schema/EnumVitalStatus.yaml create mode 100644 src/cam_expanded_enums/schema/README.md create mode 100644 src/cam_expanded_enums/schema/cam-expanded-enums.yaml create mode 100644 tests/__init__.py create mode 100644 tests/data/README.md create mode 100644 tests/data/invalid/.gitkeep create mode 100644 tests/data/problem/invalid/.gitkeep create mode 100644 tests/data/problem/valid/.gitkeep create mode 100644 tests/data/valid/.gitkeep create mode 100644 uv.lock diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..64efee3 --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,17 @@ +# Changes here will be overwritten by Copier +_commit: v0.5.0 +_src_path: https://github.com/linkml/linkml-project-copier +add_example: false +copyright_year: '2026' +email: yelena.cox@vumc.org +existing_license_file: '' +full_name: Yelena Cox +gh_action_docs_preview: false +gh_action_pypi: false +github_org: include-dcc +license: MIT +project_description: This project is a LinkML model containing expanded enumerations + from the Common Access Model. +project_name: cam-expanded-enums +project_slug: cam_expanded_enums + diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..bee5e78 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,18 @@ +# Check http://editorconfig.org for more information +# This is the main config file for this project: +root = true + +[*] +charset = utf-8 +end_of_line = lf +insert_final_newline = true +indent_style = space +indent_size = 2 +trim_trailing_whitespace = true + +[*.py] +indent_style = space +indent_size = 4 + +[*.md] +trim_trailing_whitespace = false diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..127295b --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,13 @@ +# Please see the documentation for all configuration options: +# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference + +version: 2 +updates: + - package-ecosystem: github-actions + directory: "/" + schedule: + interval: monthly + groups: + github-actions: + patterns: + - "*" diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml new file mode 100644 index 0000000..fbf11d5 --- /dev/null +++ b/.github/workflows/deploy-docs.yaml @@ -0,0 +1,62 @@ +--- +name: Deploy docs +on: # yamllint disable-line rule:truthy + push: + branches: [main] + workflow_dispatch: + +permissions: {} + +jobs: + build-docs: + runs-on: ubuntu-latest + + strategy: + matrix: + pyversion: ["3.13"] + + # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment + permissions: + contents: write # to let mkdocs write the new docs + pages: write # to deploy to Pages + id-token: write # allow to generate an OpenID Connect (OIDC) token + + steps: + # https://github.com/actions/checkout + - name: Checkout + uses: actions/checkout@v6.0.2 + with: + fetch-depth: 0 # otherwise, you will fail to push refs to dest repo + + - name: Configure git for the bot + # Gives the bot that commits to gh-pages a name & email address + # so that the commits have an author in the commit log. + run: | + git config user.name github-actions[bot] + git config user.email github-actions[bot]@users.noreply.github.com + + # https://github.com/astral-sh/setup-uv + - name: Install uv + uses: astral-sh/setup-uv@v8.1.0 + with: + python-version: ${{ matrix.pyversion }} + enable-cache: true + cache-dependency-glob: "uv.lock" + + # https://github.com/actions/setup-python + - name: Set up Python + uses: actions/setup-python@v6.2.0 + with: + python-version: ${{ matrix.pyversion }} + + - name: Install just + run: | + uv tool install rust-just + + - name: Install dependencies + run: uv sync --group dev --no-progress + + - name: Generate schema documentation + run: | + just gen-doc + uv run mkdocs gh-deploy --force diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml new file mode 100644 index 0000000..349c7d8 --- /dev/null +++ b/.github/workflows/main.yaml @@ -0,0 +1,55 @@ +# Built from: +# https://docs.github.com/en/actions/guides/building-and-testing-python +--- +name: Build and test + +on: # yamllint disable-line rule:truthy + push: + branches: [main] + pull_request: + +env: + FORCE_COLOR: "1" # Make tools pretty. + +permissions: {} + +jobs: + test: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + fail-fast: false + + steps: + + # https://github.com/actions/checkout + - name: Check out repository + uses: actions/checkout@v6.0.2 + with: + persist-credentials: false + + # https://github.com/astral-sh/setup-uv + - name: Install uv + uses: astral-sh/setup-uv@v8.1.0 + with: + python-version: ${{ matrix.python-version }} + enable-cache: true + cache-dependency-glob: "uv.lock" + + # https://github.com/actions/setup-python + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v6.2.0 + with: + python-version: ${{ matrix.python-version }} + + - name: Install just + run: | + uv tool install rust-just + + - name: Install project + run: uv sync --group dev + + - name: Run test suite + run: just test diff --git a/.gitignore b/.gitignore index d6fcca5..421e9a9 100644 --- a/.gitignore +++ b/.gitignore @@ -1,16 +1,18 @@ +# generated part of documentation +/docs/elements/*.md +# linkml-run-examples output (not useful to have in git in its current form) +/examples/output/ + +# Derived schemas, generated from the schema.yaml +tmp/ +project/ +!project/README.md + # Byte-compiled / optimized / DLL files __pycache__/ -*.py[codz] +*.py[cod] *$py.class -# Help with managing local environments -.envrc -.bash_history_local -.direnv - -# Temp place for script to turn the design into MD -#scripts - # C extensions *.so @@ -28,6 +30,7 @@ parts/ sdist/ var/ wheels/ +pip-wheel-metadata/ share/python-wheels/ *.egg-info/ .installed.cfg @@ -35,8 +38,8 @@ share/python-wheels/ MANIFEST # PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. *.manifest *.spec @@ -54,10 +57,9 @@ htmlcov/ nosetests.xml coverage.xml *.cover -*.py.cover +*.py,cover .hypothesis/ .pytest_cache/ -cover/ # Translations *.mo @@ -80,7 +82,6 @@ instance/ docs/_build/ # PyBuilder -.pybuilder/ target/ # Jupyter Notebook @@ -91,73 +92,27 @@ profile_default/ ipython_config.py # pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version +.python-version # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. # However, in case of collaboration, if having platform-specific dependencies or dependencies # having no cross-platform support, pipenv may install dependencies that don't work, or not # install all needed dependencies. -# Pipfile.lock - -# UV -# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# uv.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -# poetry.lock -# poetry.toml - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. -# https://pdm-project.org/en/latest/usage/project/#working-with-version-control -# pdm.lock -# pdm.toml -.pdm-python -.pdm-build/ - -# pixi -# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. -# pixi.lock -# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one -# in the .venv directory. It is recommended not to include this directory in version control. -.pixi - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow __pypackages__/ # Celery stuff celerybeat-schedule celerybeat.pid -# Redis -*.rdb -*.aof -*.pid - -# RabbitMQ -mnesia/ -rabbitmq/ -rabbitmq-data/ - -# ActiveMQ -activemq-data/ - # SageMath parsed files *.sage.py # Environments .env -.envrc .venv env/ venv/ @@ -183,44 +138,7 @@ dmypy.json # Pyre type checker .pyre/ -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -# .idea/ - -# Abstra -# Abstra is an AI-powered process automation framework. -# Ignore directories containing user credentials, local state, and settings. -# Learn more at https://abstra.io/docs -.abstra/ - -# Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore -# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, -# you could uncomment the following to ignore the entire vscode folder -# .vscode/ -# Temporary file for partial code execution -tempCodeRunnerFile.py - -# Ruff stuff: -.ruff_cache/ - -# PyPI configuration file -.pypirc - -# Marimo -marimo/_static/ -marimo/_lsp/ -__marimo__/ - -# Streamlit -.streamlit/secrets.toml +# pycharm +.idea +# Local vscode editor config +.vscode diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..0e6536d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,50 @@ +--- +# https://pre-commit.com/ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 + hooks: + - id: check-toml + - id: check-yaml + # mkdocs.yml uses !!python/name tags unsupported by the safe YAML loader + exclude: ^mkdocs\.yml$ + - id: end-of-file-fixer + exclude: ^\.copier-answers\.yml$ + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + + - repo: https://github.com/adrienverge/yamllint.git + rev: v1.38.0 + hooks: + - id: yamllint + args: [-c=.yamllint.yaml] + exclude: ^\.copier-answers\.yml$ + verbose: true # Show warnings. + + - repo: https://github.com/codespell-project/codespell + rev: v2.4.2 + hooks: + - id: codespell + additional_dependencies: + - tomli + + - repo: https://github.com/crate-ci/typos + rev: v1.46.3 + hooks: + - id: typos + + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.15.14 + hooks: + # Run the linter. + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + # Run the formatter. + - id: ruff-format + + - repo: https://github.com/astral-sh/uv-pre-commit + # uv version. + rev: 0.11.16 + hooks: + - id: uv-lock diff --git a/.yamllint.yaml b/.yamllint.yaml new file mode 100644 index 0000000..7fb4fd5 --- /dev/null +++ b/.yamllint.yaml @@ -0,0 +1,19 @@ +# Configuration for https://github.com/adrienverge/yamllint + +extends: default + +# Specify files to ignore. +ignore: + # Ignore autogenerated file that does not conform to yamllint rules. + - .copier-answers.yml + # Ignore schema files that may not conform due to imports. + - docs/schema/*.yaml + +rules: + document-start: disable # Don't check if document has a start marker (---). + line-length: + max: 88 + level: warning + allow-non-breakable-words: true + allow-non-breakable-inline-mappings: true + new-lines: disable # Don't check for type of new line characters. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..2b301c6 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,76 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to make participation in our project and +our community a harassment-free experience for everyone, regardless of age, +body size, disability, ethnicity, gender identity and expression, level of +experience, nationality, personal appearance, race, religion, or sexual +identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an +appointed representative at an online or offline event. Representation of a +project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by [contacting the project team](contact.md). All complaints will be +reviewed and investigated and will result in a response that is deemed +necessary and appropriate to the circumstances. The project team is obligated +to maintain confidentiality with regard to the reporter of an incident. Further +details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This code of conduct has been derived from the excellent code of conduct of the +[ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md) +which in turn is adapted from the [Contributor Covenant][homepage], version +1.4, available at [https://contributor-covenant.org/version/1/4][version] + +[homepage]: https://contributor-covenant.org +[version]: https://contributor-covenant.org/version/1/4/ diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..57ba47b --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,121 @@ +# Contributing to cam-expanded-enums + +:+1: First of all: Thank you for taking the time to contribute! + +The following is a set of guidelines for contributing to +cam-expanded-enums. These guidelines are not strict rules. +Use your best judgment, and feel free to propose changes to this document +in a pull request. + +## Table Of Contents + +* [Code of Conduct](#code-of-conduct) +* [Guidelines for Contributions and Requests](#contributions) + * [Reporting issues and making requests](#reporting-issues) + * [Questions and Discussion](#questions-and-discussion) + * [Adding new elements yourself](#adding-elements) +* [Best Practices](#best-practices) + * [How to write a great issue](#great-issues) + * [How to create a great pull/merge request](#great-pulls) + + + +## Code of Conduct + +The cam-expanded-enums team strives to create a +welcoming environment for editors, users and other contributors. +Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md). + + + +## Guidelines for Contributions and Requests + + + +### Reporting problems and suggesting changes to with the data model + +Please use our [Issue Tracker][issues] for any of the following: + +- Reporting problems +- Requesting new schema elements + + + +### Questions and Discussions + +Please use our [Discussions forum][discussions] to ask general questions or contribute to discussions. + + + +### Adding new elements yourself + +Please submit a [Pull Request][pulls] to submit a new term for consideration. + + + +## Best Practices + + + +### GitHub Best Practice + +- Creating and curating issues + - Read ["About Issues"][[about-issues]] + - Issues should be focused and actionable + - Complex issues should be broken down into simpler issues where possible +- Pull Requests + - Read ["About Pull Requests"][about-pulls] + - Read [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/) + - Pull Requests (PRs) should be atomic and aim to close a single issue + - Long running PRs should be avoided where possible + - PRs should reference issues following standard conventions (e.g. “fixes #123”) + - Schema developers should always be working on a single issue at any one time + - Never work on the main branch, always work on an issue/feature branch + - Core developers can work on branches off origin rather than forks + - Always create a PR on a branch to maximize transparency of what you are doing + - PRs should be reviewed and merged in a timely fashion by the cam-expanded-enums technical leads + - PRs that do not pass GitHub actions should never be merged + - In the case of git conflicts, the contributor should try and resolve the conflict + - If a PR fails a GitHub action check, the contributor should try and resolve the issue in a timely fashion + +### Understanding LinkML + +Core developers should read the material on the [LinkML site](https://linkml.io/linkml), in particular: + +- [Overview](https://linkml.io/linkml/intro/overview.html) +- [Tutorial](https://linkml.io/linkml/intro/tutorial.html) +- [Schemas](https://linkml.io/linkml/schemas/index.html) +- [FAQ](https://linkml.io/linkml/faq/index.html) + +### Modeling Best Practice + +- Follow Naming conventions + - Standard LinkML naming conventions should be followed (UpperCamelCase for classes and enums, snake_case for slots) + - Know how to use the LinkML linter to check style and conventions + - The names for classes should be nouns or noun-phrases: Person, GenomeAnnotation, Address, Sample + - Spell out abbreviations and short forms, except where this goes against convention (e.g. do not spell out DNA) + - Elements that are imported from outside (e.g. schema.org) need not follow the same naming conventions + - Multivalued slots should be named as plurals +- Document model elements + - All model elements should have documentation (descriptions) and other textual annotations (e.g. comments, notes) + - Textual annotations on classes, slots and enumerations should be written with minimal jargon, clear grammar and no misspellings +- Include examples and counter-examples (intentionally invalid examples) + - Rationale: these serve as documentation and unit tests + - These will be used by the automated test suite + - All elements of the schema must be illustrated with valid and invalid data examples in src/data. New schema elements will not be merged into the main branch until examples are provided + - Invalid example data files should be invalid for one single reason, which should be reflected in the filename. It should be possible to render the invalid example files valid by addressing that single fault. +- Use enums for categorical values + - Rationale: Open-ended string ranges encourage multiple values to represent the same entity, like “water”, “H2O” and “HOH” + - Any slot whose values could be constrained to a finite set should use an Enum + - Non-categorical values, e.g. descriptive fields like `name` or `description` fall outside of this. +- Reuse + - Existing scheme elements should be reused where appropriate, rather than making duplicative elements + - More specific classes can be created by refinining classes using inheritance (`is_a`) + +[about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches +[about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues +[about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests +[issues]: https://github.com/include-dcc/cam-expanded-enums/issues/ +[pulls]: https://github.com/include-dcc/cam-expanded-enums/pulls/ + +We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/) diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..5027887 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2026 Yelena Cox + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff --git a/config.public.mk b/config.public.mk new file mode 100644 index 0000000..2bf9daa --- /dev/null +++ b/config.public.mk @@ -0,0 +1,29 @@ +# config.public.mk + +# This file is public in git. No sensitive info allowed. + +###### schema definition variables, used by justfile + +# Note: +# - just works fine with quoted variables of dot-env files like this one +LINKML_SCHEMA_NAME="cam_expanded_enums" +LINKML_SCHEMA_AUTHOR="Yelena Cox " +LINKML_SCHEMA_DESCRIPTION="This project is a LinkML model containing expanded enumerations from the Common Access Model." +LINKML_SCHEMA_SOURCE_DIR="src/cam_expanded_enums/schema" + +###### linkml generator variables, used by justfile + +## gen-project configuration file +LINKML_GENERATORS_CONFIG_YAML=config.yaml + +## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports) +LINKML_GENERATORS_DOC_ARGS= + +## pass args to workaround genowl rdfs config bug (linkml#1453) +## (i.e. --no-type-objects --no-metaclasses --metadata-profile=rdfs) +# LINKML_GENERATORS_OWL_ARGS="--no-type-objects --no-metaclasses --metadata-profile=rdfs" +LINKML_GENERATORS_OWL_ARGS= + +## pass args to pydantic generator which isn't supported by gen-project +## https://github.com/linkml/linkml/issues/2537 +LINKML_GENERATORS_PYDANTIC_ARGS= diff --git a/config.yaml b/config.yaml new file mode 100644 index 0000000..e945783 --- /dev/null +++ b/config.yaml @@ -0,0 +1,63 @@ +# Configuration of generators (defaults illustrated) +--- +# The directory where the generated files are stored +# directory: "tmp" + +# By default all generators are run. Specify here the ones to skip. +excludes: + - markdown + +# Alternatively only specify the generators to run +# (comment out the above "excludes" section) +# includes: +# - markdown +# - excel + +# Set the arguments for the generators (no matter if they run or not) +generator_args: + excel: + mergeimports: true + owl: + mergeimports: true + metaclasses: false + type_objects: false + add_root_classes: true + mixins_as_expressions: true + markdown: + mergeimports: true + directory: "docs/elements" + graphql: + mergeimports: true + # gen-java is not yet supported by gen-project. + # https://github.com/linkml/linkml/issues/2537 + # java: + # mergeimports: true + # metadata: true + jsonld: + mergeimports: true + jsonschema: + mergeimports: true + jsonldcontext: + mergeimports: true + # gen-pydantic is not yet supported by gen-project. + # https://github.com/linkml/linkml/issues/2537 + # pydantic: + # mergeimports: true + python: + mergeimports: true + # head: true # Why does this not work? + prefixmap: + mergeimports: true + proto: + mergeimports: true + shacl: + mergeimports: true + shex: + mergeimports: true + sqlddl: + mergeimports: true + typescript: + mergeimports: true + metadata: true + +... diff --git a/docs/about.md b/docs/about.md new file mode 100644 index 0000000..472932d --- /dev/null +++ b/docs/about.md @@ -0,0 +1,3 @@ +# About cam-expanded-enums + +This project is a LinkML model containing expanded enumerations from the Common Access Model. diff --git a/docs/elements/.gitkeep b/docs/elements/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..a446eb8 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,5 @@ +# cam-expanded-enums + +This project is a LinkML model containing expanded enumerations from the Common Access Model. + +- Auto-generated [schema documentation](elements/index.md) diff --git a/docs/js/extra-loader.js b/docs/js/extra-loader.js new file mode 100644 index 0000000..b095c53 --- /dev/null +++ b/docs/js/extra-loader.js @@ -0,0 +1,2 @@ +// See https://facelessuser.github.io/pymdown-extensions/extras/mermaid/#custom-loader +// And https://github.com/facelessuser/pymdown-extensions/blob/main/docs/src/js/material-extra-3rdparty.js diff --git a/docs/templates-linkml/README.md b/docs/templates-linkml/README.md new file mode 100644 index 0000000..91ce079 --- /dev/null +++ b/docs/templates-linkml/README.md @@ -0,0 +1,7 @@ +# Templates for the LinkML documentation generator + +Use this folder to store templates to customize the generated model documentation. +The templates are written in Jinja2 and are used to generate the HTML documentation for the schema. + +The default templates are available in the [linkml repository](https://github.com/linkml/linkml/tree/main/packages/linkml/src/linkml/generators/docgen/). +If you want to use these as a starting point, you can copy them into this folder and modify them as needed. diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000..88d6329 --- /dev/null +++ b/examples/README.md @@ -0,0 +1,9 @@ +# Examples of using cam-expanded-enums + +This folder contains examples using the datamodel. + +The source of the data used in the example is [tests/data](../tests/data/). + +The command `just test` creates different representations of the data in [tests/data](../tests/data/) and writes them to the subfolder `output`. +It also generates a markdown documentation of the examples which is not very useful in its current form. +Hence, the `output` sub-folder is git-ignored. diff --git a/input/cam_imports_model.yaml b/input/cam_imports_model.yaml new file mode 100644 index 0000000..6c5d12d --- /dev/null +++ b/input/cam_imports_model.yaml @@ -0,0 +1,54 @@ +default_prefix: cam +default_range: string +description: LinkML Schema for the Common Access Model +id: https://includedcc.org/common-access-model +imports: +- linkml:types +- EnumDataUsePermission +- EnumDataUseModifier +- EnumProgram +- EnumResearchDomain +- EnumParticipantLifespanStage +- EnumStudyDesign +- EnumClinicalDataSourceType +- EnumDataCategory +- EnumSubjectType +- EnumSex +- EnumRace +- EnumEthnicity +- EnumVitalStatus +- EnumNull +- EnumFamilyType +- EnumConsanguinityAssertion +- EnumAssertionProvenance +- EnumAvailabilityStatus +- EnumSampleCollectionMethod +- EnumSite +- EnumSpatialQualifiers +- EnumLaterality +- EnumEDAMFormats +- EnumEDAMDataTypes +- EnumFileHashType +license: MIT +name: common-access-model +prefixes: + DUO: http://purl.obolibrary.org/obo/DUO_ + HP: http://purl.obolibrary.org/obo/HP_ + MONDO: http://purl.obolibrary.org/obo/MONDO_ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + PATO: http://purl.obolibrary.org/obo/PATO_ + cam: https://includedcc.org/common-access-model/ + cdc_race_eth: urn:oid:2.16.840.1.113883.6.238/ + hl7_null: http://terminology.hl7.org/CodeSystem/v3-NullFlavor/ + ig2_biospecimen_availability: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/ + ig2dac: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/ + ig2dat: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/ + ig_dob_method: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/ + igcondtype: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/ + linkml: https://w3id.org/linkml/ + mesh: http://id.nlm.nih.gov/mesh/ + schema: http://schema.org/ + snomed_ct: http://snomed.info/id/ +see_also: +- https://includedcc.github.io/common-access-model +title: Common Access Model diff --git a/input/common_access_model.yaml b/input/common_access_model.yaml new file mode 100644 index 0000000..7819155 --- /dev/null +++ b/input/common_access_model.yaml @@ -0,0 +1,1332 @@ +--- +id: https://includedcc.org/common-access-model +name: common-access-model +title: Common Access Model +description: LinkML Schema for the Common Access Model +license: MIT +see_also: + - https://includedcc.github.io/common-access-model + +prefixes: + cam: https://includedcc.org/common-access-model/ + linkml: https://w3id.org/linkml/ + schema: http://schema.org/ + # subset of CDC Race and Ethnicity Code Set Version 1.0 + cdc_race_eth: urn:oid:2.16.840.1.113883.6.238/ + hl7_null: http://terminology.hl7.org/CodeSystem/v3-NullFlavor/ + ig_dob_method: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/ + igcondtype: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/ + ig2dac: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/ + ig2dat: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/ + ig2_biospecimen_availability: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/ + snomed_ct: http://snomed.info/id/ + MONDO: http://purl.obolibrary.org/obo/MONDO_ + HP: http://purl.obolibrary.org/obo/HP_ + mesh: http://id.nlm.nih.gov/mesh/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + PATO: http://purl.obolibrary.org/obo/PATO_ + DUO: http://purl.obolibrary.org/obo/DUO_ + +default_prefix: cam +default_range: string + +imports: + - linkml:types + +classes: + Record: + description: One row / entity within the database + title: Record + abstract: true + slots: + - external_id + - access_policy_id + - study_id + AccessPolicy: + title: Access Policy + description: The access policy that describes the controls around use of data + slots: + - access_policy_id + - data_use_accession + - data_use_permission + - data_use_modifier + - disease_limitation + - access_description + - website + slot_usage: + access_policy_id: + range: string + required: true + identifier: true + Study: + title: Research Study + description: Study Metadata + is_a: Record + slots: + #TODO: Split out core Study items and additional study metadata? + #- study_id Inherits study_id from Record now. + - parent_study + - study_title + - study_code + - study_short_name + - program + - funding_source + - principal_investigator + - contact + - study_description + - website + # - dbgap : Should we call this out specifically or just use an external id? + - publication + - acknowledgments + - citation_statement + - do_id + slot_usage: + study_id: + range: string + required: true + identifier: true + StudyMetadata: + title: Study Metadata + description: Additional features about studies that may not apply to all studies + is_a: Record + slots: + - study_id + - participant_lifespan_stage + - selection_criteria + - study_design + - clinical_data_source_type + - data_category + - vbr_id + - research_domain + - expected_number_of_participants + - actual_number_of_participants + # Do we need this info, or should it be documented elsewhere? + #- guidType + #- guidMapped + slot_usage: + study_id: + required: true + identifier: true + data_category: + required: true + multivalued: true + + VirtualBiorepository: + title: Virtual BioRepository (VBR) + description: An organization that can provide access to specimen for further analysis. + is_a: Record + slots: + - vbr_id + - name + - institution + - contact + - website + - vbr_readme + slot_usage: + vbr_id: + range: string + required: true + identifier: true + + DOI: + title: Digital Object Identifier (DOI) + description: A DOI is a permanent reference with metadata about a digital object. + is_a: Record + slots: + - do_id + - bibliographic_reference + slot_usage: + do_id: + range: string + required: true + identifier: true + Investigator: + title: Investigator + description: An individual who made contributions to the collection, analysis, or sharing of data. + is_a: Record + slots: + - name + - institution + # - orcid : Should we call this out specifically or just use an external id? + - investigator_title + - email + Publication: + title: Publication + description: Information about a specific publication. + is_a: Record + #Could add more here + slots: + - bibliographic_reference + - website + Subject: + title: Subject + description: + This entity is the subject about which data or references are recorded. + This includes the idea of a human participant in a study, a cell line, an animal model, + or any other similar entity. + is_a: Record + slots: + - subject_id + - subject_type + - organism_type + slot_usage: + subject_id: + range: string + required: true + identifier: true + Demographics: + title: Demographics + description: Basic participant demographics summary + is_a: Record + slots: + - subject_id + - sex + - race + - ethnicity + - age_at_last_vital_status + - vital_status + - age_at_first_engagement + slot_usage: + subject_id: + required: true + identifier: true + Family: + title: Family + description: A group of individuals of some relation who are grouped together in a study. + is_a: Record + slots: + - family_id + - family_type + - family_description + - consanguinity + - family_study_focus + slot_usage: + family_id: + range: string + required: true + identifier: true + FamilyRelationship: + title: Family Member Relationship + description: A relationship between two Subjects. Directed as follows + + + is_a: Record + slots: + - family_relationship_id + - family_member_id + - relationship + - subject_id + slot_usage: + family_relationship_id: + range: string + required: true + identifier: true + subject_id: + required: true + description: The family member Subject who is the relationship "object". + FamilyMember: + title: Family Member + description: Designates a Subject as a member of a family with a specified role. + is_a: Record + slots: + - family_id + - subject_id + - family_role + unique_keys: + main: + description: Family membership is defined by family and subject ids. + unique_key_slots: + - family_id + - subject_id + slot_usage: + family_id: + required: true + subject_id: + required: true + SubjectAssertion: + title: Subject Assertion + description: Assertion about a particular Subject. May include Conditions, Measurements, etc. + is_a: Record + slots: + - assertion_id + - subject_id + - encounter_id + - assertion_provenance + - age_at_assertion + - age_at_event + - age_at_resolution + - concept + - concept_source + - value_concept + - value_number + - value_source + - value_unit + - value_unit_source + slot_usage: + assertion_id: + range: string + required: true + identifier: true + Concept: + title: Concept + description: A standardized concept with display information. + slots: + - concept_curie + - display + slot_usage: + concept_curie: + required: true + identifier: true + Sample: + title: Sample + description: A functionally equivalent specimen taken from a participant or processed from such a sample. + is_a: Record + slots: + - sample_id + - biospecimen_collection_id + - parent_sample_id + - sample_type + - processing + - availablity_status + - storage_method + - quantity_number + - quantity_unit + slot_usage: + sample_id: + range: string + required: true + identifier: true + biospecimen_collection_id: + description: Biospecimen Collection during which this sample was generated. + BiospecimenCollection: + title: BiospecimenCollection + description: A biospecimen collection event which yields one or more Samples. + is_a: Record + slots: + - biospecimen_collection_id + - age_at_collection + - method + - site + - spatial_qualifier + - laterality + - encounter_id + slot_usage: + biospecimen_collection_id: + range: string + required: true + identifier: true + Aliquot: + title: Aliquot + description: A specific tube or amount of a biospecimen associated with a Sample. + is_a: Record + slots: + - aliquot_id + - sample_id + - availablity_status + - quantity_number + - quantity_unit + - concentration_number + - concentration_unit + slot_usage: + aliquot_id: + range: string + required: true + identifier: true + Encounter: + title: Participant Encounter + description: An event at which data was collected about a participant, + an intervention was made, or information about a participant was recorded. + is_a: Record + slots: + - encounter_id + - subject_id + #TODO: Should this alternatively be an "encounter type", ie, to not require a full definition? + - encounter_definition_id + - age_at_event + slot_usage: + encounter_id: + range: string + required: true + identifier: true + EncounterDefinition: + title: Encounter Definition + description: A definition of an encounter type in this study, ie, + an event at which data was collected about a participant, + an intervention was made, or information about a participant was recorded. + This may be something planned by a study or a type of data collection. + #TODO: These are metadata and may not need the same Record basis. + is_a: Record + slots: + - encounter_definition_id + - name + - description + - activity_definition_id + slot_usage: + encounter_definition_id: + range: string + required: true + identifier: true + activity_definition_id: + multivalued: true + ActivityDefinition: + title: Activity Definition + description: A definition of an activity in this study, eg, + a biospecimen collection, intervention, survey, or assessment. + #TODO: These are metadata and may not need the same Record basis. + is_a: Record + slots: + - activity_definition_id + - name + - description + #TODO: Probably want an "expected data generated" slot, eg, + #observation definitions or dd refs + slot_usage: + activity_definition_id: + range: string + required: true + identifier: true + File: + title: File + description: File + is_a: Record + slots: + - file_id + - subject_id + - sample_id + - filename + - format + - data_category + - data_type + - format + - size + #TODO: I'm not convinced this is the right strategy- access model vs operations + - staging_url + - release_url + - drs_uri + - hash + slot_usage: + file_id: + range: string + required: true + identifier: true + subject_id: + multivalued: true + sample_id: + multivalued: true + FileHash: + title: File Hash + description: Type and value of a file content hash. + slots: + - hash_type + - hash_value + Dataset: + title: Dataset + description: Set of files grouped together for release. + slots: + - dataset_id + - name + - description + - do_id + - file_id + - publication + #TODO: Are these good elements for the core entity? + - data_collection_start + - data_collection_end + + slot_usage: + dataset_id: + range: string + required: true + identifier: true + file_id: + multivalued: true + description: The list of files comprising this dataset. + +slots: + study_id: + title: Study ID + description: INCLUDE Global ID for the study + range: Study + multivalued: false + access_policy_id: + title: Access Policy ID + description: Global identifier for the access policy that applies to + this row of data. + range: AccessPolicy + data_use_accession: + title: Data Use Accession + description: Accession used to provision access to the record, eg, + a dbGaP phsID. + range: uriorcurie + data_use_permission: + title: Data Use Permission + description: Broad category of restrictions on data use. + range: EnumDataUsePermission + required: true + data_use_modifier: + title: Data Use Modifier + description: Additional modifiers that limit data use. + range: EnumDataUseModifier + disease_limitation: + title: Data Use Disease Limitation + description: If the access is limited to a specific disease purpose, + it is specified here. + range: string + access_description: + title: Access Description + description: Any additional information to support access requests. + range: string + do_id: + title: DOI + description: Digital Object Identifier (DOI) for this Record. + range: DOI + multivalued: false + subject_id: + title: Study ID + description: INCLUDE Global ID for the Subject + range: Subject + multivalued: false + assertion_id: + title: Assertion ID + description: INCLUDE Global ID for the Assertion + range: SubjectAssertion + multivalued: false + external_id: + title: External Identifiers + description: Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP + required: false + range: uriorcurie + multivalued: true + parent_study: + title: Parent Study + description: The parent study for this study, if it is a nested study. + required: false + range: Study + multivalued: false + funding_source: + title: Funding Source + description: The funding source(s) of the study. + required: false + range: string + multivalued: true + principal_investigator: + title: Principal Investigator + description: The Principal Investigator(s) responsible for the study. + required: true + range: Investigator + multivalued: true + study_title: + description: Full Study Title + required: true + range: string + multivalued: false + study_code: + description: Unique identifier for the study (generally a short acronym) + title: Study Code + range: string + required: true + study_short_name: + title: Study Code + description: Short name for the study + range: string + required: false + investigator_title: + title: Investigator Title + description: The title of the Investigator, eg, "Assistant Professor" + range: string + required: false + name: + title: Name + description: Name of the entity. + range: string + required: false + email: + title: Email Address + description: An email address to reach the entity. + range: string + required: false + institution: + title: Institution + description: Name of the institution this record is associated with. + range: string + required: false + program: + title: Program + description: Funding source(s) for the study + range: EnumProgram + required: true + multivalued: true + study_description: + title: Study Description + description: Brief description of the study (2-4 sentences) + range: string + required: true + website: + title: Website + description: Website with more information about this entity. + range: uri + contact: + title: Contact Person + description: The individual to contact with questions about this record. + required: true + range: Investigator + multivalued: true + vbr_id: + title: Virtual Biorepository + description: Information about the study's Virtual Biorepository, if participating + range: VirtualBiorepository + vbr_readme: + title: VBR Readme + description: Instructions for contacting or requesting samples from Virtual Biorepository, if participating + range: string + research_domain: + description: Main research domain(s) of the study, other than Down syndrome + range: EnumResearchDomain + required: true + multivalued: true + participant_lifespan_stage: + title: Participant Lifespan Stage + description: Focus age group(s) of the study population + range: EnumParticipantLifespanStage + required: true + multivalued: true + selection_criteria: + title: Selection Criteria + description: Brief description of inclusion and/or exclusion criteria for the study + range: string + study_design: + title: Study Design + description: Overall design of study, including whether it is longitudinal and whether family members/unrelated controls are also enrolled + range: EnumStudyDesign + required: true + multivalued: true + data_category: + title: Data Category + description: General category of data in this Record (e.g. Clinical, Genomics, etc) + range: EnumDataCategory + clinical_data_source_type: + title: Clinical Data Source Type + description: Source(s) of data collected from study participants + range: EnumClinicalDataSourceType + required: true + multivalued: true + publication: + title: Publication + description: Publications associated with this Record. + range: Publication + multivalued: true + expected_number_of_participants: + title: Expected Number of Participants + description: Total expected number of participants to be recruited. + range: integer + required: true + actual_number_of_participants: + title: Actual Number of Participants + description: Total participants included at this time. + range: integer + required: true + acknowledgments: + title: Acknowledgments + description: Funding statement and acknowledgments for this study + range: string + citation_statement: + title: Citation Statement + description: + Statement that secondary data users should use to acknowledge use of this study or dataset. E.g., + "The results analyzed and here are based in whole or in part upon data generated by the INCLUDE + (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project , and were accessed from the INCLUDE Data Hub and ." + range: string + bibliographic_reference: + title: Bibiliographic Reference + description: Text use to reference this Record. + range: string + organism_type: + title: Organism Type + description: Organism Type, typically from NCBITaxon. For reference, Human is NCBITaxon:9606. + range: uriorcurie + subject_type: + title: Subject Type + description: Type of entity this record represents + required: true + range: EnumSubjectType + sex: + title: Sex + description: Sex of Participant + range: EnumSex + required: true + race: + title: Race + description: Race of Participant + range: EnumRace + required: true + multivalued: true + ethnicity: + title: Ethnicity + description: Ethnicity of Participant + range: EnumEthnicity + required: true + age_at_first_engagement: + #Should this just be a reference out to an encounter? + title: Age at First Participant Engagement + description: + Age in days of Participant at first recorded study event (enrollment, visit, observation, + sample collection, survey completion, etc.). Age at enrollment is preferred, if available. + range: integer + unit: + ucum_code: d + #Range -1 year to 89*365.25 (Privacy upper bound for ages over 89 years) + minimum_value: -365 + maximum_value: 32507 + vital_status: + title: Vital Status + description: Whether participant is alive or dead + range: EnumVitalStatus + age_at_last_vital_status: + title: Age at Last Vital Status + description: Age in days when participant's vital status was last recorded + range: integer + unit: + ucum_code: d + minimum_value: -365 + maximum_value: 32507 + family_id: + title: Family ID + description: Global ID for the Family + range: Family + family_type: + description: Describes the 'type' of study family, eg, trio. + range: EnumFamilyType + family_description: + description: Free text describing the study family, such as potential + inheritance or details about consanguinity + range: string + consanguinity: + description: Is there known or suspected consanguinity in this study family? + range: EnumConsanguinityAssertion + family_study_focus: + description: The specific focus of the investigation, eg, a condition. + range: uriorcurie + family_relationship_id: + title: Family Relationship ID + description: Global ID for the Family Relationship + range: FamilyRelationship + family_member_id: + description: The family member Subject who is the relationship "subject". + required: true + range: Subject + inlined: false + relationship: + description: + Code definting the relationship predicate. Relationship of the "Family Member" + to the "Subject", eg, mother of. + required: true + range: uriorcurie + family_role: + description: The "role" of this individual in this family. Could include terms like "proband", "mother", etc. + range: uriorcurie + assertion_provenance: + title: Assertion Provenance + description: The original source of this assertion + range: EnumAssertionProvenance + age_at_assertion: + title: Age at assertion + description: The age in days of the Subject when the assertion was made. + range: integer + unit: + ucum_code: d + age_at_event: + title: Age at event + description: + The age in days of the Subject at the time point which the assertion describes, + eg, age of onset or when a measurement was performed. + range: integer + unit: + ucum_code: d + age_at_resolution: + title: Age at resolution + description: The age in days of the Subject when the asserted state was resolved. + range: integer + unit: + ucum_code: d + concept: + title: Concept + description: The structured term defining the meaning of the assertion. + range: Concept + multivalued: true + concept_curie: + title: Concept Curie + description: The standardized curie for the term. + range: uriorcurie + display: + title: Display String + description: The friendly display string of the coded term. + range: string + concept_source: + title: Concept Source Text + description: The source text yielding the standardized concept. + range: string + value_concept: + title: Value concept + description: The structured term defining the value of the assertion. + range: Concept + multivalued: true + value_number: + title: Value Number + description: The numeric value of the assertion. + range: float + value_source: + title: Value Source Text + description: The source text yielding the value. + range: string + value_unit: + title: Value Units + description: The structured term defining the units of the value. + range: Concept + value_unit_source: + title: Value Units Source Text + description: The source text yielding the value's units. + range: string + sample_id: + title: Sample ID + description: The unique identifier for this Sample. + range: Sample + parent_sample_id: + title: Parent Sample ID + description: Sample from which this sample is derived + range: Sample + inlined: false + biospecimen_collection_id: + title: Biospecimen Collection ID + description: Unique identifier for this Biospecimen Collection. + range: BiospecimenCollection + aliquot_id: + title: Aliquot ID + description: Unique identifier for an Aliquot. + range: Aliquot + sample_type: + title: Sample Type + description: Type of material of which this Sample is comprised. UBERON is recommended. + required: true + range: uriorcurie + processing: + title: Sample Processing + description: + Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded + this distinct sample. OBI is recommended. + range: uriorcurie + multivalued: true + availablity_status: + title: Sample Availability + description: Can this Sample be requested for further analysis? + range: EnumAvailabilityStatus + storage_method: + title: Sample Storage Method + description: Sample storage method, eg, Frozen or with additives. OBI may be suitable, or ChEBI for additives. + range: uriorcurie + multivalued: true + quantity_number: + title: Quantity + description: The total quantity of the specimen + range: float + quantity_unit: + title: Quantity Units + description: The structured term defining the units of the quantity. + range: Concept + concentration_number: + title: Concentration + description: What is the concentration of the analyte in the Aliquot? + range: float + concentration_unit: + title: Concentration Units + description: Units associated with the concentration of the analyte in the Aliquot. + range: Concept + age_at_collection: + title: Age at Biospecimen Collection + description: The age at which this biospecimen was collected in decimal years. + range: float + unit: + ucum_code: a + method: + title: Biospecimen Collection Method + description: The approach used to collect the biospecimen. + range: EnumSampleCollectionMethod + site: + title: Biospecimen Collection Site + description: The location of the specimen collection. + range: EnumSite + spatial_qualifier: + title: Spatial Qualifier + description: Qualifier that further refine the specific location of biospecimen collection + range: EnumSpatialQualifiers + laterality: + title: Location Laterality + description: Laterality that further refine the specific location of biospecimen collection + range: EnumLaterality + encounter_id: + title: Encounter ID + description: Unique identifier for this Encounter. + range: Encounter + description: + title: Description + description: Description for this entity. + range: string + encounter_definition_id: + title: Encounter Definition ID + description: Unique identifier for this Encounter Definition. + range: EncounterDefinition + activity_definition_id: + title: Activity Definition ID + description: Unique identifier for this Activity Definition. + range: ActivityDefinition + file_id: + title: File ID + description: Unique identifier for this File. + range: File + filename: + title: Filename + description: The name of the file. + range: string + format: + title: File Format + description: The format of the file. + range: EnumEDAMFormats + data_type: + title: Data Type + description: The type of data within this file. + range: EnumEDAMDataTypes + size: + title: File Size + description: Size of the file, in Bytes. + range: integer + unit: + ucum_code: By + staging_url: + title: Staging Location + description: URL for internal access to the data. May be temporary. + range: uriorcurie + release_url: + title: Release Location + description: URL for controlled or open access to the data. + range: uriorcurie + drs_uri: + title: DRS URI + description: DRS location to access the data. + range: uriorcurie + hash: + title: File Hash + description: File hash information + range: FileHash + hash_type: + title: File Hash Type + description: The type of file hash, eg, md5 + range: EnumFileHashType + hash_value: + title: File Hash Value + description: The value of the file hash + range: string + dataset_id: + title: Dataset ID + description: Unique identifier for a Dataset. + range: Dataset + data_collection_start: + title: Data Collection Start + description: The date that data collection started. May include only a year. + #TODO: We could re-evaluate these as dates, but that may be too implementation specific + range: string + data_collection_end: + title: Data Collection End + description: The date that data collection started. May include only a year. + #TODO: We could re-evaluate these as dates, but that may be too implementation specific + range: string + +enums: + EnumDataUsePermission: + title: Data Use Permission + description: + Data Use Ontology (DUO) terms for data use permissions. + #Do we need a "registered tier" item? + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000001 + is_direct: false + relationship_types: + - rdfs:subClassOf + EnumDataUseModifier: + title: Data Use Modifier + description: Data Use Ontology (DUO) terms for data use modifiers. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000017 + is_direct: false + relationship_types: + - rdfs:subClassOf + EnumProgram: + title: Funding Programs + description: Funding programs relevant to inform operations. + permissible_values: + include: + title: INCLUDE + kf: + title: KF + other: + title: Other + EnumResearchDomain: + title: Research Domain + description: Domains of Research used to find studies. + #TODO: replace/add NIH internal categories from Huiqing + permissible_values: + behavior_and_behavior_mechanisms: + title: Behavior and Behavior Mechanisms + meaning: mesh:D001520 + congenital_heart_defects: + title: Congenital Heart Defects + meaning: mesh:D006330 + immune_system_diseases: + title: Immune System Diseases + meaning: mesh:D007154 + hematologic_diseases: + title: Hematologic Diseases + meaning: mesh:D006402 + neurodevelopment: + title: Neurodevelopment + meaning: mesh:D065886 + sleep_wake_disorders: + title: Sleep Wake Disorders + meaning: mesh:D012893 + all_co_occurring_conditions: + title: All Co-occurring Conditions + meaning: mesh:D013568 + physical_fitness: + title: Physical Fitness + meaning: mesh:D010809 + other: + title: Other + EnumParticipantLifespanStage: + title: Participant Lifespan Stage + description: Stages of life during which participants may be recruited. + permissible_values: + fetal: + title: Fetal + description: Before birth + neonatal: + title: Neonatal + description: 0-28 days old + pediatric: + title: Pediatric + description: Birth-17 years old + adult: + title: Adult + description: 18+ years old + EnumStudyDesign: + title: Study Design + description: Approaches for collecting data, investigating interventions, and/or analyzing data. + #TODO: Add meanings + permissible_values: + case_control: + title: Case-Control + case_set: + title: Case Set + control_set: + title: Control Set + clinical_trial: + title: Clinical Trial + cross_sectional: + title: Cross-Sectional + family_twins_trios: + title: Family/Twins/Trios + interventional: + title: Interventional + longitudinal: + title: Longitudinal + trial_readiness_study: + title: Trial Readiness Study + tumor_vs_matched_normal: + title: Tumor vs Matched Normal + EnumClinicalDataSourceType: + title: Clinical Data Source Type + description: Approaches to ascertain clinical information about a participant. + #TODO: Add meanings + permissible_values: + medical_record: + title: Medical Record + description: Data obtained directly from medical record + investigator_assessment: + title: Investigator Assessment + description: Data obtained by examination, interview, etc. with investigator + participant_or_caregiver_report: + title: Participant or Caregiver Report + description: Data obtained from survey, questionnaire, etc. filled out by participant or caregiver + other: + title: Other + description: Data obtained from other source, such as tissue bank + unknown: + title: Unknown + EnumDataCategory: + title: Data Category + description: Categories of data which may be collected about participants. + #TODO: Add meanings + permissible_values: + #Should we have these two demo/clinical data categories? + unharmonized_demographic_clinical_data: + title: Unharmonized Demographic/Clinical Data + harmonized_demographic_clinical_data: + title: Harmonized Demographic/Clinical Data + genomics: + title: Genomics + transcriptomics: + title: Transcriptomics + epigenomics: + title: Epigenomics + proteomics: + title: Proteomics + metabolomics: + title: Metabolomics + cognitive_behavioral: + title: Cognitive/Behavioral + immune_profiling: + title: Immune Profiling + imaging: + title: Imaging + microbiome: + title: Microbiome + #What is the difference between these two? + fitness: + title: Fitness + physical_activity: + title: Physical Activity + other: + title: Other + sleep_study: + title: Sleep Study + EnumSubjectType: + description: Types of Subject entities + permissible_values: + participant: + description: Study participant with consent, assent, or waiver of consent. + non_participant: + description: + An individual associated with a study who was not explictly consented, eg, the subject + of a reported family history. + cell_line: + description: Cell Line + animal_model: + description: Animal model + group: + description: A group of individuals or entities. + other: + description: A different entity type- ideally this will be resolved! + EnumSex: + description: Subject Sex + permissible_values: + female: + title: Female + meaning: NCIT:C16576 + male: + title: Male + meaning: NCIT:C20197 + other: + title: Other + meaning: NCIT:C17649 + unknown: + title: Unknown + meaning: NCIT:C17998 + EnumRace: + description: Participant Race + permissible_values: + american_indian_or_alaska_native: + title: American Indian or Alaska Native + meaning: NCIT:C41259 + asian: + title: Asian + meaning: NCIT:C41260 + black_or_african_american: + title: Black or African American + meaning: NCIT:C16352 + more_than_one_race: + title: More than one race + meaning: NCIT:C67109 + native_hawaiian_or_other_pacific_islander: + title: Native Hawaiian or Other Pacific Islander + meaning: NCIT:C41219 + other: + title: Other + meaning: NCIT:C17649 + white: + title: White + meaning: NCIT:C41261 + prefer_not_to_answer: + title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + title: Unknown + meaning: NCIT:C17998 + east_asian: + title: East Asian + description: UK only; do not use for US data + meaning: NCIT:C161419 + latin_american: + title: Latin American + description: UK only; do not use for US data + meaning: NCIT:C126531 + middle_eastern_or_north_african: + title: Middle Eastern or North African + description: UK only; do not use for US data + meaning: NCIT:C43866 + south_asian: + title: South Asian + description: UK only; do not use for US data + meaning: NCIT:C41263 + EnumEthnicity: + description: Participant ethnicity, specific to Hispanic or Latino. + permissible_values: + # asked_but_unknown: + # text: asked_but_unknown + # title: Asked but unknown + hispanic_or_latino: + title: Hispanic or Latino + meaning: NCIT:C17459 + not_hispanic_or_latino: + title: Not Hispanic or Latino + meaning: NCIT:C41222 + #This should likely be rolled into a null flavor + prefer_not_to_answer: + title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + title: Unknown + meaning: NCIT:C17998 + EnumVitalStatus: + description: Descriptions of a Subject's vital status + is_a: EnumNull + permissible_values: + dead: + title: Dead + meaning: NCIT:C28554 + alive: + title: Alive + meaning: NCIT:C37987 + EnumNull: + description: Base enumeration providing null options. + permissible_values: + unknown: + title: Unknown + meaning: NCIT:C17998 + EnumFamilyType: + description: Enumerations describing research family type + is_a: EnumNull + permissible_values: + control_only: + title: Control-only + description: Control Only + duo: + title: Duo + description: Duo + proband_only: + title: Proband-only + description: Proband Only + trio: + title: Trio + description: Trio (2 parents and affected child) + trio_plus: + title: Trio+ + description: 2 Parents and 2 or more children + EnumConsanguinityAssertion: + description: Asserts known or suspected consanguinity in this study family + permissible_values: + not_suspected: + title: not-suspected + description: Not suspected + meaning: snomed_ct:428263003 + suspected: + title: suspected + description: Suspected + meaning: snomed_ct:415684004 + known_present: + title: known-present + description: Known Present + meaning: snomed_ct:410515003 + unknown: + title: unknown + description: Unknown + meaning: snomed_ct:261665006 + EnumAssertionProvenance: + description: Possible data sources for assertions. + is_a: EnumNull + permissible_values: + medical_record: + title: Medical Record + description: Data obtained from a medical record + investigator_assessment: + title: Investigator Assessment + description: Data obtained by examination, interview, etc. with investigator + participant_or_caregiver_report: + title: Participant or Caregiver Report + description: Data obtained from survey, questionnaire, etc. filled out by participant or caregiver + other: + title: Other + description: Data obtained from other source, such as tissue bank + #TODO: Revisit these bindings / enumerations + EnumAvailabilityStatus: + description: Is the biospecimen available for use? + permissible_values: + available: + title: Available + meaning: ig2_biospecimen_availability:available + description: Biospecimen is Available + unavailable: + title: Unavailable + meaning: ig2_biospecimen_availability:unavailable + description: Biospecimen is Unavailable + EnumSampleCollectionMethod: + description: The approach used to collect the biospecimen. [LOINC](https://loinc.org) is recommended. + EnumSite: + description: The location of the specimen collection. [SNOMED Body Site](https://hl7.org/fhir/R4B/valueset-body-site.html) is recommended. + EnumSpatialQualifiers: + description: Any spatial/location qualifiers. + enum_uri: http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs + reachable_from: + source_ontology: bioregistry:snomedct + source_nodes: + - snomedct:106233006 + - snomedct:272424004 + - snomedct:51440002 + - snomedct:399488007 + - snomedct:24028007 + - snomedct:7771000 + is_direct: false + relationship_types: + - rdfs:subClassOf + EnumLaterality: + description: Laterality information for the site + EnumEDAMFormats: + description: Data formats from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:format_1915 #Format + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + EnumEDAMDataTypes: + description: Data types from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:data_0006 #Data + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + EnumFileHashType: + description: Types of file hashes supported. + permissible_values: + md5: + title: MD5 + etag: + title: ETag + sha1: + title: SHA-1 diff --git a/justfile b/justfile new file mode 100644 index 0000000..fbb1b6b --- /dev/null +++ b/justfile @@ -0,0 +1,295 @@ +# ============ Shell configuration for Windows ============ + +# On Windows the "bash" shell from Git for Windows is used. +# If Git is installed in a non-standard location, edit the path below. +set windows-shell := ["C:/Program Files/Git/bin/bash", "-cu"] + +# ============ Variables used in recipes ============ + +# Detect WSL2 variable +_wsl2_check := `[ -n "${WSL_INTEROP:-}" ] && [ -z "${JUST_TEMPDIR:-}" ] && echo "ERROR" || echo "OK"` + +# Load environment variables from config.public.mk or specified file +set dotenv-load := true +# set dotenv-filename := env_var_or_default("LINKML_ENVIRONMENT_FILENAME", "config.public.mk") +set dotenv-filename := x'${LINKML_ENVIRONMENT_FILENAME:-config.public.mk}' + +# Set shebang line for cross-platform Python recipes (assumes presence of launcher on Windows) +shebang := if os() == 'windows' { + 'py' +} else { + '/usr/bin/env python3' +} + +# Environment variables with defaults +schema_name := env_var_or_default("LINKML_SCHEMA_NAME", "_no_schema_given_") +source_schema_dir := env_var_or_default("LINKML_SCHEMA_SOURCE_DIR", "") +config_yaml := if env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "") != "" { + "--config-file " + env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "") +} else { + "" +} +gen_doc_args := env_var_or_default("LINKML_GENERATORS_DOC_ARGS", "") +gen_java_args := env_var_or_default("LINKML_GENERATORS_JAVA_ARGS", "") +gen_owl_args := env_var_or_default("LINKML_GENERATORS_OWL_ARGS", "") +gen_pydantic_args := env_var_or_default("LINKML_GENERATORS_PYDANTIC_ARGS", "") +gen_ts_args := env_var_or_default("LINKML_GENERATORS_TYPESCRIPT_ARGS", "") + +# Directory variables +src := "src" +dest := "project" +pymodel := src / schema_name / "datamodel" +source_schema_path := source_schema_dir / schema_name + ".yaml" +docdir := "docs/elements" # Directory for generated documentation +distrib_schema_path := "docs/schema" # Directory for publishing schema artifacts + +# ============== Project recipes ============== + +# List all commands as default command. The prefix "_" hides the command. +_default: _status + @{{ if _wsl2_check == "ERROR" { "echo 'WSL2 detected: run export JUST_TEMPDIR=/tmp'" } else { "" } }} + @just --list + +# WSL2 status check - warns but does not abort (safe to use in _status/_default) +[private] +_wsl2_status_check: + @if [ -n "${WSL_INTEROP:-}" ] && [ -z "${JUST_TEMPDIR:-}" ]; then \ + echo "WARNING: WSL2 detected but JUST_TEMPDIR is not set."; \ + echo "Shebang recipes will fail with 'Permission denied' errors."; \ + echo "Fix: run 'export JUST_TEMPDIR=/tmp'"; \ + fi + +# WSL2 compatibility check - fails early with helpful message +[private] +_wsl2_compat_check: + @if [ -n "${WSL_INTEROP:-}" ] && [ -z "${JUST_TEMPDIR:-}" ]; then \ + echo "ERROR: WSL2 detected but JUST_TEMPDIR is not set."; \ + echo "Shebang recipes will fail with 'Permission denied' errors."; \ + echo ""; \ + echo "Fix: run this command:"; \ + echo ""; \ + echo " export JUST_TEMPDIR=/tmp"; \ + echo ""; \ + echo "Or add it to your ~/.bashrc for persistence."; \ + exit 1; \ + fi + +# Initialize a new project (use this for projects not yet under version control) +[group('project management')] +setup: _wsl2_compat_check _check-config _git-init install _git-add && _setup_part2 + git commit -m "Initialise git with minimal project" -a || true + +_setup_part2: gen-project gen-doc + @echo + @echo '=== Setup completed! ===' + @echo 'Various model representations have been created under directory "project". By default' + @echo 'they are ignored by git. You decide whether you want to add them to git tracking or' + @echo 'continue to git-ignore them as they can be regenerated if needed.' + @echo 'For tracking specific subfolders, add !project/[foldername]/* line(s) to ".gitignore".' + +# Install project dependencies +[group('project management')] +install: + uv sync --group dev + +# Updates project template and LinkML package +[group('project management')] +update: _update-template _update-linkml + +# Clean all generated files +[group('project management')] +clean: _wsl2_compat_check _clean_project + rm -rf tmp + rm -rf {{docdir}}/*.md + +# (Re-)Generate project and documentation locally +[group('model development')] +site: gen-project gen-doc + +# Deploy documentation site to Github Pages +[group('deployment')] +deploy: site + mkd-gh-deploy + +# Run all tests +[group('model development')] +test: _test-schema _test-python _test-examples + +# Run linting +[group('model development')] +lint: + uv run linkml-lint {{source_schema_dir}} + +# Generate md documentation for the schema and add artifacts +[group('model development')] +gen-doc: _gen-yaml && _add-artifacts + uv run gen-doc {{gen_doc_args}} -d {{docdir}} {{source_schema_path}} + +# Build docs and run test server +[group('model development')] +testdoc: gen-doc _serve + +# Generate the Python data models (dataclasses & pydantic) +gen-python: + uv run gen-project -d {{pymodel}} -I python {{source_schema_path}} + uv run gen-pydantic {{gen_pydantic_args}} {{source_schema_path}} > {{pymodel}}/{{schema_name}}_pydantic.py + +# Generate project files including Python data model +[group('model development')] +gen-project: + uv run gen-project {{config_yaml}} -d {{dest}} {{source_schema_path}} + mkdir -p {{pymodel}} + mv {{dest}}/*.py {{pymodel}}/ + uv run gen-pydantic {{gen_pydantic_args}} {{source_schema_path}} > {{pymodel}}/{{schema_name}}_pydantic.py + + @# Some generators ignore config_yaml or cannot create directories, so we run them separately. + uv run gen-java {{gen_java_args}} --output-directory {{dest}}/java/ {{source_schema_path}} + + @if [ ! -d "{{dest}}/typescript" ]; then \ + mkdir -p {{dest}}/typescript ; \ + fi + uv run gen-typescript {{gen_ts_args}} {{source_schema_path}} > {{dest}}/typescript/{{schema_name}}.ts + + @if [ ! -d "{{dest}}/owl" ]; then \ + mkdir -p {{dest}}/owl ; \ + fi + uv run gen-owl {{gen_owl_args}} {{source_schema_path}} > "{{dest}}/owl/{{schema_name}}.owl.ttl" + +# ============== Migrations recipes for Copier ============== + +# Hidden command to adjust the directory layout on upgrading a project +# created with linkml-project-copier v0.1.x to v0.2.0 or newer. +# Use with care! - It may not work for customized projects. +_post_upgrade_v020: _wsl2_compat_check && _post_upgrade_v020py + mv docs/*.md docs/elements + +_post_upgrade_v020py: + #!{{shebang}} + import subprocess + from pathlib import Path + # Git move files from folder src to folder dest + tasks = [ + (Path("src/docs/files"), Path("docs")), + (Path("src/docs/templates"), Path("docs/templates-linkml")), + (Path("src/data/examples"), Path("tests/data/")), + ] + for src, dest in tasks: + for path_obj in src.rglob("*"): + if not path_obj.is_file(): + continue + file_dest = dest / path_obj.relative_to(src) + if not file_dest.parent.exists(): + file_dest.parent.mkdir(parents=True) + print(f"Moving {path_obj} --> {file_dest}") + subprocess.run(["git", "mv", str(path_obj), str(file_dest)]) + print( + "Migration to v0.2.x completed! Check the changes carefully before committing." + ) + +# ============== Hidden internal recipes ============== + +# Show current project status +_status: _wsl2_status_check _check-config + @echo "Project: {{schema_name}}" + @echo "Source: {{source_schema_path}}" + +# Check project configuration +_check-config: + #!{{shebang}} + import os + schema_name = os.getenv('LINKML_SCHEMA_NAME') + if not schema_name: + print('**Project not configured**:\n - See \'.env.public\'') + exit(1) + print('Project-status: Ok') + +# Update project template +_update-template: + copier update --trust --skip-answered + +# Update LinkML runtime and LinkML to latest versions +_update-linkml: + uv lock --upgrade-package linkml-runtime --upgrade-package linkml + +# Test schema generation +_test-schema: + uv run gen-project {{config_yaml}} -d tmp {{source_schema_path}} + +# Run Python unit tests with pytest +_test-python: gen-python + uv run python -m pytest + +# Run example tests +_test-examples: _ensure_examples_output + uv run linkml-run-examples \ + --input-formats json \ + --input-formats yaml \ + --output-formats json \ + --output-formats yaml \ + --counter-example-input-directory tests/data/invalid \ + --input-directory tests/data/valid \ + --output-directory examples/output \ + --schema {{source_schema_path}} > examples/output/README.md + +# Add the merged model to docs/schema. +_gen-yaml: + -mkdir -p {{distrib_schema_path}} + uv run gen-yaml {{source_schema_path}} > {{distrib_schema_path}}/{{schema_name}}.yaml + +# Overridable recipe to add project-specific artifacts to the distribution schema path +_add-artifacts: + +# Run documentation server +_serve: + uv run mkdocs serve + +# Initialize git repository +_git-init: + git init + +# Add files to git +_git-add: + git add . + +# Commit files to git +_git-commit: + git commit -m 'chore: just setup was run' -a + +# Show git status +_git-status: + git status + +_clean_project: + #!{{shebang}} + import shutil, pathlib + # remove the generated project files + for d in pathlib.Path("{{dest}}").iterdir(): + if d.is_dir(): + print(f'removing "{d}"') + shutil.rmtree(d, ignore_errors=True) + # remove the generated python data model + for d in pathlib.Path("{{pymodel}}").iterdir(): + if d.name == "__init__.py": + continue + print(f'removing "{d}"') + if d.is_dir(): + shutil.rmtree(d, ignore_errors=True) + else: + d.unlink() + +_ensure_examples_output: # Ensure a clean examples/output directory exists + -mkdir -p examples/output + -rm -rf examples/output/*.* + +# ============== Include project-specific recipes ============== + +import "project.justfile" + +# ====== Override recipes from above with custom versions ======= + +# Uncomment the following line to allow duplicate recipe names +#set allow-duplicate-recipes + +# Overriding recipes from the root justfile by adding a recipe with the same +# name in an imported file is not possible until a known issue in just is fixed, +# https://github.com/casey/just/issues/2540 - So we need to override them here. diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..0a2ca40 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,78 @@ +--- +site_name: "cam-expanded-enums" +theme: + # https://www.mkdocs.org/user-guide/configuration/#theme + name: material + icon: + logo: material/book-open-page-variant + # palette: + # scheme: slate + # primary: cyan + features: + - content.tabs.link + - header.autohide # maximum screen space during scrolling + - navigation.expand # optimize user experience + - navigation.instant # optimize user experience + - navigation.instant.progress + - navigation.tracking # update address bar + - search.suggest # suggest good completions + - content.code.copy # enable copy to clipboard + +# extra css/js see https://www.mkdocs.org/user-guide/customizing-your-theme/ +extra_css: [] +extra_javascript: [] + +plugins: + - search + - mknotebooks: + execute: false + - mermaid2: + version: 11.4.1 + # https://pypi.org/project/mkdocs-pymdownx-material-extras + - mkdocs_pymdownx_material_extras: + +markdown_extensions: + - pymdownx.superfences: + # https://mkdocs-mermaid2.readthedocs.io/en/latest/superfences + # custom code highlighting rules + custom_fences: + - name: mermaid + # disable code highlighting to display diagrams + format: !!python/name:pymdownx.superfences.fence_code_format + class: mermaid + # https://facelessuser.github.io/pymdown-extensions/extensions/magiclink/ + # auto-link HTML, FTP, and email links + - pymdownx.magiclink + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition + # support for call-outs + - admonition + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#tables + # create tables + - tables + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists + # enables use of HTML attributes and CSS classes to applicable elements + - attr_list + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#markdown-in-html + # write markdown inside of HTML + - md_in_html + +watch: + - src/cam_expanded_enums/schema + +nav: + - Home: index.md + - Schema: elements/index.md + - About: about.md + +exclude_docs: | + /templates-linkml/ + +site_url: https://include-dcc.github.io/cam-expanded-enums +repo_url: https://github.com/include-dcc/cam-expanded-enums + +# Uncomment this block to enable use of Google Analytics. +# Replace the property value with your own ID. +# extra: +# analytics: +# provider: google +# property: G-XXXXXXXXXX diff --git a/output/EnumAssertionProvenance.yaml b/output/EnumAssertionProvenance.yaml new file mode 100644 index 0000000..1f1e5fb --- /dev/null +++ b/output/EnumAssertionProvenance.yaml @@ -0,0 +1,21 @@ +--- +id: https://includedcc.org/common-access-model/EnumAssertionProvenance +name: EnumAssertionProvenance +enums: + EnumAssertionProvenance: + description: Possible data sources for assertions. + is_a: EnumNull + permissible_values: + medical_record: + title: Medical Record + description: Data obtained from a medical record + investigator_assessment: + title: Investigator Assessment + description: Data obtained by examination, interview, etc. with investigator + participant_or_caregiver_report: + title: Participant or Caregiver Report + description: Data obtained from survey, questionnaire, etc. filled out by + participant or caregiver + other: + title: Other + description: Data obtained from other source, such as tissue bank diff --git a/output/EnumAvailabilityStatus.yaml b/output/EnumAvailabilityStatus.yaml new file mode 100644 index 0000000..2bd4d68 --- /dev/null +++ b/output/EnumAvailabilityStatus.yaml @@ -0,0 +1,15 @@ +--- +id: https://includedcc.org/common-access-model/EnumAvailabilityStatus +name: EnumAvailabilityStatus +enums: + EnumAvailabilityStatus: + description: Is the biospecimen available for use? + permissible_values: + available: + title: Available + meaning: ig2_biospecimen_availability:available + description: Biospecimen is Available + unavailable: + title: Unavailable + meaning: ig2_biospecimen_availability:unavailable + description: Biospecimen is Unavailable diff --git a/output/EnumClinicalDataSourceType.yaml b/output/EnumClinicalDataSourceType.yaml new file mode 100644 index 0000000..af096af --- /dev/null +++ b/output/EnumClinicalDataSourceType.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumClinicalDataSourceType +name: EnumClinicalDataSourceType +enums: + EnumClinicalDataSourceType: + title: Clinical Data Source Type + description: Approaches to ascertain clinical information about a participant. + permissible_values: + medical_record: + title: Medical Record + description: Data obtained directly from medical record + investigator_assessment: + title: Investigator Assessment + description: Data obtained by examination, interview, etc. with investigator + participant_or_caregiver_report: + title: Participant or Caregiver Report + description: Data obtained from survey, questionnaire, etc. filled out by + participant or caregiver + other: + title: Other + description: Data obtained from other source, such as tissue bank + unknown: + title: Unknown diff --git a/output/EnumConsanguinityAssertion.yaml b/output/EnumConsanguinityAssertion.yaml new file mode 100644 index 0000000..0a47e27 --- /dev/null +++ b/output/EnumConsanguinityAssertion.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumConsanguinityAssertion +name: EnumConsanguinityAssertion +enums: + EnumConsanguinityAssertion: + description: Asserts known or suspected consanguinity in this study family + permissible_values: + not_suspected: + title: not-suspected + description: Not suspected + meaning: snomed_ct:428263003 + suspected: + title: suspected + description: Suspected + meaning: snomed_ct:415684004 + known_present: + title: known-present + description: Known Present + meaning: snomed_ct:410515003 + unknown: + title: unknown + description: Unknown + meaning: snomed_ct:261665006 diff --git a/output/EnumDataCategory.yaml b/output/EnumDataCategory.yaml new file mode 100644 index 0000000..f223487 --- /dev/null +++ b/output/EnumDataCategory.yaml @@ -0,0 +1,38 @@ +--- +id: https://includedcc.org/common-access-model/EnumDataCategory +name: EnumDataCategory +enums: + EnumDataCategory: + title: Data Category + description: Categories of data which may be collected about participants. + permissible_values: + unharmonized_demographic_clinical_data: + title: Unharmonized Demographic/Clinical Data + harmonized_demographic_clinical_data: + title: Harmonized Demographic/Clinical Data + genomics: + title: Genomics + transcriptomics: + title: Transcriptomics + epigenomics: + title: Epigenomics + proteomics: + title: Proteomics + metabolomics: + title: Metabolomics + cognitive_behavioral: + title: Cognitive/Behavioral + immune_profiling: + title: Immune Profiling + imaging: + title: Imaging + microbiome: + title: Microbiome + fitness: + title: Fitness + physical_activity: + title: Physical Activity + other: + title: Other + sleep_study: + title: Sleep Study diff --git a/output/EnumDataUseModifier.yaml b/output/EnumDataUseModifier.yaml new file mode 100644 index 0000000..4552ffc --- /dev/null +++ b/output/EnumDataUseModifier.yaml @@ -0,0 +1,86 @@ +id: https://includedcc.org/common-access-model/EnumDataUseModifier +name: EnumDataUseModifier +enums: + EnumDataUseModifier: + title: Data Use Modifier + description: Data Use Ontology (DUO) terms for data use modifiers. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000017 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + DUO:00000044: + text: DUO:00000044 + description: population origins or ancestry research prohibited + title: population origins or ancestry research prohibited + DUO:0000012: + text: DUO:0000012 + description: research specific restrictions + title: research specific restrictions + DUO:0000015: + text: DUO:0000015 + description: no general methods research + title: no general methods research + DUO:0000016: + text: DUO:0000016 + description: genetic studies only + title: genetic studies only + DUO:0000018: + text: DUO:0000018 + description: not for profit, non commercial use only + title: not for profit, non commercial use only + DUO:0000019: + text: DUO:0000019 + description: publication required + title: publication required + DUO:0000020: + text: DUO:0000020 + description: collaboration required + title: collaboration required + DUO:0000021: + text: DUO:0000021 + description: ethics approval required + title: ethics approval required + DUO:0000022: + text: DUO:0000022 + description: geographical restriction + title: geographical restriction + DUO:0000024: + text: DUO:0000024 + description: publication moratorium + title: publication moratorium + DUO:0000025: + text: DUO:0000025 + description: time limit on use + title: time limit on use + DUO:0000026: + text: DUO:0000026 + description: user specific restriction + title: user specific restriction + DUO:0000027: + text: DUO:0000027 + description: project specific restriction + title: project specific restriction + DUO:0000028: + text: DUO:0000028 + description: institution specific restriction + title: institution specific restriction + DUO:0000029: + text: DUO:0000029 + description: return to database or resource + title: return to database or resource + DUO:0000043: + text: DUO:0000043 + description: clinical care use + title: clinical care use + DUO:0000045: + text: DUO:0000045 + description: not for profit organisation use only + title: not for profit organisation use only + DUO:0000046: + text: DUO:0000046 + description: non-commercial use only + title: non-commercial use only diff --git a/output/EnumDataUsePermission.yaml b/output/EnumDataUsePermission.yaml new file mode 100644 index 0000000..74a70dc --- /dev/null +++ b/output/EnumDataUsePermission.yaml @@ -0,0 +1,34 @@ +id: https://includedcc.org/common-access-model/EnumDataUsePermission +name: EnumDataUsePermission +enums: + EnumDataUsePermission: + title: Data Use Permission + description: Data Use Ontology (DUO) terms for data use permissions. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000001 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + DUO:0000004: + text: DUO:0000004 + description: no restriction + title: no restriction + DUO:0000006: + text: DUO:0000006 + description: health or medical or biomedical research + title: health or medical or biomedical research + DUO:0000007: + text: DUO:0000007 + description: disease specific research + title: disease specific research + DUO:0000011: + text: DUO:0000011 + description: population origins or ancestry research only + title: population origins or ancestry research only + DUO:0000042: + text: DUO:0000042 + description: general research use + title: general research use diff --git a/output/EnumEDAMDataTypes.yaml b/output/EnumEDAMDataTypes.yaml new file mode 100644 index 0000000..62f72fe --- /dev/null +++ b/output/EnumEDAMDataTypes.yaml @@ -0,0 +1,3806 @@ +id: https://includedcc.org/common-access-model/EnumEDAMDataTypes +name: EnumEDAMDataTypes +enums: + EnumEDAMDataTypes: + description: Data types from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:data_0006 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + EDAM_data:0582: + text: EDAM_data:0582 + description: Ontology + title: Ontology + EDAM_data:0842: + text: EDAM_data:0842 + description: Identifier + title: Identifier + EDAM_data:0844: + text: EDAM_data:0844 + description: Molecular mass + title: Molecular mass + EDAM_data:0845: + text: EDAM_data:0845 + description: Molecular charge + title: Molecular charge + EDAM_data:0846: + text: EDAM_data:0846 + description: Chemical formula + title: Chemical formula + EDAM_data:0847: + text: EDAM_data:0847 + description: QSAR descriptor + title: QSAR descriptor + EDAM_data:0849: + text: EDAM_data:0849 + description: Sequence record + title: Sequence record + EDAM_data:0850: + text: EDAM_data:0850 + description: Sequence set + title: Sequence set + EDAM_data:0856: + text: EDAM_data:0856 + description: Sequence feature source + title: Sequence feature source + EDAM_data:0857: + text: EDAM_data:0857 + description: Sequence search results + title: Sequence search results + EDAM_data:0858: + text: EDAM_data:0858 + description: Sequence signature matches + title: Sequence signature matches + EDAM_data:0860: + text: EDAM_data:0860 + description: Sequence signature data + title: Sequence signature data + EDAM_data:0862: + text: EDAM_data:0862 + description: Dotplot + title: Dotplot + EDAM_data:0863: + text: EDAM_data:0863 + description: Sequence alignment + title: Sequence alignment + EDAM_data:0865: + text: EDAM_data:0865 + description: Sequence similarity score + title: Sequence similarity score + EDAM_data:0867: + text: EDAM_data:0867 + description: Sequence alignment report + title: Sequence alignment report + EDAM_data:0870: + text: EDAM_data:0870 + description: Sequence distance matrix + title: Sequence distance matrix + EDAM_data:0871: + text: EDAM_data:0871 + description: Phylogenetic character data + title: Phylogenetic character data + EDAM_data:0872: + text: EDAM_data:0872 + description: Phylogenetic tree + title: Phylogenetic tree + EDAM_data:0874: + text: EDAM_data:0874 + description: Comparison matrix + title: Comparison matrix + EDAM_data:0878: + text: EDAM_data:0878 + description: Protein secondary structure alignment + title: Protein secondary structure alignment + EDAM_data:0880: + text: EDAM_data:0880 + description: RNA secondary structure + title: RNA secondary structure + EDAM_data:0881: + text: EDAM_data:0881 + description: RNA secondary structure alignment + title: RNA secondary structure alignment + EDAM_data:0883: + text: EDAM_data:0883 + description: Structure + title: Structure + EDAM_data:0886: + text: EDAM_data:0886 + description: Structure alignment + title: Structure alignment + EDAM_data:0887: + text: EDAM_data:0887 + description: Structure alignment report + title: Structure alignment report + EDAM_data:0888: + text: EDAM_data:0888 + description: Structure similarity score + title: Structure similarity score + EDAM_data:0889: + text: EDAM_data:0889 + description: Structural profile + title: Structural profile + EDAM_data:0890: + text: EDAM_data:0890 + description: Structural (3D) profile alignment + title: Structural (3D) profile alignment + EDAM_data:0892: + text: EDAM_data:0892 + description: Protein sequence-structure scoring matrix + title: Protein sequence-structure scoring matrix + EDAM_data:0893: + text: EDAM_data:0893 + description: Sequence-structure alignment + title: Sequence-structure alignment + EDAM_data:0896: + text: EDAM_data:0896 + description: Protein report + title: Protein report + EDAM_data:0897: + text: EDAM_data:0897 + description: Protein property + title: Protein property + EDAM_data:0905: + text: EDAM_data:0905 + description: Protein interaction raw data + title: Protein interaction raw data + EDAM_data:0906: + text: EDAM_data:0906 + description: Protein interaction data + title: Protein interaction data + EDAM_data:0907: + text: EDAM_data:0907 + description: Protein family report + title: Protein family report + EDAM_data:0909: + text: EDAM_data:0909 + description: Vmax + title: Vmax + EDAM_data:0910: + text: EDAM_data:0910 + description: Km + title: Km + EDAM_data:0912: + text: EDAM_data:0912 + description: Nucleic acid property + title: Nucleic acid property + EDAM_data:0914: + text: EDAM_data:0914 + description: Codon usage data + title: Codon usage data + EDAM_data:0916: + text: EDAM_data:0916 + description: Gene report + title: Gene report + EDAM_data:0919: + text: EDAM_data:0919 + description: Chromosome report + title: Chromosome report + EDAM_data:0920: + text: EDAM_data:0920 + description: Genotype/phenotype report + title: Genotype/phenotype report + EDAM_data:0924: + text: EDAM_data:0924 + description: Sequence trace + title: Sequence trace + EDAM_data:0925: + text: EDAM_data:0925 + description: Sequence assembly + title: Sequence assembly + EDAM_data:0926: + text: EDAM_data:0926 + description: RH scores + title: RH scores + EDAM_data:0927: + text: EDAM_data:0927 + description: Genetic linkage report + title: Genetic linkage report + EDAM_data:0928: + text: EDAM_data:0928 + description: Gene expression profile + title: Gene expression profile + EDAM_data:0937: + text: EDAM_data:0937 + description: Electron density map + title: Electron density map + EDAM_data:0938: + text: EDAM_data:0938 + description: Raw NMR data + title: Raw NMR data + EDAM_data:0939: + text: EDAM_data:0939 + description: CD spectra + title: CD spectra + EDAM_data:0940: + text: EDAM_data:0940 + description: Volume map + title: Volume map + EDAM_data:0942: + text: EDAM_data:0942 + description: 2D PAGE image + title: 2D PAGE image + EDAM_data:0943: + text: EDAM_data:0943 + description: Mass spectrum + title: Mass spectrum + EDAM_data:0944: + text: EDAM_data:0944 + description: Peptide mass fingerprint + title: Peptide mass fingerprint + EDAM_data:0945: + text: EDAM_data:0945 + description: Peptide identification + title: Peptide identification + EDAM_data:0949: + text: EDAM_data:0949 + description: Workflow metadata + title: Workflow metadata + EDAM_data:0950: + text: EDAM_data:0950 + description: Mathematical model + title: Mathematical model + EDAM_data:0951: + text: EDAM_data:0951 + description: Statistical estimate score + title: Statistical estimate score + EDAM_data:0954: + text: EDAM_data:0954 + description: Database cross-mapping + title: Database cross-mapping + EDAM_data:0955: + text: EDAM_data:0955 + description: Data index + title: Data index + EDAM_data:0956: + text: EDAM_data:0956 + description: Data index report + title: Data index report + EDAM_data:0957: + text: EDAM_data:0957 + description: Database metadata + title: Database metadata + EDAM_data:0958: + text: EDAM_data:0958 + description: Tool metadata + title: Tool metadata + EDAM_data:0960: + text: EDAM_data:0960 + description: User metadata + title: User metadata + EDAM_data:0962: + text: EDAM_data:0962 + description: Small molecule report + title: Small molecule report + EDAM_data:0963: + text: EDAM_data:0963 + description: Cell line report + title: Cell line report + EDAM_data:0966: + text: EDAM_data:0966 + description: Ontology term + title: Ontology term + EDAM_data:0967: + text: EDAM_data:0967 + description: Ontology concept data + title: Ontology concept data + EDAM_data:0968: + text: EDAM_data:0968 + description: Keyword + title: Keyword + EDAM_data:0970: + text: EDAM_data:0970 + description: Citation + title: Citation + EDAM_data:0971: + text: EDAM_data:0971 + description: Article + title: Article + EDAM_data:0972: + text: EDAM_data:0972 + description: Text mining report + title: Text mining report + EDAM_data:0976: + text: EDAM_data:0976 + description: Identifier (by type of entity) + title: Identifier (by type of entity) + EDAM_data:0977: + text: EDAM_data:0977 + description: Tool identifier + title: Tool identifier + EDAM_data:0982: + text: EDAM_data:0982 + description: Molecule identifier + title: Molecule identifier + EDAM_data:0983: + text: EDAM_data:0983 + description: Atom ID + title: Atom ID + EDAM_data:0984: + text: EDAM_data:0984 + description: Molecule name + title: Molecule name + EDAM_data:0987: + text: EDAM_data:0987 + description: Chromosome name + title: Chromosome name + EDAM_data:0988: + text: EDAM_data:0988 + description: Peptide identifier + title: Peptide identifier + EDAM_data:0989: + text: EDAM_data:0989 + description: Protein identifier + title: Protein identifier + EDAM_data:0990: + text: EDAM_data:0990 + description: Compound name + title: Compound name + EDAM_data:0991: + text: EDAM_data:0991 + description: Chemical registry number + title: Chemical registry number + EDAM_data:0993: + text: EDAM_data:0993 + description: Drug identifier + title: Drug identifier + EDAM_data:0994: + text: EDAM_data:0994 + description: Amino acid identifier + title: Amino acid identifier + EDAM_data:0995: + text: EDAM_data:0995 + description: Nucleotide identifier + title: Nucleotide identifier + EDAM_data:0996: + text: EDAM_data:0996 + description: Monosaccharide identifier + title: Monosaccharide identifier + EDAM_data:0997: + text: EDAM_data:0997 + description: Chemical name (ChEBI) + title: Chemical name (ChEBI) + EDAM_data:0998: + text: EDAM_data:0998 + description: Chemical name (IUPAC) + title: Chemical name (IUPAC) + EDAM_data:0999: + text: EDAM_data:0999 + description: Chemical name (INN) + title: Chemical name (INN) + EDAM_data:1000: + text: EDAM_data:1000 + description: Chemical name (brand) + title: Chemical name (brand) + EDAM_data:1001: + text: EDAM_data:1001 + description: Chemical name (synonymous) + title: Chemical name (synonymous) + EDAM_data:1002: + text: EDAM_data:1002 + description: CAS number + title: CAS number + EDAM_data:1003: + text: EDAM_data:1003 + description: Chemical registry number (Beilstein) + title: Chemical registry number (Beilstein) + EDAM_data:1004: + text: EDAM_data:1004 + description: Chemical registry number (Gmelin) + title: Chemical registry number (Gmelin) + EDAM_data:1005: + text: EDAM_data:1005 + description: HET group name + title: HET group name + EDAM_data:1006: + text: EDAM_data:1006 + description: Amino acid name + title: Amino acid name + EDAM_data:1007: + text: EDAM_data:1007 + description: Nucleotide code + title: Nucleotide code + EDAM_data:1008: + text: EDAM_data:1008 + description: Polypeptide chain ID + title: Polypeptide chain ID + EDAM_data:1009: + text: EDAM_data:1009 + description: Protein name + title: Protein name + EDAM_data:1010: + text: EDAM_data:1010 + description: Enzyme identifier + title: Enzyme identifier + EDAM_data:1011: + text: EDAM_data:1011 + description: EC number + title: EC number + EDAM_data:1012: + text: EDAM_data:1012 + description: Enzyme name + title: Enzyme name + EDAM_data:1013: + text: EDAM_data:1013 + description: Restriction enzyme name + title: Restriction enzyme name + EDAM_data:1015: + text: EDAM_data:1015 + description: Sequence feature ID + title: Sequence feature ID + EDAM_data:1016: + text: EDAM_data:1016 + description: Sequence position + title: Sequence position + EDAM_data:1017: + text: EDAM_data:1017 + description: Sequence range + title: Sequence range + EDAM_data:1020: + text: EDAM_data:1020 + description: Sequence feature key + title: Sequence feature key + EDAM_data:1021: + text: EDAM_data:1021 + description: Sequence feature qualifier + title: Sequence feature qualifier + EDAM_data:1022: + text: EDAM_data:1022 + description: Sequence feature label + title: Sequence feature label + EDAM_data:1023: + text: EDAM_data:1023 + description: EMBOSS Uniform Feature Object + title: EMBOSS Uniform Feature Object + EDAM_data:1025: + text: EDAM_data:1025 + description: Gene identifier + title: Gene identifier + EDAM_data:1026: + text: EDAM_data:1026 + description: Gene symbol + title: Gene symbol + EDAM_data:1027: + text: EDAM_data:1027 + description: Gene ID (NCBI) + title: Gene ID (NCBI) + EDAM_data:1031: + text: EDAM_data:1031 + description: Gene ID (CGD) + title: Gene ID (CGD) + EDAM_data:1032: + text: EDAM_data:1032 + description: Gene ID (DictyBase) + title: Gene ID (DictyBase) + EDAM_data:1033: + text: EDAM_data:1033 + description: Ensembl gene ID + title: Ensembl gene ID + EDAM_data:1034: + text: EDAM_data:1034 + description: Gene ID (SGD) + title: Gene ID (SGD) + EDAM_data:1035: + text: EDAM_data:1035 + description: Gene ID (GeneDB) + title: Gene ID (GeneDB) + EDAM_data:1036: + text: EDAM_data:1036 + description: TIGR identifier + title: TIGR identifier + EDAM_data:1037: + text: EDAM_data:1037 + description: TAIR accession (gene) + title: TAIR accession (gene) + EDAM_data:1038: + text: EDAM_data:1038 + description: Protein domain ID + title: Protein domain ID + EDAM_data:1039: + text: EDAM_data:1039 + description: SCOP domain identifier + title: SCOP domain identifier + EDAM_data:1040: + text: EDAM_data:1040 + description: CATH domain ID + title: CATH domain ID + EDAM_data:1041: + text: EDAM_data:1041 + description: SCOP concise classification string (sccs) + title: SCOP concise classification string (sccs) + EDAM_data:1042: + text: EDAM_data:1042 + description: SCOP sunid + title: SCOP sunid + EDAM_data:1043: + text: EDAM_data:1043 + description: CATH node ID + title: CATH node ID + EDAM_data:1044: + text: EDAM_data:1044 + description: Kingdom name + title: Kingdom name + EDAM_data:1045: + text: EDAM_data:1045 + description: Species name + title: Species name + EDAM_data:1046: + text: EDAM_data:1046 + description: Strain name + title: Strain name + EDAM_data:1047: + text: EDAM_data:1047 + description: URI + title: URI + EDAM_data:1048: + text: EDAM_data:1048 + description: Database ID + title: Database ID + EDAM_data:1049: + text: EDAM_data:1049 + description: Directory name + title: Directory name + EDAM_data:1050: + text: EDAM_data:1050 + description: File name + title: File name + EDAM_data:1051: + text: EDAM_data:1051 + description: Ontology name + title: Ontology name + EDAM_data:1052: + text: EDAM_data:1052 + description: URL + title: URL + EDAM_data:1053: + text: EDAM_data:1053 + description: URN + title: URN + EDAM_data:1055: + text: EDAM_data:1055 + description: LSID + title: LSID + EDAM_data:1056: + text: EDAM_data:1056 + description: Database name + title: Database name + EDAM_data:1058: + text: EDAM_data:1058 + description: Enumerated file name + title: Enumerated file name + EDAM_data:1059: + text: EDAM_data:1059 + description: File name extension + title: File name extension + EDAM_data:1060: + text: EDAM_data:1060 + description: File base name + title: File base name + EDAM_data:1061: + text: EDAM_data:1061 + description: QSAR descriptor name + title: QSAR descriptor name + EDAM_data:1063: + text: EDAM_data:1063 + description: Sequence identifier + title: Sequence identifier + EDAM_data:1064: + text: EDAM_data:1064 + description: Sequence set ID + title: Sequence set ID + EDAM_data:1066: + text: EDAM_data:1066 + description: Sequence alignment ID + title: Sequence alignment ID + EDAM_data:1068: + text: EDAM_data:1068 + description: Phylogenetic tree ID + title: Phylogenetic tree ID + EDAM_data:1069: + text: EDAM_data:1069 + description: Comparison matrix identifier + title: Comparison matrix identifier + EDAM_data:1070: + text: EDAM_data:1070 + description: Structure ID + title: Structure ID + EDAM_data:1071: + text: EDAM_data:1071 + description: Structural (3D) profile ID + title: Structural (3D) profile ID + EDAM_data:1072: + text: EDAM_data:1072 + description: Structure alignment ID + title: Structure alignment ID + EDAM_data:1073: + text: EDAM_data:1073 + description: Amino acid index ID + title: Amino acid index ID + EDAM_data:1074: + text: EDAM_data:1074 + description: Protein interaction ID + title: Protein interaction ID + EDAM_data:1075: + text: EDAM_data:1075 + description: Protein family identifier + title: Protein family identifier + EDAM_data:1076: + text: EDAM_data:1076 + description: Codon usage table name + title: Codon usage table name + EDAM_data:1077: + text: EDAM_data:1077 + description: Transcription factor identifier + title: Transcription factor identifier + EDAM_data:1078: + text: EDAM_data:1078 + description: Experiment annotation ID + title: Experiment annotation ID + EDAM_data:1079: + text: EDAM_data:1079 + description: Electron microscopy model ID + title: Electron microscopy model ID + EDAM_data:1080: + text: EDAM_data:1080 + description: Gene expression report ID + title: Gene expression report ID + EDAM_data:1081: + text: EDAM_data:1081 + description: Genotype and phenotype annotation ID + title: Genotype and phenotype annotation ID + EDAM_data:1082: + text: EDAM_data:1082 + description: Pathway or network identifier + title: Pathway or network identifier + EDAM_data:1083: + text: EDAM_data:1083 + description: Workflow ID + title: Workflow ID + EDAM_data:1084: + text: EDAM_data:1084 + description: Data resource definition ID + title: Data resource definition ID + EDAM_data:1085: + text: EDAM_data:1085 + description: Biological model ID + title: Biological model ID + EDAM_data:1086: + text: EDAM_data:1086 + description: Compound identifier + title: Compound identifier + EDAM_data:1087: + text: EDAM_data:1087 + description: Ontology concept ID + title: Ontology concept ID + EDAM_data:1088: + text: EDAM_data:1088 + description: Article ID + title: Article ID + EDAM_data:1089: + text: EDAM_data:1089 + description: FlyBase ID + title: FlyBase ID + EDAM_data:1091: + text: EDAM_data:1091 + description: WormBase name + title: WormBase name + EDAM_data:1092: + text: EDAM_data:1092 + description: WormBase class + title: WormBase class + EDAM_data:1093: + text: EDAM_data:1093 + description: Sequence accession + title: Sequence accession + EDAM_data:1095: + text: EDAM_data:1095 + description: EMBOSS Uniform Sequence Address + title: EMBOSS Uniform Sequence Address + EDAM_data:1096: + text: EDAM_data:1096 + description: Sequence accession (protein) + title: Sequence accession (protein) + EDAM_data:1097: + text: EDAM_data:1097 + description: Sequence accession (nucleic acid) + title: Sequence accession (nucleic acid) + EDAM_data:1098: + text: EDAM_data:1098 + description: RefSeq accession + title: RefSeq accession + EDAM_data:1100: + text: EDAM_data:1100 + description: PIR identifier + title: PIR identifier + EDAM_data:1102: + text: EDAM_data:1102 + description: Gramene primary identifier + title: Gramene primary identifier + EDAM_data:1103: + text: EDAM_data:1103 + description: EMBL/GenBank/DDBJ ID + title: EMBL/GenBank/DDBJ ID + EDAM_data:1104: + text: EDAM_data:1104 + description: Sequence cluster ID (UniGene) + title: Sequence cluster ID (UniGene) + EDAM_data:1105: + text: EDAM_data:1105 + description: dbEST accession + title: dbEST accession + EDAM_data:1106: + text: EDAM_data:1106 + description: dbSNP ID + title: dbSNP ID + EDAM_data:1112: + text: EDAM_data:1112 + description: Sequence cluster ID + title: Sequence cluster ID + EDAM_data:1113: + text: EDAM_data:1113 + description: Sequence cluster ID (COG) + title: Sequence cluster ID (COG) + EDAM_data:1114: + text: EDAM_data:1114 + description: Sequence motif identifier + title: Sequence motif identifier + EDAM_data:1115: + text: EDAM_data:1115 + description: Sequence profile ID + title: Sequence profile ID + EDAM_data:1116: + text: EDAM_data:1116 + description: ELM ID + title: ELM ID + EDAM_data:1117: + text: EDAM_data:1117 + description: Prosite accession number + title: Prosite accession number + EDAM_data:1118: + text: EDAM_data:1118 + description: HMMER hidden Markov model ID + title: HMMER hidden Markov model ID + EDAM_data:1119: + text: EDAM_data:1119 + description: JASPAR profile ID + title: JASPAR profile ID + EDAM_data:1123: + text: EDAM_data:1123 + description: TreeBASE study accession number + title: TreeBASE study accession number + EDAM_data:1124: + text: EDAM_data:1124 + description: TreeFam accession number + title: TreeFam accession number + EDAM_data:1126: + text: EDAM_data:1126 + description: Comparison matrix name + title: Comparison matrix name + EDAM_data:1127: + text: EDAM_data:1127 + description: PDB ID + title: PDB ID + EDAM_data:1128: + text: EDAM_data:1128 + description: AAindex ID + title: AAindex ID + EDAM_data:1129: + text: EDAM_data:1129 + description: BIND accession number + title: BIND accession number + EDAM_data:1130: + text: EDAM_data:1130 + description: IntAct accession number + title: IntAct accession number + EDAM_data:1131: + text: EDAM_data:1131 + description: Protein family name + title: Protein family name + EDAM_data:1132: + text: EDAM_data:1132 + description: InterPro entry name + title: InterPro entry name + EDAM_data:1133: + text: EDAM_data:1133 + description: InterPro accession + title: InterPro accession + EDAM_data:1134: + text: EDAM_data:1134 + description: InterPro secondary accession + title: InterPro secondary accession + EDAM_data:1135: + text: EDAM_data:1135 + description: Gene3D ID + title: Gene3D ID + EDAM_data:1136: + text: EDAM_data:1136 + description: PIRSF ID + title: PIRSF ID + EDAM_data:1137: + text: EDAM_data:1137 + description: PRINTS code + title: PRINTS code + EDAM_data:1138: + text: EDAM_data:1138 + description: Pfam accession number + title: Pfam accession number + EDAM_data:1139: + text: EDAM_data:1139 + description: SMART accession number + title: SMART accession number + EDAM_data:1140: + text: EDAM_data:1140 + description: Superfamily hidden Markov model number + title: Superfamily hidden Markov model number + EDAM_data:1141: + text: EDAM_data:1141 + description: TIGRFam ID + title: TIGRFam ID + EDAM_data:1142: + text: EDAM_data:1142 + description: ProDom accession number + title: ProDom accession number + EDAM_data:1143: + text: EDAM_data:1143 + description: TRANSFAC accession number + title: TRANSFAC accession number + EDAM_data:1144: + text: EDAM_data:1144 + description: ArrayExpress accession number + title: ArrayExpress accession number + EDAM_data:1145: + text: EDAM_data:1145 + description: PRIDE experiment accession number + title: PRIDE experiment accession number + EDAM_data:1146: + text: EDAM_data:1146 + description: EMDB ID + title: EMDB ID + EDAM_data:1147: + text: EDAM_data:1147 + description: GEO accession number + title: GEO accession number + EDAM_data:1148: + text: EDAM_data:1148 + description: GermOnline ID + title: GermOnline ID + EDAM_data:1149: + text: EDAM_data:1149 + description: EMAGE ID + title: EMAGE ID + EDAM_data:1150: + text: EDAM_data:1150 + description: Disease ID + title: Disease ID + EDAM_data:1151: + text: EDAM_data:1151 + description: HGVbase ID + title: HGVbase ID + EDAM_data:1153: + text: EDAM_data:1153 + description: OMIM ID + title: OMIM ID + EDAM_data:1154: + text: EDAM_data:1154 + description: KEGG object identifier + title: KEGG object identifier + EDAM_data:1155: + text: EDAM_data:1155 + description: Pathway ID (reactome) + title: Pathway ID (reactome) + EDAM_data:1157: + text: EDAM_data:1157 + description: Pathway ID (BioCyc) + title: Pathway ID (BioCyc) + EDAM_data:1158: + text: EDAM_data:1158 + description: Pathway ID (INOH) + title: Pathway ID (INOH) + EDAM_data:1159: + text: EDAM_data:1159 + description: Pathway ID (PATIKA) + title: Pathway ID (PATIKA) + EDAM_data:1160: + text: EDAM_data:1160 + description: Pathway ID (CPDB) + title: Pathway ID (CPDB) + EDAM_data:1161: + text: EDAM_data:1161 + description: Pathway ID (Panther) + title: Pathway ID (Panther) + EDAM_data:1162: + text: EDAM_data:1162 + description: MIRIAM identifier + title: MIRIAM identifier + EDAM_data:1163: + text: EDAM_data:1163 + description: MIRIAM data type name + title: MIRIAM data type name + EDAM_data:1164: + text: EDAM_data:1164 + description: MIRIAM URI + title: MIRIAM URI + EDAM_data:1165: + text: EDAM_data:1165 + description: MIRIAM data type primary name + title: MIRIAM data type primary name + EDAM_data:1166: + text: EDAM_data:1166 + description: MIRIAM data type synonymous name + title: MIRIAM data type synonymous name + EDAM_data:1167: + text: EDAM_data:1167 + description: Taverna workflow ID + title: Taverna workflow ID + EDAM_data:1170: + text: EDAM_data:1170 + description: Biological model name + title: Biological model name + EDAM_data:1171: + text: EDAM_data:1171 + description: BioModel ID + title: BioModel ID + EDAM_data:1172: + text: EDAM_data:1172 + description: PubChem CID + title: PubChem CID + EDAM_data:1173: + text: EDAM_data:1173 + description: ChemSpider ID + title: ChemSpider ID + EDAM_data:1174: + text: EDAM_data:1174 + description: ChEBI ID + title: ChEBI ID + EDAM_data:1175: + text: EDAM_data:1175 + description: BioPax concept ID + title: BioPax concept ID + EDAM_data:1176: + text: EDAM_data:1176 + description: GO concept ID + title: GO concept ID + EDAM_data:1177: + text: EDAM_data:1177 + description: MeSH concept ID + title: MeSH concept ID + EDAM_data:1178: + text: EDAM_data:1178 + description: HGNC concept ID + title: HGNC concept ID + EDAM_data:1179: + text: EDAM_data:1179 + description: NCBI taxonomy ID + title: NCBI taxonomy ID + EDAM_data:1180: + text: EDAM_data:1180 + description: Plant Ontology concept ID + title: Plant Ontology concept ID + EDAM_data:1181: + text: EDAM_data:1181 + description: UMLS concept ID + title: UMLS concept ID + EDAM_data:1182: + text: EDAM_data:1182 + description: FMA concept ID + title: FMA concept ID + EDAM_data:1183: + text: EDAM_data:1183 + description: EMAP concept ID + title: EMAP concept ID + EDAM_data:1184: + text: EDAM_data:1184 + description: ChEBI concept ID + title: ChEBI concept ID + EDAM_data:1185: + text: EDAM_data:1185 + description: MGED concept ID + title: MGED concept ID + EDAM_data:1186: + text: EDAM_data:1186 + description: myGrid concept ID + title: myGrid concept ID + EDAM_data:1187: + text: EDAM_data:1187 + description: PubMed ID + title: PubMed ID + EDAM_data:1188: + text: EDAM_data:1188 + description: DOI + title: DOI + EDAM_data:1189: + text: EDAM_data:1189 + description: Medline UI + title: Medline UI + EDAM_data:1190: + text: EDAM_data:1190 + description: Tool name + title: Tool name + EDAM_data:1191: + text: EDAM_data:1191 + description: Tool name (signature) + title: Tool name (signature) + EDAM_data:1192: + text: EDAM_data:1192 + description: Tool name (BLAST) + title: Tool name (BLAST) + EDAM_data:1193: + text: EDAM_data:1193 + description: Tool name (FASTA) + title: Tool name (FASTA) + EDAM_data:1194: + text: EDAM_data:1194 + description: Tool name (EMBOSS) + title: Tool name (EMBOSS) + EDAM_data:1195: + text: EDAM_data:1195 + description: Tool name (EMBASSY package) + title: Tool name (EMBASSY package) + EDAM_data:1201: + text: EDAM_data:1201 + description: QSAR descriptor (constitutional) + title: QSAR descriptor (constitutional) + EDAM_data:1202: + text: EDAM_data:1202 + description: QSAR descriptor (electronic) + title: QSAR descriptor (electronic) + EDAM_data:1203: + text: EDAM_data:1203 + description: QSAR descriptor (geometrical) + title: QSAR descriptor (geometrical) + EDAM_data:1204: + text: EDAM_data:1204 + description: QSAR descriptor (topological) + title: QSAR descriptor (topological) + EDAM_data:1205: + text: EDAM_data:1205 + description: QSAR descriptor (molecular) + title: QSAR descriptor (molecular) + EDAM_data:1233: + text: EDAM_data:1233 + description: Sequence set (protein) + title: Sequence set (protein) + EDAM_data:1234: + text: EDAM_data:1234 + description: Sequence set (nucleic acid) + title: Sequence set (nucleic acid) + EDAM_data:1235: + text: EDAM_data:1235 + description: Sequence cluster + title: Sequence cluster + EDAM_data:1238: + text: EDAM_data:1238 + description: Proteolytic digest + title: Proteolytic digest + EDAM_data:1239: + text: EDAM_data:1239 + description: Restriction digest + title: Restriction digest + EDAM_data:1240: + text: EDAM_data:1240 + description: PCR primers + title: PCR primers + EDAM_data:1245: + text: EDAM_data:1245 + description: Sequence cluster (protein) + title: Sequence cluster (protein) + EDAM_data:1246: + text: EDAM_data:1246 + description: Sequence cluster (nucleic acid) + title: Sequence cluster (nucleic acid) + EDAM_data:1249: + text: EDAM_data:1249 + description: Sequence length + title: Sequence length + EDAM_data:1254: + text: EDAM_data:1254 + description: Sequence property + title: Sequence property + EDAM_data:1255: + text: EDAM_data:1255 + description: Sequence features + title: Sequence features + EDAM_data:1259: + text: EDAM_data:1259 + description: Sequence complexity report + title: Sequence complexity report + EDAM_data:1260: + text: EDAM_data:1260 + description: Sequence ambiguity report + title: Sequence ambiguity report + EDAM_data:1261: + text: EDAM_data:1261 + description: Sequence composition report + title: Sequence composition report + EDAM_data:1262: + text: EDAM_data:1262 + description: Peptide molecular weight hits + title: Peptide molecular weight hits + EDAM_data:1263: + text: EDAM_data:1263 + description: Base position variability plot + title: Base position variability plot + EDAM_data:1265: + text: EDAM_data:1265 + description: Base frequencies table + title: Base frequencies table + EDAM_data:1266: + text: EDAM_data:1266 + description: Base word frequencies table + title: Base word frequencies table + EDAM_data:1267: + text: EDAM_data:1267 + description: Amino acid frequencies table + title: Amino acid frequencies table + EDAM_data:1268: + text: EDAM_data:1268 + description: Amino acid word frequencies table + title: Amino acid word frequencies table + EDAM_data:1270: + text: EDAM_data:1270 + description: Feature table + title: Feature table + EDAM_data:1274: + text: EDAM_data:1274 + description: Map + title: Map + EDAM_data:1276: + text: EDAM_data:1276 + description: Nucleic acid features + title: Nucleic acid features + EDAM_data:1277: + text: EDAM_data:1277 + description: Protein features + title: Protein features + EDAM_data:1278: + text: EDAM_data:1278 + description: Genetic map + title: Genetic map + EDAM_data:1279: + text: EDAM_data:1279 + description: Sequence map + title: Sequence map + EDAM_data:1280: + text: EDAM_data:1280 + description: Physical map + title: Physical map + EDAM_data:1283: + text: EDAM_data:1283 + description: Cytogenetic map + title: Cytogenetic map + EDAM_data:1284: + text: EDAM_data:1284 + description: DNA transduction map + title: DNA transduction map + EDAM_data:1285: + text: EDAM_data:1285 + description: Gene map + title: Gene map + EDAM_data:1286: + text: EDAM_data:1286 + description: Plasmid map + title: Plasmid map + EDAM_data:1288: + text: EDAM_data:1288 + description: Genome map + title: Genome map + EDAM_data:1289: + text: EDAM_data:1289 + description: Restriction map + title: Restriction map + EDAM_data:1347: + text: EDAM_data:1347 + description: Dirichlet distribution + title: Dirichlet distribution + EDAM_data:1352: + text: EDAM_data:1352 + description: Regular expression + title: Regular expression + EDAM_data:1353: + text: EDAM_data:1353 + description: Sequence motif + title: Sequence motif + EDAM_data:1354: + text: EDAM_data:1354 + description: Sequence profile + title: Sequence profile + EDAM_data:1355: + text: EDAM_data:1355 + description: Protein signature + title: Protein signature + EDAM_data:1361: + text: EDAM_data:1361 + description: Position frequency matrix + title: Position frequency matrix + EDAM_data:1362: + text: EDAM_data:1362 + description: Position weight matrix + title: Position weight matrix + EDAM_data:1363: + text: EDAM_data:1363 + description: Information content matrix + title: Information content matrix + EDAM_data:1364: + text: EDAM_data:1364 + description: Hidden Markov model + title: Hidden Markov model + EDAM_data:1365: + text: EDAM_data:1365 + description: Fingerprint + title: Fingerprint + EDAM_data:1381: + text: EDAM_data:1381 + description: Pair sequence alignment + title: Pair sequence alignment + EDAM_data:1383: + text: EDAM_data:1383 + description: Nucleic acid sequence alignment + title: Nucleic acid sequence alignment + EDAM_data:1384: + text: EDAM_data:1384 + description: Protein sequence alignment + title: Protein sequence alignment + EDAM_data:1385: + text: EDAM_data:1385 + description: Hybrid sequence alignment + title: Hybrid sequence alignment + EDAM_data:1394: + text: EDAM_data:1394 + description: Alignment score or penalty + title: Alignment score or penalty + EDAM_data:1397: + text: EDAM_data:1397 + description: Gap opening penalty + title: Gap opening penalty + EDAM_data:1398: + text: EDAM_data:1398 + description: Gap extension penalty + title: Gap extension penalty + EDAM_data:1399: + text: EDAM_data:1399 + description: Gap separation penalty + title: Gap separation penalty + EDAM_data:1401: + text: EDAM_data:1401 + description: Match reward score + title: Match reward score + EDAM_data:1402: + text: EDAM_data:1402 + description: Mismatch penalty score + title: Mismatch penalty score + EDAM_data:1403: + text: EDAM_data:1403 + description: Drop off score + title: Drop off score + EDAM_data:1410: + text: EDAM_data:1410 + description: Terminal gap opening penalty + title: Terminal gap opening penalty + EDAM_data:1411: + text: EDAM_data:1411 + description: Terminal gap extension penalty + title: Terminal gap extension penalty + EDAM_data:1412: + text: EDAM_data:1412 + description: Sequence identity + title: Sequence identity + EDAM_data:1413: + text: EDAM_data:1413 + description: Sequence similarity + title: Sequence similarity + EDAM_data:1426: + text: EDAM_data:1426 + description: Phylogenetic continuous quantitative data + title: Phylogenetic continuous quantitative data + EDAM_data:1427: + text: EDAM_data:1427 + description: Phylogenetic discrete data + title: Phylogenetic discrete data + EDAM_data:1428: + text: EDAM_data:1428 + description: Phylogenetic character cliques + title: Phylogenetic character cliques + EDAM_data:1429: + text: EDAM_data:1429 + description: Phylogenetic invariants + title: Phylogenetic invariants + EDAM_data:1439: + text: EDAM_data:1439 + description: DNA substitution model + title: DNA substitution model + EDAM_data:1442: + text: EDAM_data:1442 + description: Phylogenetic tree distances + title: Phylogenetic tree distances + EDAM_data:1444: + text: EDAM_data:1444 + description: Phylogenetic character contrasts + title: Phylogenetic character contrasts + EDAM_data:1448: + text: EDAM_data:1448 + description: Comparison matrix (nucleotide) + title: Comparison matrix (nucleotide) + EDAM_data:1449: + text: EDAM_data:1449 + description: Comparison matrix (amino acid) + title: Comparison matrix (amino acid) + EDAM_data:1459: + text: EDAM_data:1459 + description: Nucleic acid structure + title: Nucleic acid structure + EDAM_data:1460: + text: EDAM_data:1460 + description: Protein structure + title: Protein structure + EDAM_data:1461: + text: EDAM_data:1461 + description: Protein-ligand complex + title: Protein-ligand complex + EDAM_data:1462: + text: EDAM_data:1462 + description: Carbohydrate structure + title: Carbohydrate structure + EDAM_data:1463: + text: EDAM_data:1463 + description: Small molecule structure + title: Small molecule structure + EDAM_data:1464: + text: EDAM_data:1464 + description: DNA structure + title: DNA structure + EDAM_data:1465: + text: EDAM_data:1465 + description: RNA structure + title: RNA structure + EDAM_data:1466: + text: EDAM_data:1466 + description: tRNA structure + title: tRNA structure + EDAM_data:1467: + text: EDAM_data:1467 + description: Protein chain + title: Protein chain + EDAM_data:1468: + text: EDAM_data:1468 + description: Protein domain + title: Protein domain + EDAM_data:1470: + text: EDAM_data:1470 + description: C-alpha trace + title: C-alpha trace + EDAM_data:1479: + text: EDAM_data:1479 + description: Structure alignment (pair) + title: Structure alignment (pair) + EDAM_data:1481: + text: EDAM_data:1481 + description: Protein structure alignment + title: Protein structure alignment + EDAM_data:1482: + text: EDAM_data:1482 + description: Nucleic acid structure alignment + title: Nucleic acid structure alignment + EDAM_data:1493: + text: EDAM_data:1493 + description: RNA structure alignment + title: RNA structure alignment + EDAM_data:1494: + text: EDAM_data:1494 + description: Structural transformation matrix + title: Structural transformation matrix + EDAM_data:1497: + text: EDAM_data:1497 + description: Root-mean-square deviation + title: Root-mean-square deviation + EDAM_data:1498: + text: EDAM_data:1498 + description: Tanimoto similarity score + title: Tanimoto similarity score + EDAM_data:1499: + text: EDAM_data:1499 + description: 3D-1D scoring matrix + title: 3D-1D scoring matrix + EDAM_data:1501: + text: EDAM_data:1501 + description: Amino acid index + title: Amino acid index + EDAM_data:1502: + text: EDAM_data:1502 + description: Amino acid index (chemical classes) + title: Amino acid index (chemical classes) + EDAM_data:1503: + text: EDAM_data:1503 + description: Amino acid pair-wise contact potentials + title: Amino acid pair-wise contact potentials + EDAM_data:1505: + text: EDAM_data:1505 + description: Amino acid index (molecular weight) + title: Amino acid index (molecular weight) + EDAM_data:1506: + text: EDAM_data:1506 + description: Amino acid index (hydropathy) + title: Amino acid index (hydropathy) + EDAM_data:1507: + text: EDAM_data:1507 + description: Amino acid index (White-Wimley data) + title: Amino acid index (White-Wimley data) + EDAM_data:1508: + text: EDAM_data:1508 + description: Amino acid index (van der Waals radii) + title: Amino acid index (van der Waals radii) + EDAM_data:1519: + text: EDAM_data:1519 + description: Peptide molecular weights + title: Peptide molecular weights + EDAM_data:1520: + text: EDAM_data:1520 + description: Peptide hydrophobic moment + title: Peptide hydrophobic moment + EDAM_data:1521: + text: EDAM_data:1521 + description: Protein aliphatic index + title: Protein aliphatic index + EDAM_data:1522: + text: EDAM_data:1522 + description: Protein sequence hydropathy plot + title: Protein sequence hydropathy plot + EDAM_data:1523: + text: EDAM_data:1523 + description: Protein charge plot + title: Protein charge plot + EDAM_data:1524: + text: EDAM_data:1524 + description: Protein solubility + title: Protein solubility + EDAM_data:1525: + text: EDAM_data:1525 + description: Protein crystallizability + title: Protein crystallizability + EDAM_data:1526: + text: EDAM_data:1526 + description: Protein globularity + title: Protein globularity + EDAM_data:1527: + text: EDAM_data:1527 + description: Protein titration curve + title: Protein titration curve + EDAM_data:1528: + text: EDAM_data:1528 + description: Protein isoelectric point + title: Protein isoelectric point + EDAM_data:1529: + text: EDAM_data:1529 + description: Protein pKa value + title: Protein pKa value + EDAM_data:1530: + text: EDAM_data:1530 + description: Protein hydrogen exchange rate + title: Protein hydrogen exchange rate + EDAM_data:1531: + text: EDAM_data:1531 + description: Protein extinction coefficient + title: Protein extinction coefficient + EDAM_data:1532: + text: EDAM_data:1532 + description: Protein optical density + title: Protein optical density + EDAM_data:1534: + text: EDAM_data:1534 + description: Peptide immunogenicity data + title: Peptide immunogenicity data + EDAM_data:1537: + text: EDAM_data:1537 + description: Protein structure report + title: Protein structure report + EDAM_data:1539: + text: EDAM_data:1539 + description: Protein structural quality report + title: Protein structural quality report + EDAM_data:1542: + text: EDAM_data:1542 + description: Protein solvent accessibility + title: Protein solvent accessibility + EDAM_data:1544: + text: EDAM_data:1544 + description: Ramachandran plot + title: Ramachandran plot + EDAM_data:1545: + text: EDAM_data:1545 + description: Protein dipole moment + title: Protein dipole moment + EDAM_data:1546: + text: EDAM_data:1546 + description: Protein distance matrix + title: Protein distance matrix + EDAM_data:1547: + text: EDAM_data:1547 + description: Protein contact map + title: Protein contact map + EDAM_data:1548: + text: EDAM_data:1548 + description: Protein residue 3D cluster + title: Protein residue 3D cluster + EDAM_data:1549: + text: EDAM_data:1549 + description: Protein hydrogen bonds + title: Protein hydrogen bonds + EDAM_data:1566: + text: EDAM_data:1566 + description: Protein-ligand interaction report + title: Protein-ligand interaction report + EDAM_data:1583: + text: EDAM_data:1583 + description: Nucleic acid melting profile + title: Nucleic acid melting profile + EDAM_data:1584: + text: EDAM_data:1584 + description: Nucleic acid enthalpy + title: Nucleic acid enthalpy + EDAM_data:1585: + text: EDAM_data:1585 + description: Nucleic acid entropy + title: Nucleic acid entropy + EDAM_data:1588: + text: EDAM_data:1588 + description: DNA base pair stacking energies data + title: DNA base pair stacking energies data + EDAM_data:1589: + text: EDAM_data:1589 + description: DNA base pair twist angle data + title: DNA base pair twist angle data + EDAM_data:1590: + text: EDAM_data:1590 + description: DNA base trimer roll angles data + title: DNA base trimer roll angles data + EDAM_data:1595: + text: EDAM_data:1595 + description: Base pairing probability matrix dotplot + title: Base pairing probability matrix dotplot + EDAM_data:1596: + text: EDAM_data:1596 + description: Nucleic acid folding report + title: Nucleic acid folding report + EDAM_data:1597: + text: EDAM_data:1597 + description: Codon usage table + title: Codon usage table + EDAM_data:1598: + text: EDAM_data:1598 + description: Genetic code + title: Genetic code + EDAM_data:1600: + text: EDAM_data:1600 + description: Codon usage bias plot + title: Codon usage bias plot + EDAM_data:1602: + text: EDAM_data:1602 + description: Codon usage fraction difference + title: Codon usage fraction difference + EDAM_data:1621: + text: EDAM_data:1621 + description: Pharmacogenomic test report + title: Pharmacogenomic test report + EDAM_data:1622: + text: EDAM_data:1622 + description: Disease report + title: Disease report + EDAM_data:1636: + text: EDAM_data:1636 + description: Heat map + title: Heat map + EDAM_data:1667: + text: EDAM_data:1667 + description: E-value + title: E-value + EDAM_data:1668: + text: EDAM_data:1668 + description: Z-value + title: Z-value + EDAM_data:1669: + text: EDAM_data:1669 + description: P-value + title: P-value + EDAM_data:1689: + text: EDAM_data:1689 + description: Username + title: Username + EDAM_data:1690: + text: EDAM_data:1690 + description: Password + title: Password + EDAM_data:1691: + text: EDAM_data:1691 + description: Email address + title: Email address + EDAM_data:1692: + text: EDAM_data:1692 + description: Person name + title: Person name + EDAM_data:1696: + text: EDAM_data:1696 + description: Drug report + title: Drug report + EDAM_data:1707: + text: EDAM_data:1707 + description: Phylogenetic tree image + title: Phylogenetic tree image + EDAM_data:1708: + text: EDAM_data:1708 + description: RNA secondary structure image + title: RNA secondary structure image + EDAM_data:1709: + text: EDAM_data:1709 + description: Protein secondary structure image + title: Protein secondary structure image + EDAM_data:1710: + text: EDAM_data:1710 + description: Structure image + title: Structure image + EDAM_data:1711: + text: EDAM_data:1711 + description: Sequence alignment image + title: Sequence alignment image + EDAM_data:1712: + text: EDAM_data:1712 + description: Chemical structure image + title: Chemical structure image + EDAM_data:1713: + text: EDAM_data:1713 + description: Fate map + title: Fate map + EDAM_data:1714: + text: EDAM_data:1714 + description: Microarray spots image + title: Microarray spots image + EDAM_data:1731: + text: EDAM_data:1731 + description: Ontology concept definition + title: Ontology concept definition + EDAM_data:1742: + text: EDAM_data:1742 + description: PDB residue number + title: PDB residue number + EDAM_data:1743: + text: EDAM_data:1743 + description: Atomic coordinate + title: Atomic coordinate + EDAM_data:1748: + text: EDAM_data:1748 + description: PDB atom name + title: PDB atom name + EDAM_data:1755: + text: EDAM_data:1755 + description: Protein atom + title: Protein atom + EDAM_data:1756: + text: EDAM_data:1756 + description: Protein residue + title: Protein residue + EDAM_data:1757: + text: EDAM_data:1757 + description: Atom name + title: Atom name + EDAM_data:1758: + text: EDAM_data:1758 + description: PDB residue name + title: PDB residue name + EDAM_data:1759: + text: EDAM_data:1759 + description: PDB model number + title: PDB model number + EDAM_data:1771: + text: EDAM_data:1771 + description: Sequence version + title: Sequence version + EDAM_data:1772: + text: EDAM_data:1772 + description: Score + title: Score + EDAM_data:1794: + text: EDAM_data:1794 + description: Gene ID (PlasmoDB) + title: Gene ID (PlasmoDB) + EDAM_data:1795: + text: EDAM_data:1795 + description: Gene ID (EcoGene) + title: Gene ID (EcoGene) + EDAM_data:1796: + text: EDAM_data:1796 + description: Gene ID (FlyBase) + title: Gene ID (FlyBase) + EDAM_data:1802: + text: EDAM_data:1802 + description: Gene ID (Gramene) + title: Gene ID (Gramene) + EDAM_data:1803: + text: EDAM_data:1803 + description: Gene ID (Virginia microbial) + title: Gene ID (Virginia microbial) + EDAM_data:1804: + text: EDAM_data:1804 + description: Gene ID (SGN) + title: Gene ID (SGN) + EDAM_data:1805: + text: EDAM_data:1805 + description: Gene ID (WormBase) + title: Gene ID (WormBase) + EDAM_data:1807: + text: EDAM_data:1807 + description: ORF name + title: ORF name + EDAM_data:1855: + text: EDAM_data:1855 + description: Clone ID + title: Clone ID + EDAM_data:1856: + text: EDAM_data:1856 + description: PDB insertion code + title: PDB insertion code + EDAM_data:1857: + text: EDAM_data:1857 + description: Atomic occupancy + title: Atomic occupancy + EDAM_data:1858: + text: EDAM_data:1858 + description: Isotropic B factor + title: Isotropic B factor + EDAM_data:1859: + text: EDAM_data:1859 + description: Deletion map + title: Deletion map + EDAM_data:1860: + text: EDAM_data:1860 + description: QTL map + title: QTL map + EDAM_data:1863: + text: EDAM_data:1863 + description: Haplotype map + title: Haplotype map + EDAM_data:1867: + text: EDAM_data:1867 + description: Protein fold name + title: Protein fold name + EDAM_data:1868: + text: EDAM_data:1868 + description: Taxon + title: Taxon + EDAM_data:1869: + text: EDAM_data:1869 + description: Organism identifier + title: Organism identifier + EDAM_data:1870: + text: EDAM_data:1870 + description: Genus name + title: Genus name + EDAM_data:1872: + text: EDAM_data:1872 + description: Taxonomic classification + title: Taxonomic classification + EDAM_data:1873: + text: EDAM_data:1873 + description: iHOP organism ID + title: iHOP organism ID + EDAM_data:1874: + text: EDAM_data:1874 + description: Genbank common name + title: Genbank common name + EDAM_data:1875: + text: EDAM_data:1875 + description: NCBI taxon + title: NCBI taxon + EDAM_data:1881: + text: EDAM_data:1881 + description: Author ID + title: Author ID + EDAM_data:1882: + text: EDAM_data:1882 + description: DragonDB author identifier + title: DragonDB author identifier + EDAM_data:1883: + text: EDAM_data:1883 + description: Annotated URI + title: Annotated URI + EDAM_data:1885: + text: EDAM_data:1885 + description: Gene ID (GeneFarm) + title: Gene ID (GeneFarm) + EDAM_data:1886: + text: EDAM_data:1886 + description: Blattner number + title: Blattner number + EDAM_data:1891: + text: EDAM_data:1891 + description: iHOP symbol + title: iHOP symbol + EDAM_data:1893: + text: EDAM_data:1893 + description: Locus ID + title: Locus ID + EDAM_data:1895: + text: EDAM_data:1895 + description: Locus ID (AGI) + title: Locus ID (AGI) + EDAM_data:1896: + text: EDAM_data:1896 + description: Locus ID (ASPGD) + title: Locus ID (ASPGD) + EDAM_data:1897: + text: EDAM_data:1897 + description: Locus ID (MGG) + title: Locus ID (MGG) + EDAM_data:1898: + text: EDAM_data:1898 + description: Locus ID (CGD) + title: Locus ID (CGD) + EDAM_data:1899: + text: EDAM_data:1899 + description: Locus ID (CMR) + title: Locus ID (CMR) + EDAM_data:1900: + text: EDAM_data:1900 + description: NCBI locus tag + title: NCBI locus tag + EDAM_data:1901: + text: EDAM_data:1901 + description: Locus ID (SGD) + title: Locus ID (SGD) + EDAM_data:1902: + text: EDAM_data:1902 + description: Locus ID (MMP) + title: Locus ID (MMP) + EDAM_data:1903: + text: EDAM_data:1903 + description: Locus ID (DictyBase) + title: Locus ID (DictyBase) + EDAM_data:1904: + text: EDAM_data:1904 + description: Locus ID (EntrezGene) + title: Locus ID (EntrezGene) + EDAM_data:1905: + text: EDAM_data:1905 + description: Locus ID (MaizeGDB) + title: Locus ID (MaizeGDB) + EDAM_data:1907: + text: EDAM_data:1907 + description: Gene ID (KOME) + title: Gene ID (KOME) + EDAM_data:1908: + text: EDAM_data:1908 + description: Locus ID (Tropgene) + title: Locus ID (Tropgene) + EDAM_data:1916: + text: EDAM_data:1916 + description: Alignment + title: Alignment + EDAM_data:1917: + text: EDAM_data:1917 + description: Atomic property + title: Atomic property + EDAM_data:2007: + text: EDAM_data:2007 + description: UniProt keyword + title: UniProt keyword + EDAM_data:2012: + text: EDAM_data:2012 + description: Sequence coordinates + title: Sequence coordinates + EDAM_data:2016: + text: EDAM_data:2016 + description: Amino acid property + title: Amino acid property + EDAM_data:2019: + text: EDAM_data:2019 + description: Map data + title: Map data + EDAM_data:2024: + text: EDAM_data:2024 + description: Enzyme kinetics data + title: Enzyme kinetics data + EDAM_data:2025: + text: EDAM_data:2025 + description: Michaelis Menten plot + title: Michaelis Menten plot + EDAM_data:2026: + text: EDAM_data:2026 + description: Hanes Woolf plot + title: Hanes Woolf plot + EDAM_data:2042: + text: EDAM_data:2042 + description: Evidence + title: Evidence + EDAM_data:2044: + text: EDAM_data:2044 + description: Sequence + title: Sequence + EDAM_data:2048: + text: EDAM_data:2048 + description: Report + title: Report + EDAM_data:2050: + text: EDAM_data:2050 + description: Molecular property (general) + title: Molecular property (general) + EDAM_data:2070: + text: EDAM_data:2070 + description: Sequence motif (nucleic acid) + title: Sequence motif (nucleic acid) + EDAM_data:2071: + text: EDAM_data:2071 + description: Sequence motif (protein) + title: Sequence motif (protein) + EDAM_data:2080: + text: EDAM_data:2080 + description: Database search results + title: Database search results + EDAM_data:2082: + text: EDAM_data:2082 + description: Matrix + title: Matrix + EDAM_data:2084: + text: EDAM_data:2084 + description: Nucleic acid report + title: Nucleic acid report + EDAM_data:2085: + text: EDAM_data:2085 + description: Structure report + title: Structure report + EDAM_data:2087: + text: EDAM_data:2087 + description: Molecular property + title: Molecular property + EDAM_data:2088: + text: EDAM_data:2088 + description: DNA base structural data + title: DNA base structural data + EDAM_data:2091: + text: EDAM_data:2091 + description: Accession + title: Accession + EDAM_data:2093: + text: EDAM_data:2093 + description: Data reference + title: Data reference + EDAM_data:2098: + text: EDAM_data:2098 + description: Job identifier + title: Job identifier + EDAM_data:2099: + text: EDAM_data:2099 + description: Name + title: Name + EDAM_data:2101: + text: EDAM_data:2101 + description: Account authentication + title: Account authentication + EDAM_data:2102: + text: EDAM_data:2102 + description: KEGG organism code + title: KEGG organism code + EDAM_data:2104: + text: EDAM_data:2104 + description: BioCyc ID + title: BioCyc ID + EDAM_data:2105: + text: EDAM_data:2105 + description: Compound ID (BioCyc) + title: Compound ID (BioCyc) + EDAM_data:2106: + text: EDAM_data:2106 + description: Reaction ID (BioCyc) + title: Reaction ID (BioCyc) + EDAM_data:2107: + text: EDAM_data:2107 + description: Enzyme ID (BioCyc) + title: Enzyme ID (BioCyc) + EDAM_data:2108: + text: EDAM_data:2108 + description: Reaction ID + title: Reaction ID + EDAM_data:2109: + text: EDAM_data:2109 + description: Identifier (hybrid) + title: Identifier (hybrid) + EDAM_data:2110: + text: EDAM_data:2110 + description: Molecular property identifier + title: Molecular property identifier + EDAM_data:2111: + text: EDAM_data:2111 + description: Codon usage table ID + title: Codon usage table ID + EDAM_data:2112: + text: EDAM_data:2112 + description: FlyBase primary identifier + title: FlyBase primary identifier + EDAM_data:2113: + text: EDAM_data:2113 + description: WormBase identifier + title: WormBase identifier + EDAM_data:2114: + text: EDAM_data:2114 + description: WormBase wormpep ID + title: WormBase wormpep ID + EDAM_data:2117: + text: EDAM_data:2117 + description: Map identifier + title: Map identifier + EDAM_data:2118: + text: EDAM_data:2118 + description: Person identifier + title: Person identifier + EDAM_data:2119: + text: EDAM_data:2119 + description: Nucleic acid identifier + title: Nucleic acid identifier + EDAM_data:2127: + text: EDAM_data:2127 + description: Genetic code identifier + title: Genetic code identifier + EDAM_data:2128: + text: EDAM_data:2128 + description: Genetic code name + title: Genetic code name + EDAM_data:2129: + text: EDAM_data:2129 + description: File format name + title: File format name + EDAM_data:2131: + text: EDAM_data:2131 + description: Operating system name + title: Operating system name + EDAM_data:2133: + text: EDAM_data:2133 + description: Logical operator + title: Logical operator + EDAM_data:2137: + text: EDAM_data:2137 + description: Gap penalty + title: Gap penalty + EDAM_data:2139: + text: EDAM_data:2139 + description: Nucleic acid melting temperature + title: Nucleic acid melting temperature + EDAM_data:2140: + text: EDAM_data:2140 + description: Concentration + title: Concentration + EDAM_data:2154: + text: EDAM_data:2154 + description: Sequence name + title: Sequence name + EDAM_data:2160: + text: EDAM_data:2160 + description: Fickett testcode plot + title: Fickett testcode plot + EDAM_data:2161: + text: EDAM_data:2161 + description: Sequence similarity plot + title: Sequence similarity plot + EDAM_data:2162: + text: EDAM_data:2162 + description: Helical wheel + title: Helical wheel + EDAM_data:2163: + text: EDAM_data:2163 + description: Helical net + title: Helical net + EDAM_data:2165: + text: EDAM_data:2165 + description: Protein ionisation curve + title: Protein ionisation curve + EDAM_data:2166: + text: EDAM_data:2166 + description: Sequence composition plot + title: Sequence composition plot + EDAM_data:2167: + text: EDAM_data:2167 + description: Nucleic acid density plot + title: Nucleic acid density plot + EDAM_data:2168: + text: EDAM_data:2168 + description: Sequence trace image + title: Sequence trace image + EDAM_data:2174: + text: EDAM_data:2174 + description: FlyBase secondary identifier + title: FlyBase secondary identifier + EDAM_data:2190: + text: EDAM_data:2190 + description: Sequence checksum + title: Sequence checksum + EDAM_data:2193: + text: EDAM_data:2193 + description: Database entry metadata + title: Database entry metadata + EDAM_data:2208: + text: EDAM_data:2208 + description: Plasmid identifier + title: Plasmid identifier + EDAM_data:2209: + text: EDAM_data:2209 + description: Mutation ID + title: Mutation ID + EDAM_data:2216: + text: EDAM_data:2216 + description: Codon number + title: Codon number + EDAM_data:2219: + text: EDAM_data:2219 + description: Database field name + title: Database field name + EDAM_data:2220: + text: EDAM_data:2220 + description: Sequence cluster ID (SYSTERS) + title: Sequence cluster ID (SYSTERS) + EDAM_data:2223: + text: EDAM_data:2223 + description: Ontology metadata + title: Ontology metadata + EDAM_data:2253: + text: EDAM_data:2253 + description: Data resource definition name + title: Data resource definition name + EDAM_data:2254: + text: EDAM_data:2254 + description: OBO file format name + title: OBO file format name + EDAM_data:2285: + text: EDAM_data:2285 + description: Gene ID (MIPS) + title: Gene ID (MIPS) + EDAM_data:2290: + text: EDAM_data:2290 + description: EMBL accession + title: EMBL accession + EDAM_data:2291: + text: EDAM_data:2291 + description: UniProt ID + title: UniProt ID + EDAM_data:2292: + text: EDAM_data:2292 + description: GenBank accession + title: GenBank accession + EDAM_data:2293: + text: EDAM_data:2293 + description: Gramene secondary identifier + title: Gramene secondary identifier + EDAM_data:2294: + text: EDAM_data:2294 + description: Sequence variation ID + title: Sequence variation ID + EDAM_data:2295: + text: EDAM_data:2295 + description: Gene ID + title: Gene ID + EDAM_data:2297: + text: EDAM_data:2297 + description: Gene ID (ECK) + title: Gene ID (ECK) + EDAM_data:2298: + text: EDAM_data:2298 + description: Gene ID (HGNC) + title: Gene ID (HGNC) + EDAM_data:2299: + text: EDAM_data:2299 + description: Gene name + title: Gene name + EDAM_data:2301: + text: EDAM_data:2301 + description: SMILES string + title: SMILES string + EDAM_data:2302: + text: EDAM_data:2302 + description: STRING ID + title: STRING ID + EDAM_data:2309: + text: EDAM_data:2309 + description: Reaction ID (SABIO-RK) + title: Reaction ID (SABIO-RK) + EDAM_data:2313: + text: EDAM_data:2313 + description: Carbohydrate report + title: Carbohydrate report + EDAM_data:2314: + text: EDAM_data:2314 + description: GI number + title: GI number + EDAM_data:2315: + text: EDAM_data:2315 + description: NCBI version + title: NCBI version + EDAM_data:2316: + text: EDAM_data:2316 + description: Cell line name + title: Cell line name + EDAM_data:2317: + text: EDAM_data:2317 + description: Cell line name (exact) + title: Cell line name (exact) + EDAM_data:2318: + text: EDAM_data:2318 + description: Cell line name (truncated) + title: Cell line name (truncated) + EDAM_data:2319: + text: EDAM_data:2319 + description: Cell line name (no punctuation) + title: Cell line name (no punctuation) + EDAM_data:2320: + text: EDAM_data:2320 + description: Cell line name (assonant) + title: Cell line name (assonant) + EDAM_data:2321: + text: EDAM_data:2321 + description: Enzyme ID + title: Enzyme ID + EDAM_data:2325: + text: EDAM_data:2325 + description: REBASE enzyme number + title: REBASE enzyme number + EDAM_data:2326: + text: EDAM_data:2326 + description: DrugBank ID + title: DrugBank ID + EDAM_data:2327: + text: EDAM_data:2327 + description: GI number (protein) + title: GI number (protein) + EDAM_data:2335: + text: EDAM_data:2335 + description: Bit score + title: Bit score + EDAM_data:2337: + text: EDAM_data:2337 + description: Resource metadata + title: Resource metadata + EDAM_data:2338: + text: EDAM_data:2338 + description: Ontology identifier + title: Ontology identifier + EDAM_data:2339: + text: EDAM_data:2339 + description: Ontology concept name + title: Ontology concept name + EDAM_data:2340: + text: EDAM_data:2340 + description: Genome build identifier + title: Genome build identifier + EDAM_data:2342: + text: EDAM_data:2342 + description: Pathway or network name + title: Pathway or network name + EDAM_data:2343: + text: EDAM_data:2343 + description: Pathway ID (KEGG) + title: Pathway ID (KEGG) + EDAM_data:2344: + text: EDAM_data:2344 + description: Pathway ID (NCI-Nature) + title: Pathway ID (NCI-Nature) + EDAM_data:2345: + text: EDAM_data:2345 + description: Pathway ID (ConsensusPathDB) + title: Pathway ID (ConsensusPathDB) + EDAM_data:2346: + text: EDAM_data:2346 + description: Sequence cluster ID (UniRef) + title: Sequence cluster ID (UniRef) + EDAM_data:2347: + text: EDAM_data:2347 + description: Sequence cluster ID (UniRef100) + title: Sequence cluster ID (UniRef100) + EDAM_data:2348: + text: EDAM_data:2348 + description: Sequence cluster ID (UniRef90) + title: Sequence cluster ID (UniRef90) + EDAM_data:2349: + text: EDAM_data:2349 + description: Sequence cluster ID (UniRef50) + title: Sequence cluster ID (UniRef50) + EDAM_data:2353: + text: EDAM_data:2353 + description: Ontology data + title: Ontology data + EDAM_data:2354: + text: EDAM_data:2354 + description: RNA family report + title: RNA family report + EDAM_data:2355: + text: EDAM_data:2355 + description: RNA family identifier + title: RNA family identifier + EDAM_data:2356: + text: EDAM_data:2356 + description: RFAM accession + title: RFAM accession + EDAM_data:2362: + text: EDAM_data:2362 + description: Sequence accession (hybrid) + title: Sequence accession (hybrid) + EDAM_data:2365: + text: EDAM_data:2365 + description: Pathway or network accession + title: Pathway or network accession + EDAM_data:2366: + text: EDAM_data:2366 + description: Secondary structure alignment + title: Secondary structure alignment + EDAM_data:2367: + text: EDAM_data:2367 + description: ASTD ID + title: ASTD ID + EDAM_data:2368: + text: EDAM_data:2368 + description: ASTD ID (exon) + title: ASTD ID (exon) + EDAM_data:2369: + text: EDAM_data:2369 + description: ASTD ID (intron) + title: ASTD ID (intron) + EDAM_data:2370: + text: EDAM_data:2370 + description: ASTD ID (polya) + title: ASTD ID (polya) + EDAM_data:2371: + text: EDAM_data:2371 + description: ASTD ID (tss) + title: ASTD ID (tss) + EDAM_data:2373: + text: EDAM_data:2373 + description: Spot ID + title: Spot ID + EDAM_data:2374: + text: EDAM_data:2374 + description: Spot serial number + title: Spot serial number + EDAM_data:2375: + text: EDAM_data:2375 + description: Spot ID (HSC-2DPAGE) + title: Spot ID (HSC-2DPAGE) + EDAM_data:2379: + text: EDAM_data:2379 + description: Strain identifier + title: Strain identifier + EDAM_data:2380: + text: EDAM_data:2380 + description: CABRI accession + title: CABRI accession + EDAM_data:2382: + text: EDAM_data:2382 + description: Genotype experiment ID + title: Genotype experiment ID + EDAM_data:2383: + text: EDAM_data:2383 + description: EGA accession + title: EGA accession + EDAM_data:2384: + text: EDAM_data:2384 + description: IPI protein ID + title: IPI protein ID + EDAM_data:2385: + text: EDAM_data:2385 + description: RefSeq accession (protein) + title: RefSeq accession (protein) + EDAM_data:2386: + text: EDAM_data:2386 + description: EPD ID + title: EPD ID + EDAM_data:2387: + text: EDAM_data:2387 + description: TAIR accession + title: TAIR accession + EDAM_data:2388: + text: EDAM_data:2388 + description: TAIR accession (At gene) + title: TAIR accession (At gene) + EDAM_data:2389: + text: EDAM_data:2389 + description: UniSTS accession + title: UniSTS accession + EDAM_data:2390: + text: EDAM_data:2390 + description: UNITE accession + title: UNITE accession + EDAM_data:2391: + text: EDAM_data:2391 + description: UTR accession + title: UTR accession + EDAM_data:2392: + text: EDAM_data:2392 + description: UniParc accession + title: UniParc accession + EDAM_data:2393: + text: EDAM_data:2393 + description: mFLJ/mKIAA number + title: mFLJ/mKIAA number + EDAM_data:2398: + text: EDAM_data:2398 + description: Ensembl protein ID + title: Ensembl protein ID + EDAM_data:2523: + text: EDAM_data:2523 + description: Phylogenetic data + title: Phylogenetic data + EDAM_data:2526: + text: EDAM_data:2526 + description: Text data + title: Text data + EDAM_data:2530: + text: EDAM_data:2530 + description: Organism report + title: Organism report + EDAM_data:2531: + text: EDAM_data:2531 + description: Protocol + title: Protocol + EDAM_data:2534: + text: EDAM_data:2534 + description: Sequence attribute + title: Sequence attribute + EDAM_data:2535: + text: EDAM_data:2535 + description: Sequence tag profile + title: Sequence tag profile + EDAM_data:2536: + text: EDAM_data:2536 + description: Mass spectrometry data + title: Mass spectrometry data + EDAM_data:2537: + text: EDAM_data:2537 + description: Protein structure raw data + title: Protein structure raw data + EDAM_data:2538: + text: EDAM_data:2538 + description: Mutation identifier + title: Mutation identifier + EDAM_data:2563: + text: EDAM_data:2563 + description: Amino acid name (single letter) + title: Amino acid name (single letter) + EDAM_data:2564: + text: EDAM_data:2564 + description: Amino acid name (three letter) + title: Amino acid name (three letter) + EDAM_data:2565: + text: EDAM_data:2565 + description: Amino acid name (full name) + title: Amino acid name (full name) + EDAM_data:2576: + text: EDAM_data:2576 + description: Toxin identifier + title: Toxin identifier + EDAM_data:2578: + text: EDAM_data:2578 + description: ArachnoServer ID + title: ArachnoServer ID + EDAM_data:2580: + text: EDAM_data:2580 + description: BindingDB Monomer ID + title: BindingDB Monomer ID + EDAM_data:2582: + text: EDAM_data:2582 + description: GO concept ID (biological process) + title: GO concept ID (biological process) + EDAM_data:2583: + text: EDAM_data:2583 + description: GO concept ID (molecular function) + title: GO concept ID (molecular function) + EDAM_data:2586: + text: EDAM_data:2586 + description: Northern blot image + title: Northern blot image + EDAM_data:2587: + text: EDAM_data:2587 + description: Blot ID + title: Blot ID + EDAM_data:2588: + text: EDAM_data:2588 + description: BlotBase blot ID + title: BlotBase blot ID + EDAM_data:2589: + text: EDAM_data:2589 + description: Hierarchy + title: Hierarchy + EDAM_data:2591: + text: EDAM_data:2591 + description: Brite hierarchy ID + title: Brite hierarchy ID + EDAM_data:2593: + text: EDAM_data:2593 + description: BRENDA organism ID + title: BRENDA organism ID + EDAM_data:2594: + text: EDAM_data:2594 + description: UniGene taxon + title: UniGene taxon + EDAM_data:2595: + text: EDAM_data:2595 + description: UTRdb taxon + title: UTRdb taxon + EDAM_data:2596: + text: EDAM_data:2596 + description: Catalogue ID + title: Catalogue ID + EDAM_data:2597: + text: EDAM_data:2597 + description: CABRI catalogue name + title: CABRI catalogue name + EDAM_data:2600: + text: EDAM_data:2600 + description: Pathway or network + title: Pathway or network + EDAM_data:2603: + text: EDAM_data:2603 + description: Expression data + title: Expression data + EDAM_data:2605: + text: EDAM_data:2605 + description: Compound ID (KEGG) + title: Compound ID (KEGG) + EDAM_data:2606: + text: EDAM_data:2606 + description: RFAM name + title: RFAM name + EDAM_data:2608: + text: EDAM_data:2608 + description: Reaction ID (KEGG) + title: Reaction ID (KEGG) + EDAM_data:2609: + text: EDAM_data:2609 + description: Drug ID (KEGG) + title: Drug ID (KEGG) + EDAM_data:2610: + text: EDAM_data:2610 + description: Ensembl ID + title: Ensembl ID + EDAM_data:2611: + text: EDAM_data:2611 + description: ICD identifier + title: ICD identifier + EDAM_data:2612: + text: EDAM_data:2612 + description: Sequence cluster ID (CluSTr) + title: Sequence cluster ID (CluSTr) + EDAM_data:2613: + text: EDAM_data:2613 + description: KEGG Glycan ID + title: KEGG Glycan ID + EDAM_data:2614: + text: EDAM_data:2614 + description: TCDB ID + title: TCDB ID + EDAM_data:2615: + text: EDAM_data:2615 + description: MINT ID + title: MINT ID + EDAM_data:2616: + text: EDAM_data:2616 + description: DIP ID + title: DIP ID + EDAM_data:2617: + text: EDAM_data:2617 + description: Signaling Gateway protein ID + title: Signaling Gateway protein ID + EDAM_data:2618: + text: EDAM_data:2618 + description: Protein modification ID + title: Protein modification ID + EDAM_data:2619: + text: EDAM_data:2619 + description: RESID ID + title: RESID ID + EDAM_data:2620: + text: EDAM_data:2620 + description: RGD ID + title: RGD ID + EDAM_data:2621: + text: EDAM_data:2621 + description: TAIR accession (protein) + title: TAIR accession (protein) + EDAM_data:2622: + text: EDAM_data:2622 + description: Compound ID (HMDB) + title: Compound ID (HMDB) + EDAM_data:2625: + text: EDAM_data:2625 + description: LIPID MAPS ID + title: LIPID MAPS ID + EDAM_data:2626: + text: EDAM_data:2626 + description: PeptideAtlas ID + title: PeptideAtlas ID + EDAM_data:2628: + text: EDAM_data:2628 + description: BioGRID interaction ID + title: BioGRID interaction ID + EDAM_data:2629: + text: EDAM_data:2629 + description: Enzyme ID (MEROPS) + title: Enzyme ID (MEROPS) + EDAM_data:2630: + text: EDAM_data:2630 + description: Mobile genetic element ID + title: Mobile genetic element ID + EDAM_data:2631: + text: EDAM_data:2631 + description: ACLAME ID + title: ACLAME ID + EDAM_data:2632: + text: EDAM_data:2632 + description: SGD ID + title: SGD ID + EDAM_data:2633: + text: EDAM_data:2633 + description: Book ID + title: Book ID + EDAM_data:2634: + text: EDAM_data:2634 + description: ISBN + title: ISBN + EDAM_data:2635: + text: EDAM_data:2635 + description: Compound ID (3DMET) + title: Compound ID (3DMET) + EDAM_data:2636: + text: EDAM_data:2636 + description: MatrixDB interaction ID + title: MatrixDB interaction ID + EDAM_data:2637: + text: EDAM_data:2637 + description: cPath ID + title: cPath ID + EDAM_data:2638: + text: EDAM_data:2638 + description: PubChem bioassay ID + title: PubChem bioassay ID + EDAM_data:2639: + text: EDAM_data:2639 + description: PubChem ID + title: PubChem ID + EDAM_data:2641: + text: EDAM_data:2641 + description: Reaction ID (MACie) + title: Reaction ID (MACie) + EDAM_data:2642: + text: EDAM_data:2642 + description: Gene ID (miRBase) + title: Gene ID (miRBase) + EDAM_data:2643: + text: EDAM_data:2643 + description: Gene ID (ZFIN) + title: Gene ID (ZFIN) + EDAM_data:2644: + text: EDAM_data:2644 + description: Reaction ID (Rhea) + title: Reaction ID (Rhea) + EDAM_data:2645: + text: EDAM_data:2645 + description: Pathway ID (Unipathway) + title: Pathway ID (Unipathway) + EDAM_data:2646: + text: EDAM_data:2646 + description: Compound ID (ChEMBL) + title: Compound ID (ChEMBL) + EDAM_data:2647: + text: EDAM_data:2647 + description: LGICdb identifier + title: LGICdb identifier + EDAM_data:2648: + text: EDAM_data:2648 + description: Reaction kinetics ID (SABIO-RK) + title: Reaction kinetics ID (SABIO-RK) + EDAM_data:2649: + text: EDAM_data:2649 + description: PharmGKB ID + title: PharmGKB ID + EDAM_data:2650: + text: EDAM_data:2650 + description: Pathway ID (PharmGKB) + title: Pathway ID (PharmGKB) + EDAM_data:2651: + text: EDAM_data:2651 + description: Disease ID (PharmGKB) + title: Disease ID (PharmGKB) + EDAM_data:2652: + text: EDAM_data:2652 + description: Drug ID (PharmGKB) + title: Drug ID (PharmGKB) + EDAM_data:2653: + text: EDAM_data:2653 + description: Drug ID (TTD) + title: Drug ID (TTD) + EDAM_data:2654: + text: EDAM_data:2654 + description: Target ID (TTD) + title: Target ID (TTD) + EDAM_data:2655: + text: EDAM_data:2655 + description: Cell type identifier + title: Cell type identifier + EDAM_data:2656: + text: EDAM_data:2656 + description: NeuronDB ID + title: NeuronDB ID + EDAM_data:2657: + text: EDAM_data:2657 + description: NeuroMorpho ID + title: NeuroMorpho ID + EDAM_data:2658: + text: EDAM_data:2658 + description: Compound ID (ChemIDplus) + title: Compound ID (ChemIDplus) + EDAM_data:2659: + text: EDAM_data:2659 + description: Pathway ID (SMPDB) + title: Pathway ID (SMPDB) + EDAM_data:2660: + text: EDAM_data:2660 + description: BioNumbers ID + title: BioNumbers ID + EDAM_data:2662: + text: EDAM_data:2662 + description: T3DB ID + title: T3DB ID + EDAM_data:2663: + text: EDAM_data:2663 + description: Carbohydrate identifier + title: Carbohydrate identifier + EDAM_data:2664: + text: EDAM_data:2664 + description: GlycomeDB ID + title: GlycomeDB ID + EDAM_data:2665: + text: EDAM_data:2665 + description: LipidBank ID + title: LipidBank ID + EDAM_data:2666: + text: EDAM_data:2666 + description: CDD ID + title: CDD ID + EDAM_data:2667: + text: EDAM_data:2667 + description: MMDB ID + title: MMDB ID + EDAM_data:2668: + text: EDAM_data:2668 + description: iRefIndex ID + title: iRefIndex ID + EDAM_data:2669: + text: EDAM_data:2669 + description: ModelDB ID + title: ModelDB ID + EDAM_data:2670: + text: EDAM_data:2670 + description: Pathway ID (DQCS) + title: Pathway ID (DQCS) + EDAM_data:2700: + text: EDAM_data:2700 + description: CATH identifier + title: CATH identifier + EDAM_data:2701: + text: EDAM_data:2701 + description: CATH node ID (family) + title: CATH node ID (family) + EDAM_data:2702: + text: EDAM_data:2702 + description: Enzyme ID (CAZy) + title: Enzyme ID (CAZy) + EDAM_data:2704: + text: EDAM_data:2704 + description: Clone ID (IMAGE) + title: Clone ID (IMAGE) + EDAM_data:2705: + text: EDAM_data:2705 + description: GO concept ID (cellular component) + title: GO concept ID (cellular component) + EDAM_data:2706: + text: EDAM_data:2706 + description: Chromosome name (BioCyc) + title: Chromosome name (BioCyc) + EDAM_data:2709: + text: EDAM_data:2709 + description: CleanEx entry name + title: CleanEx entry name + EDAM_data:2710: + text: EDAM_data:2710 + description: CleanEx dataset code + title: CleanEx dataset code + EDAM_data:2711: + text: EDAM_data:2711 + description: Genome report + title: Genome report + EDAM_data:2713: + text: EDAM_data:2713 + description: Protein ID (CORUM) + title: Protein ID (CORUM) + EDAM_data:2714: + text: EDAM_data:2714 + description: CDD PSSM-ID + title: CDD PSSM-ID + EDAM_data:2715: + text: EDAM_data:2715 + description: Protein ID (CuticleDB) + title: Protein ID (CuticleDB) + EDAM_data:2716: + text: EDAM_data:2716 + description: DBD ID + title: DBD ID + EDAM_data:2717: + text: EDAM_data:2717 + description: Oligonucleotide probe annotation + title: Oligonucleotide probe annotation + EDAM_data:2718: + text: EDAM_data:2718 + description: Oligonucleotide ID + title: Oligonucleotide ID + EDAM_data:2719: + text: EDAM_data:2719 + description: dbProbe ID + title: dbProbe ID + EDAM_data:2720: + text: EDAM_data:2720 + description: Dinucleotide property + title: Dinucleotide property + EDAM_data:2721: + text: EDAM_data:2721 + description: DiProDB ID + title: DiProDB ID + EDAM_data:2723: + text: EDAM_data:2723 + description: Protein ID (DisProt) + title: Protein ID (DisProt) + EDAM_data:2725: + text: EDAM_data:2725 + description: Ensembl transcript ID + title: Ensembl transcript ID + EDAM_data:2727: + text: EDAM_data:2727 + description: Promoter ID + title: Promoter ID + EDAM_data:2728: + text: EDAM_data:2728 + description: EST accession + title: EST accession + EDAM_data:2729: + text: EDAM_data:2729 + description: COGEME EST ID + title: COGEME EST ID + EDAM_data:2730: + text: EDAM_data:2730 + description: COGEME unisequence ID + title: COGEME unisequence ID + EDAM_data:2731: + text: EDAM_data:2731 + description: Protein family ID (GeneFarm) + title: Protein family ID (GeneFarm) + EDAM_data:2732: + text: EDAM_data:2732 + description: Family name + title: Family name + EDAM_data:2736: + text: EDAM_data:2736 + description: Sequence feature ID (SwissRegulon) + title: Sequence feature ID (SwissRegulon) + EDAM_data:2737: + text: EDAM_data:2737 + description: FIG ID + title: FIG ID + EDAM_data:2738: + text: EDAM_data:2738 + description: Gene ID (Xenbase) + title: Gene ID (Xenbase) + EDAM_data:2739: + text: EDAM_data:2739 + description: Gene ID (Genolist) + title: Gene ID (Genolist) + EDAM_data:2741: + text: EDAM_data:2741 + description: ABS ID + title: ABS ID + EDAM_data:2742: + text: EDAM_data:2742 + description: AraC-XylS ID + title: AraC-XylS ID + EDAM_data:2744: + text: EDAM_data:2744 + description: Locus ID (PseudoCAP) + title: Locus ID (PseudoCAP) + EDAM_data:2745: + text: EDAM_data:2745 + description: Locus ID (UTR) + title: Locus ID (UTR) + EDAM_data:2746: + text: EDAM_data:2746 + description: MonosaccharideDB ID + title: MonosaccharideDB ID + EDAM_data:2749: + text: EDAM_data:2749 + description: Genome identifier + title: Genome identifier + EDAM_data:2752: + text: EDAM_data:2752 + description: GlycoMap ID + title: GlycoMap ID + EDAM_data:2753: + text: EDAM_data:2753 + description: Carbohydrate conformational map + title: Carbohydrate conformational map + EDAM_data:2755: + text: EDAM_data:2755 + description: Transcription factor name + title: Transcription factor name + EDAM_data:2756: + text: EDAM_data:2756 + description: TCID + title: TCID + EDAM_data:2757: + text: EDAM_data:2757 + description: Pfam domain name + title: Pfam domain name + EDAM_data:2758: + text: EDAM_data:2758 + description: Pfam clan ID + title: Pfam clan ID + EDAM_data:2759: + text: EDAM_data:2759 + description: Gene ID (VectorBase) + title: Gene ID (VectorBase) + EDAM_data:2761: + text: EDAM_data:2761 + description: UTRSite ID + title: UTRSite ID + EDAM_data:2762: + text: EDAM_data:2762 + description: Sequence signature report + title: Sequence signature report + EDAM_data:2764: + text: EDAM_data:2764 + description: Protein name (UniProt) + title: Protein name (UniProt) + EDAM_data:2766: + text: EDAM_data:2766 + description: HAMAP ID + title: HAMAP ID + EDAM_data:2769: + text: EDAM_data:2769 + description: Transcript ID + title: Transcript ID + EDAM_data:2770: + text: EDAM_data:2770 + description: HIT ID + title: HIT ID + EDAM_data:2771: + text: EDAM_data:2771 + description: HIX ID + title: HIX ID + EDAM_data:2772: + text: EDAM_data:2772 + description: HPA antibody id + title: HPA antibody id + EDAM_data:2773: + text: EDAM_data:2773 + description: IMGT/HLA ID + title: IMGT/HLA ID + EDAM_data:2774: + text: EDAM_data:2774 + description: Gene ID (JCVI) + title: Gene ID (JCVI) + EDAM_data:2775: + text: EDAM_data:2775 + description: Kinase name + title: Kinase name + EDAM_data:2776: + text: EDAM_data:2776 + description: ConsensusPathDB entity ID + title: ConsensusPathDB entity ID + EDAM_data:2777: + text: EDAM_data:2777 + description: ConsensusPathDB entity name + title: ConsensusPathDB entity name + EDAM_data:2778: + text: EDAM_data:2778 + description: CCAP strain number + title: CCAP strain number + EDAM_data:2779: + text: EDAM_data:2779 + description: Stock number + title: Stock number + EDAM_data:2780: + text: EDAM_data:2780 + description: Stock number (TAIR) + title: Stock number (TAIR) + EDAM_data:2781: + text: EDAM_data:2781 + description: REDIdb ID + title: REDIdb ID + EDAM_data:2782: + text: EDAM_data:2782 + description: SMART domain name + title: SMART domain name + EDAM_data:2783: + text: EDAM_data:2783 + description: Protein family ID (PANTHER) + title: Protein family ID (PANTHER) + EDAM_data:2784: + text: EDAM_data:2784 + description: RNAVirusDB ID + title: RNAVirusDB ID + EDAM_data:2785: + text: EDAM_data:2785 + description: Virus identifier + title: Virus identifier + EDAM_data:2786: + text: EDAM_data:2786 + description: NCBI Genome Project ID + title: NCBI Genome Project ID + EDAM_data:2787: + text: EDAM_data:2787 + description: NCBI genome accession + title: NCBI genome accession + EDAM_data:2789: + text: EDAM_data:2789 + description: Protein ID (TopDB) + title: Protein ID (TopDB) + EDAM_data:2790: + text: EDAM_data:2790 + description: Gel ID + title: Gel ID + EDAM_data:2791: + text: EDAM_data:2791 + description: Reference map name (SWISS-2DPAGE) + title: Reference map name (SWISS-2DPAGE) + EDAM_data:2792: + text: EDAM_data:2792 + description: Protein ID (PeroxiBase) + title: Protein ID (PeroxiBase) + EDAM_data:2793: + text: EDAM_data:2793 + description: SISYPHUS ID + title: SISYPHUS ID + EDAM_data:2794: + text: EDAM_data:2794 + description: ORF ID + title: ORF ID + EDAM_data:2795: + text: EDAM_data:2795 + description: ORF identifier + title: ORF identifier + EDAM_data:2796: + text: EDAM_data:2796 + description: LINUCS ID + title: LINUCS ID + EDAM_data:2797: + text: EDAM_data:2797 + description: Protein ID (LGICdb) + title: Protein ID (LGICdb) + EDAM_data:2798: + text: EDAM_data:2798 + description: MaizeDB ID + title: MaizeDB ID + EDAM_data:2799: + text: EDAM_data:2799 + description: Gene ID (MfunGD) + title: Gene ID (MfunGD) + EDAM_data:2800: + text: EDAM_data:2800 + description: Orpha number + title: Orpha number + EDAM_data:2802: + text: EDAM_data:2802 + description: Protein ID (EcID) + title: Protein ID (EcID) + EDAM_data:2803: + text: EDAM_data:2803 + description: Clone ID (RefSeq) + title: Clone ID (RefSeq) + EDAM_data:2804: + text: EDAM_data:2804 + description: Protein ID (ConoServer) + title: Protein ID (ConoServer) + EDAM_data:2805: + text: EDAM_data:2805 + description: GeneSNP ID + title: GeneSNP ID + EDAM_data:2812: + text: EDAM_data:2812 + description: Lipid identifier + title: Lipid identifier + EDAM_data:2835: + text: EDAM_data:2835 + description: Gene ID (VBASE2) + title: Gene ID (VBASE2) + EDAM_data:2836: + text: EDAM_data:2836 + description: DPVweb ID + title: DPVweb ID + EDAM_data:2837: + text: EDAM_data:2837 + description: Pathway ID (BioSystems) + title: Pathway ID (BioSystems) + EDAM_data:2849: + text: EDAM_data:2849 + description: Abstract + title: Abstract + EDAM_data:2850: + text: EDAM_data:2850 + description: Lipid structure + title: Lipid structure + EDAM_data:2851: + text: EDAM_data:2851 + description: Drug structure + title: Drug structure + EDAM_data:2852: + text: EDAM_data:2852 + description: Toxin structure + title: Toxin structure + EDAM_data:2854: + text: EDAM_data:2854 + description: Position-specific scoring matrix + title: Position-specific scoring matrix + EDAM_data:2855: + text: EDAM_data:2855 + description: Distance matrix + title: Distance matrix + EDAM_data:2856: + text: EDAM_data:2856 + description: Structural distance matrix + title: Structural distance matrix + EDAM_data:2858: + text: EDAM_data:2858 + description: Ontology concept + title: Ontology concept + EDAM_data:2865: + text: EDAM_data:2865 + description: Codon usage bias + title: Codon usage bias + EDAM_data:2870: + text: EDAM_data:2870 + description: Radiation hybrid map + title: Radiation hybrid map + EDAM_data:2872: + text: EDAM_data:2872 + description: ID list + title: ID list + EDAM_data:2873: + text: EDAM_data:2873 + description: Phylogenetic gene frequencies data + title: Phylogenetic gene frequencies data + EDAM_data:2877: + text: EDAM_data:2877 + description: Protein complex + title: Protein complex + EDAM_data:2878: + text: EDAM_data:2878 + description: Protein structural motif + title: Protein structural motif + EDAM_data:2879: + text: EDAM_data:2879 + description: Lipid report + title: Lipid report + EDAM_data:2884: + text: EDAM_data:2884 + description: Plot + title: Plot + EDAM_data:2886: + text: EDAM_data:2886 + description: Protein sequence record + title: Protein sequence record + EDAM_data:2887: + text: EDAM_data:2887 + description: Nucleic acid sequence record + title: Nucleic acid sequence record + EDAM_data:2891: + text: EDAM_data:2891 + description: Biological model accession + title: Biological model accession + EDAM_data:2892: + text: EDAM_data:2892 + description: Cell type name + title: Cell type name + EDAM_data:2893: + text: EDAM_data:2893 + description: Cell type accession + title: Cell type accession + EDAM_data:2894: + text: EDAM_data:2894 + description: Compound accession + title: Compound accession + EDAM_data:2895: + text: EDAM_data:2895 + description: Drug accession + title: Drug accession + EDAM_data:2896: + text: EDAM_data:2896 + description: Toxin name + title: Toxin name + EDAM_data:2897: + text: EDAM_data:2897 + description: Toxin accession + title: Toxin accession + EDAM_data:2898: + text: EDAM_data:2898 + description: Monosaccharide accession + title: Monosaccharide accession + EDAM_data:2899: + text: EDAM_data:2899 + description: Drug name + title: Drug name + EDAM_data:2900: + text: EDAM_data:2900 + description: Carbohydrate accession + title: Carbohydrate accession + EDAM_data:2901: + text: EDAM_data:2901 + description: Molecule accession + title: Molecule accession + EDAM_data:2902: + text: EDAM_data:2902 + description: Data resource definition accession + title: Data resource definition accession + EDAM_data:2903: + text: EDAM_data:2903 + description: Genome accession + title: Genome accession + EDAM_data:2904: + text: EDAM_data:2904 + description: Map accession + title: Map accession + EDAM_data:2905: + text: EDAM_data:2905 + description: Lipid accession + title: Lipid accession + EDAM_data:2906: + text: EDAM_data:2906 + description: Peptide ID + title: Peptide ID + EDAM_data:2907: + text: EDAM_data:2907 + description: Protein accession + title: Protein accession + EDAM_data:2908: + text: EDAM_data:2908 + description: Organism accession + title: Organism accession + EDAM_data:2909: + text: EDAM_data:2909 + description: Organism name + title: Organism name + EDAM_data:2910: + text: EDAM_data:2910 + description: Protein family accession + title: Protein family accession + EDAM_data:2911: + text: EDAM_data:2911 + description: Transcription factor accession + title: Transcription factor accession + EDAM_data:2912: + text: EDAM_data:2912 + description: Strain accession + title: Strain accession + EDAM_data:2914: + text: EDAM_data:2914 + description: Sequence features metadata + title: Sequence features metadata + EDAM_data:2915: + text: EDAM_data:2915 + description: Gramene identifier + title: Gramene identifier + EDAM_data:2916: + text: EDAM_data:2916 + description: DDBJ accession + title: DDBJ accession + EDAM_data:2917: + text: EDAM_data:2917 + description: ConsensusPathDB identifier + title: ConsensusPathDB identifier + EDAM_data:2955: + text: EDAM_data:2955 + description: Sequence report + title: Sequence report + EDAM_data:2956: + text: EDAM_data:2956 + description: Protein secondary structure + title: Protein secondary structure + EDAM_data:2957: + text: EDAM_data:2957 + description: Hopp and Woods plot + title: Hopp and Woods plot + EDAM_data:2968: + text: EDAM_data:2968 + description: Image + title: Image + EDAM_data:2969: + text: EDAM_data:2969 + description: Sequence image + title: Sequence image + EDAM_data:2970: + text: EDAM_data:2970 + description: Protein hydropathy data + title: Protein hydropathy data + EDAM_data:2976: + text: EDAM_data:2976 + description: Protein sequence + title: Protein sequence + EDAM_data:2977: + text: EDAM_data:2977 + description: Nucleic acid sequence + title: Nucleic acid sequence + EDAM_data:2978: + text: EDAM_data:2978 + description: Reaction data + title: Reaction data + EDAM_data:2979: + text: EDAM_data:2979 + description: Peptide property + title: Peptide property + EDAM_data:2984: + text: EDAM_data:2984 + description: Pathway or network report + title: Pathway or network report + EDAM_data:2985: + text: EDAM_data:2985 + description: Nucleic acid thermodynamic data + title: Nucleic acid thermodynamic data + EDAM_data:2991: + text: EDAM_data:2991 + description: Protein geometry data + title: Protein geometry data + EDAM_data:2992: + text: EDAM_data:2992 + description: Protein structure image + title: Protein structure image + EDAM_data:2994: + text: EDAM_data:2994 + description: Phylogenetic character weights + title: Phylogenetic character weights + EDAM_data:3002: + text: EDAM_data:3002 + description: Annotation track + title: Annotation track + EDAM_data:3021: + text: EDAM_data:3021 + description: UniProt accession + title: UniProt accession + EDAM_data:3022: + text: EDAM_data:3022 + description: NCBI genetic code ID + title: NCBI genetic code ID + EDAM_data:3025: + text: EDAM_data:3025 + description: Ontology concept identifier + title: Ontology concept identifier + EDAM_data:3028: + text: EDAM_data:3028 + description: Taxonomy + title: Taxonomy + EDAM_data:3029: + text: EDAM_data:3029 + description: Protein ID (EMBL/GenBank/DDBJ) + title: Protein ID (EMBL/GenBank/DDBJ) + EDAM_data:3034: + text: EDAM_data:3034 + description: Sequence feature identifier + title: Sequence feature identifier + EDAM_data:3035: + text: EDAM_data:3035 + description: Structure identifier + title: Structure identifier + EDAM_data:3036: + text: EDAM_data:3036 + description: Matrix identifier + title: Matrix identifier + EDAM_data:3103: + text: EDAM_data:3103 + description: ATC code + title: ATC code + EDAM_data:3104: + text: EDAM_data:3104 + description: UNII + title: UNII + EDAM_data:3106: + text: EDAM_data:3106 + description: System metadata + title: System metadata + EDAM_data:3108: + text: EDAM_data:3108 + description: Experimental measurement + title: Experimental measurement + EDAM_data:3110: + text: EDAM_data:3110 + description: Raw microarray data + title: Raw microarray data + EDAM_data:3111: + text: EDAM_data:3111 + description: Processed microarray data + title: Processed microarray data + EDAM_data:3112: + text: EDAM_data:3112 + description: Gene expression matrix + title: Gene expression matrix + EDAM_data:3113: + text: EDAM_data:3113 + description: Sample annotation + title: Sample annotation + EDAM_data:3115: + text: EDAM_data:3115 + description: Microarray metadata + title: Microarray metadata + EDAM_data:3117: + text: EDAM_data:3117 + description: Microarray hybridisation data + title: Microarray hybridisation data + EDAM_data:3128: + text: EDAM_data:3128 + description: Nucleic acid structure report + title: Nucleic acid structure report + EDAM_data:3134: + text: EDAM_data:3134 + description: Gene transcript report + title: Gene transcript report + EDAM_data:3148: + text: EDAM_data:3148 + description: Gene family report + title: Gene family report + EDAM_data:3153: + text: EDAM_data:3153 + description: Protein image + title: Protein image + EDAM_data:3181: + text: EDAM_data:3181 + description: Sequence assembly report + title: Sequence assembly report + EDAM_data:3210: + text: EDAM_data:3210 + description: Genome index + title: Genome index + EDAM_data:3236: + text: EDAM_data:3236 + description: Cytoband position + title: Cytoband position + EDAM_data:3238: + text: EDAM_data:3238 + description: Cell type ontology ID + title: Cell type ontology ID + EDAM_data:3241: + text: EDAM_data:3241 + description: Kinetic model + title: Kinetic model + EDAM_data:3264: + text: EDAM_data:3264 + description: COSMIC ID + title: COSMIC ID + EDAM_data:3265: + text: EDAM_data:3265 + description: HGMD ID + title: HGMD ID + EDAM_data:3266: + text: EDAM_data:3266 + description: Sequence assembly ID + title: Sequence assembly ID + EDAM_data:3270: + text: EDAM_data:3270 + description: Ensembl gene tree ID + title: Ensembl gene tree ID + EDAM_data:3271: + text: EDAM_data:3271 + description: Gene tree + title: Gene tree + EDAM_data:3272: + text: EDAM_data:3272 + description: Species tree + title: Species tree + EDAM_data:3273: + text: EDAM_data:3273 + description: Sample ID + title: Sample ID + EDAM_data:3274: + text: EDAM_data:3274 + description: MGI accession + title: MGI accession + EDAM_data:3275: + text: EDAM_data:3275 + description: Phenotype name + title: Phenotype name + EDAM_data:3354: + text: EDAM_data:3354 + description: Transition matrix + title: Transition matrix + EDAM_data:3355: + text: EDAM_data:3355 + description: Emission matrix + title: Emission matrix + EDAM_data:3358: + text: EDAM_data:3358 + description: Format identifier + title: Format identifier + EDAM_data:3424: + text: EDAM_data:3424 + description: Raw image + title: Raw image + EDAM_data:3425: + text: EDAM_data:3425 + description: Carbohydrate property + title: Carbohydrate property + EDAM_data:3442: + text: EDAM_data:3442 + description: MRI image + title: MRI image + EDAM_data:3449: + text: EDAM_data:3449 + description: Cell migration track image + title: Cell migration track image + EDAM_data:3451: + text: EDAM_data:3451 + description: Rate of association + title: Rate of association + EDAM_data:3479: + text: EDAM_data:3479 + description: Gene order + title: Gene order + EDAM_data:3483: + text: EDAM_data:3483 + description: Spectrum + title: Spectrum + EDAM_data:3488: + text: EDAM_data:3488 + description: NMR spectrum + title: NMR spectrum + EDAM_data:3492: + text: EDAM_data:3492 + description: Nucleic acid signature + title: Nucleic acid signature + EDAM_data:3494: + text: EDAM_data:3494 + description: DNA sequence + title: DNA sequence + EDAM_data:3495: + text: EDAM_data:3495 + description: RNA sequence + title: RNA sequence + EDAM_data:3498: + text: EDAM_data:3498 + description: Sequence variations + title: Sequence variations + EDAM_data:3505: + text: EDAM_data:3505 + description: Bibliography + title: Bibliography + EDAM_data:3509: + text: EDAM_data:3509 + description: Ontology mapping + title: Ontology mapping + EDAM_data:3546: + text: EDAM_data:3546 + description: Image metadata + title: Image metadata + EDAM_data:3558: + text: EDAM_data:3558 + description: Clinical trial report + title: Clinical trial report + EDAM_data:3567: + text: EDAM_data:3567 + description: Reference sample report + title: Reference sample report + EDAM_data:3568: + text: EDAM_data:3568 + description: Gene Expression Atlas Experiment ID + title: Gene Expression Atlas Experiment ID + EDAM_data:3667: + text: EDAM_data:3667 + description: Disease identifier + title: Disease identifier + EDAM_data:3668: + text: EDAM_data:3668 + description: Disease name + title: Disease name + EDAM_data:3669: + text: EDAM_data:3669 + description: Learning material + title: Learning material + EDAM_data:3670: + text: EDAM_data:3670 + description: Online course + title: Online course + EDAM_data:3671: + text: EDAM_data:3671 + description: Text + title: Text + EDAM_data:3707: + text: EDAM_data:3707 + description: Biodiversity data + title: Biodiversity data + EDAM_data:3716: + text: EDAM_data:3716 + description: Biosafety report + title: Biosafety report + EDAM_data:3717: + text: EDAM_data:3717 + description: Isolation report + title: Isolation report + EDAM_data:3718: + text: EDAM_data:3718 + description: Pathogenicity report + title: Pathogenicity report + EDAM_data:3719: + text: EDAM_data:3719 + description: Biosafety classification + title: Biosafety classification + EDAM_data:3720: + text: EDAM_data:3720 + description: Geographic location + title: Geographic location + EDAM_data:3721: + text: EDAM_data:3721 + description: Isolation source + title: Isolation source + EDAM_data:3722: + text: EDAM_data:3722 + description: Physiology parameter + title: Physiology parameter + EDAM_data:3723: + text: EDAM_data:3723 + description: Morphology parameter + title: Morphology parameter + EDAM_data:3724: + text: EDAM_data:3724 + description: Cultivation parameter + title: Cultivation parameter + EDAM_data:3732: + text: EDAM_data:3732 + description: Sequencing metadata name + title: Sequencing metadata name + EDAM_data:3733: + text: EDAM_data:3733 + description: Flow cell identifier + title: Flow cell identifier + EDAM_data:3734: + text: EDAM_data:3734 + description: Lane identifier + title: Lane identifier + EDAM_data:3735: + text: EDAM_data:3735 + description: Run number + title: Run number + EDAM_data:3736: + text: EDAM_data:3736 + description: Ecological data + title: Ecological data + EDAM_data:3737: + text: EDAM_data:3737 + description: Alpha diversity data + title: Alpha diversity data + EDAM_data:3738: + text: EDAM_data:3738 + description: Beta diversity data + title: Beta diversity data + EDAM_data:3739: + text: EDAM_data:3739 + description: Gamma diversity data + title: Gamma diversity data + EDAM_data:3743: + text: EDAM_data:3743 + description: Ordination plot + title: Ordination plot + EDAM_data:3753: + text: EDAM_data:3753 + description: Over-representation data + title: Over-representation data + EDAM_data:3754: + text: EDAM_data:3754 + description: GO-term enrichment data + title: GO-term enrichment data + EDAM_data:3756: + text: EDAM_data:3756 + description: Localisation score + title: Localisation score + EDAM_data:3757: + text: EDAM_data:3757 + description: Unimod ID + title: Unimod ID + EDAM_data:3759: + text: EDAM_data:3759 + description: ProteomeXchange ID + title: ProteomeXchange ID + EDAM_data:3768: + text: EDAM_data:3768 + description: Clustered expression profiles + title: Clustered expression profiles + EDAM_data:3769: + text: EDAM_data:3769 + description: BRENDA ontology concept ID + title: BRENDA ontology concept ID + EDAM_data:3779: + text: EDAM_data:3779 + description: Annotated text + title: Annotated text + EDAM_data:3786: + text: EDAM_data:3786 + description: Query script + title: Query script + EDAM_data:3805: + text: EDAM_data:3805 + description: 3D EM Map + title: 3D EM Map + EDAM_data:3806: + text: EDAM_data:3806 + description: 3D EM Mask + title: 3D EM Mask + EDAM_data:3807: + text: EDAM_data:3807 + description: EM Movie + title: EM Movie + EDAM_data:3808: + text: EDAM_data:3808 + description: EM Micrograph + title: EM Micrograph + EDAM_data:3842: + text: EDAM_data:3842 + description: Molecular simulation data + title: Molecular simulation data + EDAM_data:3856: + text: EDAM_data:3856 + description: RNA central ID + title: RNA central ID + EDAM_data:3861: + text: EDAM_data:3861 + description: Electronic health record + title: Electronic health record + EDAM_data:3869: + text: EDAM_data:3869 + description: Simulation + title: Simulation + EDAM_data:3870: + text: EDAM_data:3870 + description: Trajectory data + title: Trajectory data + EDAM_data:3871: + text: EDAM_data:3871 + description: Forcefield parameters + title: Forcefield parameters + EDAM_data:3872: + text: EDAM_data:3872 + description: Topology data + title: Topology data + EDAM_data:3905: + text: EDAM_data:3905 + description: Histogram + title: Histogram + EDAM_data:3914: + text: EDAM_data:3914 + description: Quality control report + title: Quality control report + EDAM_data:3917: + text: EDAM_data:3917 + description: Count matrix + title: Count matrix + EDAM_data:3924: + text: EDAM_data:3924 + description: DNA structure alignment + title: DNA structure alignment + EDAM_data:3932: + text: EDAM_data:3932 + description: Q-value + title: Q-value + EDAM_data:3949: + text: EDAM_data:3949 + description: Profile HMM + title: Profile HMM + EDAM_data:3952: + text: EDAM_data:3952 + description: Pathway ID (WikiPathways) + title: Pathway ID (WikiPathways) + EDAM_data:3953: + text: EDAM_data:3953 + description: Pathway overrepresentation data + title: Pathway overrepresentation data + EDAM_data:4022: + text: EDAM_data:4022 + description: ORCID Identifier + title: ORCID Identifier + EDAM_data:4040: + text: EDAM_data:4040 + description: Data management plan + title: Data management plan diff --git a/output/EnumEDAMFormats.yaml b/output/EnumEDAMFormats.yaml new file mode 100644 index 0000000..8f4436c --- /dev/null +++ b/output/EnumEDAMFormats.yaml @@ -0,0 +1,2513 @@ +id: https://includedcc.org/common-access-model/EnumEDAMFormats +name: EnumEDAMFormats +enums: + EnumEDAMFormats: + description: Data formats from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:format_1915 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + EDAM_format:1196: + text: EDAM_format:1196 + description: SMILES + title: SMILES + EDAM_format:1197: + text: EDAM_format:1197 + description: InChI + title: InChI + EDAM_format:1198: + text: EDAM_format:1198 + description: mf + title: mf + EDAM_format:1199: + text: EDAM_format:1199 + description: InChIKey + title: InChIKey + EDAM_format:1200: + text: EDAM_format:1200 + description: smarts + title: smarts + EDAM_format:1206: + text: EDAM_format:1206 + description: unambiguous pure + title: unambiguous pure + EDAM_format:1207: + text: EDAM_format:1207 + description: nucleotide + title: nucleotide + EDAM_format:1208: + text: EDAM_format:1208 + description: protein + title: protein + EDAM_format:1209: + text: EDAM_format:1209 + description: consensus + title: consensus + EDAM_format:1210: + text: EDAM_format:1210 + description: pure nucleotide + title: pure nucleotide + EDAM_format:1211: + text: EDAM_format:1211 + description: unambiguous pure nucleotide + title: unambiguous pure nucleotide + EDAM_format:1212: + text: EDAM_format:1212 + description: dna + title: dna + EDAM_format:1213: + text: EDAM_format:1213 + description: rna + title: rna + EDAM_format:1214: + text: EDAM_format:1214 + description: unambiguous pure dna + title: unambiguous pure dna + EDAM_format:1215: + text: EDAM_format:1215 + description: pure dna + title: pure dna + EDAM_format:1216: + text: EDAM_format:1216 + description: unambiguous pure rna sequence + title: unambiguous pure rna sequence + EDAM_format:1217: + text: EDAM_format:1217 + description: pure rna + title: pure rna + EDAM_format:1218: + text: EDAM_format:1218 + description: unambiguous pure protein + title: unambiguous pure protein + EDAM_format:1219: + text: EDAM_format:1219 + description: pure protein + title: pure protein + EDAM_format:1248: + text: EDAM_format:1248 + description: EMBL feature location + title: EMBL feature location + EDAM_format:1295: + text: EDAM_format:1295 + description: quicktandem + title: quicktandem + EDAM_format:1296: + text: EDAM_format:1296 + description: Sanger inverted repeats + title: Sanger inverted repeats + EDAM_format:1297: + text: EDAM_format:1297 + description: EMBOSS repeat + title: EMBOSS repeat + EDAM_format:1316: + text: EDAM_format:1316 + description: est2genome format + title: est2genome format + EDAM_format:1318: + text: EDAM_format:1318 + description: restrict format + title: restrict format + EDAM_format:1319: + text: EDAM_format:1319 + description: restover format + title: restover format + EDAM_format:1320: + text: EDAM_format:1320 + description: REBASE restriction sites + title: REBASE restriction sites + EDAM_format:1332: + text: EDAM_format:1332 + description: FASTA search results format + title: FASTA search results format + EDAM_format:1333: + text: EDAM_format:1333 + description: BLAST results + title: BLAST results + EDAM_format:1334: + text: EDAM_format:1334 + description: mspcrunch + title: mspcrunch + EDAM_format:1335: + text: EDAM_format:1335 + description: Smith-Waterman format + title: Smith-Waterman format + EDAM_format:1336: + text: EDAM_format:1336 + description: dhf + title: dhf + EDAM_format:1337: + text: EDAM_format:1337 + description: lhf + title: lhf + EDAM_format:1341: + text: EDAM_format:1341 + description: InterPro hits format + title: InterPro hits format + EDAM_format:1342: + text: EDAM_format:1342 + description: InterPro protein view report format + title: InterPro protein view report format + EDAM_format:1343: + text: EDAM_format:1343 + description: InterPro match table format + title: InterPro match table format + EDAM_format:1349: + text: EDAM_format:1349 + description: HMMER Dirichlet prior + title: HMMER Dirichlet prior + EDAM_format:1350: + text: EDAM_format:1350 + description: MEME Dirichlet prior + title: MEME Dirichlet prior + EDAM_format:1351: + text: EDAM_format:1351 + description: HMMER emission and transition + title: HMMER emission and transition + EDAM_format:1356: + text: EDAM_format:1356 + description: prosite-pattern + title: prosite-pattern + EDAM_format:1357: + text: EDAM_format:1357 + description: EMBOSS sequence pattern + title: EMBOSS sequence pattern + EDAM_format:1360: + text: EDAM_format:1360 + description: meme-motif + title: meme-motif + EDAM_format:1366: + text: EDAM_format:1366 + description: prosite-profile + title: prosite-profile + EDAM_format:1367: + text: EDAM_format:1367 + description: JASPAR format + title: JASPAR format + EDAM_format:1369: + text: EDAM_format:1369 + description: MEME background Markov model + title: MEME background Markov model + EDAM_format:1370: + text: EDAM_format:1370 + description: HMMER format + title: HMMER format + EDAM_format:1391: + text: EDAM_format:1391 + description: HMMER-aln + title: HMMER-aln + EDAM_format:1392: + text: EDAM_format:1392 + description: DIALIGN format + title: DIALIGN format + EDAM_format:1393: + text: EDAM_format:1393 + description: daf + title: daf + EDAM_format:1419: + text: EDAM_format:1419 + description: Sequence-MEME profile alignment + title: Sequence-MEME profile alignment + EDAM_format:1421: + text: EDAM_format:1421 + description: HMMER profile alignment (sequences versus HMMs) + title: HMMER profile alignment (sequences versus HMMs) + EDAM_format:1422: + text: EDAM_format:1422 + description: HMMER profile alignment (HMM versus sequences) + title: HMMER profile alignment (HMM versus sequences) + EDAM_format:1423: + text: EDAM_format:1423 + description: Phylip distance matrix + title: Phylip distance matrix + EDAM_format:1424: + text: EDAM_format:1424 + description: ClustalW dendrogram + title: ClustalW dendrogram + EDAM_format:1425: + text: EDAM_format:1425 + description: Phylip tree raw + title: Phylip tree raw + EDAM_format:1430: + text: EDAM_format:1430 + description: Phylip continuous quantitative characters + title: Phylip continuous quantitative characters + EDAM_format:1432: + text: EDAM_format:1432 + description: Phylip character frequencies format + title: Phylip character frequencies format + EDAM_format:1433: + text: EDAM_format:1433 + description: Phylip discrete states format + title: Phylip discrete states format + EDAM_format:1434: + text: EDAM_format:1434 + description: Phylip cliques format + title: Phylip cliques format + EDAM_format:1435: + text: EDAM_format:1435 + description: Phylip tree format + title: Phylip tree format + EDAM_format:1436: + text: EDAM_format:1436 + description: TreeBASE format + title: TreeBASE format + EDAM_format:1437: + text: EDAM_format:1437 + description: TreeFam format + title: TreeFam format + EDAM_format:1445: + text: EDAM_format:1445 + description: Phylip tree distance format + title: Phylip tree distance format + EDAM_format:1454: + text: EDAM_format:1454 + description: dssp + title: dssp + EDAM_format:1455: + text: EDAM_format:1455 + description: hssp + title: hssp + EDAM_format:1457: + text: EDAM_format:1457 + description: Dot-bracket format + title: Dot-bracket format + EDAM_format:1458: + text: EDAM_format:1458 + description: Vienna local RNA secondary structure format + title: Vienna local RNA secondary structure format + EDAM_format:1475: + text: EDAM_format:1475 + description: PDB database entry format + title: PDB database entry format + EDAM_format:1476: + text: EDAM_format:1476 + description: PDB + title: PDB + EDAM_format:1477: + text: EDAM_format:1477 + description: mmCIF + title: mmCIF + EDAM_format:1478: + text: EDAM_format:1478 + description: PDBML + title: PDBML + EDAM_format:1504: + text: EDAM_format:1504 + description: aaindex + title: aaindex + EDAM_format:1551: + text: EDAM_format:1551 + description: Pcons report format + title: Pcons report format + EDAM_format:1552: + text: EDAM_format:1552 + description: ProQ report format + title: ProQ report format + EDAM_format:1582: + text: EDAM_format:1582 + description: findkm + title: findkm + EDAM_format:1627: + text: EDAM_format:1627 + description: Primer3 primer + title: Primer3 primer + EDAM_format:1628: + text: EDAM_format:1628 + description: ABI + title: ABI + EDAM_format:1629: + text: EDAM_format:1629 + description: mira + title: mira + EDAM_format:1630: + text: EDAM_format:1630 + description: CAF + title: CAF + EDAM_format:1631: + text: EDAM_format:1631 + description: EXP + title: EXP + EDAM_format:1632: + text: EDAM_format:1632 + description: SCF + title: SCF + EDAM_format:1633: + text: EDAM_format:1633 + description: PHD + title: PHD + EDAM_format:1637: + text: EDAM_format:1637 + description: dat + title: dat + EDAM_format:1638: + text: EDAM_format:1638 + description: cel + title: cel + EDAM_format:1639: + text: EDAM_format:1639 + description: affymetrix + title: affymetrix + EDAM_format:1641: + text: EDAM_format:1641 + description: affymetrix-exp + title: affymetrix-exp + EDAM_format:1644: + text: EDAM_format:1644 + description: CHP + title: CHP + EDAM_format:1665: + text: EDAM_format:1665 + description: Taverna workflow format + title: Taverna workflow format + EDAM_format:1705: + text: EDAM_format:1705 + description: HET group dictionary entry format + title: HET group dictionary entry format + EDAM_format:1734: + text: EDAM_format:1734 + description: PubMed citation + title: PubMed citation + EDAM_format:1735: + text: EDAM_format:1735 + description: Medline Display Format + title: Medline Display Format + EDAM_format:1736: + text: EDAM_format:1736 + description: CiteXplore-core + title: CiteXplore-core + EDAM_format:1737: + text: EDAM_format:1737 + description: CiteXplore-all + title: CiteXplore-all + EDAM_format:1739: + text: EDAM_format:1739 + description: pmc + title: pmc + EDAM_format:1740: + text: EDAM_format:1740 + description: iHOP format + title: iHOP format + EDAM_format:1741: + text: EDAM_format:1741 + description: OSCAR format + title: OSCAR format + EDAM_format:1861: + text: EDAM_format:1861 + description: PlasMapper TextMap + title: PlasMapper TextMap + EDAM_format:1910: + text: EDAM_format:1910 + description: newick + title: newick + EDAM_format:1911: + text: EDAM_format:1911 + description: TreeCon format + title: TreeCon format + EDAM_format:1912: + text: EDAM_format:1912 + description: Nexus format + title: Nexus format + EDAM_format:1919: + text: EDAM_format:1919 + description: Sequence record format + title: Sequence record format + EDAM_format:1920: + text: EDAM_format:1920 + description: Sequence feature annotation format + title: Sequence feature annotation format + EDAM_format:1921: + text: EDAM_format:1921 + description: Alignment format + title: Alignment format + EDAM_format:1923: + text: EDAM_format:1923 + description: acedb + title: acedb + EDAM_format:1925: + text: EDAM_format:1925 + description: codata + title: codata + EDAM_format:1926: + text: EDAM_format:1926 + description: dbid + title: dbid + EDAM_format:1927: + text: EDAM_format:1927 + description: EMBL format + title: EMBL format + EDAM_format:1928: + text: EDAM_format:1928 + description: Staden experiment format + title: Staden experiment format + EDAM_format:1929: + text: EDAM_format:1929 + description: FASTA + title: FASTA + EDAM_format:1930: + text: EDAM_format:1930 + description: FASTQ + title: FASTQ + EDAM_format:1931: + text: EDAM_format:1931 + description: FASTQ-illumina + title: FASTQ-illumina + EDAM_format:1932: + text: EDAM_format:1932 + description: FASTQ-sanger + title: FASTQ-sanger + EDAM_format:1933: + text: EDAM_format:1933 + description: FASTQ-solexa + title: FASTQ-solexa + EDAM_format:1934: + text: EDAM_format:1934 + description: fitch program + title: fitch program + EDAM_format:1935: + text: EDAM_format:1935 + description: GCG + title: GCG + EDAM_format:1936: + text: EDAM_format:1936 + description: GenBank format + title: GenBank format + EDAM_format:1937: + text: EDAM_format:1937 + description: genpept + title: genpept + EDAM_format:1938: + text: EDAM_format:1938 + description: GFF2-seq + title: GFF2-seq + EDAM_format:1939: + text: EDAM_format:1939 + description: GFF3-seq + title: GFF3-seq + EDAM_format:1940: + text: EDAM_format:1940 + description: giFASTA format + title: giFASTA format + EDAM_format:1941: + text: EDAM_format:1941 + description: hennig86 + title: hennig86 + EDAM_format:1942: + text: EDAM_format:1942 + description: ig + title: ig + EDAM_format:1943: + text: EDAM_format:1943 + description: igstrict + title: igstrict + EDAM_format:1944: + text: EDAM_format:1944 + description: jackknifer + title: jackknifer + EDAM_format:1945: + text: EDAM_format:1945 + description: mase format + title: mase format + EDAM_format:1946: + text: EDAM_format:1946 + description: mega-seq + title: mega-seq + EDAM_format:1947: + text: EDAM_format:1947 + description: GCG MSF + title: GCG MSF + EDAM_format:1948: + text: EDAM_format:1948 + description: nbrf/pir + title: nbrf/pir + EDAM_format:1949: + text: EDAM_format:1949 + description: nexus-seq + title: nexus-seq + EDAM_format:1950: + text: EDAM_format:1950 + description: pdbatom + title: pdbatom + EDAM_format:1951: + text: EDAM_format:1951 + description: pdbatomnuc + title: pdbatomnuc + EDAM_format:1952: + text: EDAM_format:1952 + description: pdbseqresnuc + title: pdbseqresnuc + EDAM_format:1953: + text: EDAM_format:1953 + description: pdbseqres + title: pdbseqres + EDAM_format:1954: + text: EDAM_format:1954 + description: Pearson format + title: Pearson format + EDAM_format:1957: + text: EDAM_format:1957 + description: raw + title: raw + EDAM_format:1958: + text: EDAM_format:1958 + description: refseqp + title: refseqp + EDAM_format:1960: + text: EDAM_format:1960 + description: Staden format + title: Staden format + EDAM_format:1961: + text: EDAM_format:1961 + description: Stockholm format + title: Stockholm format + EDAM_format:1962: + text: EDAM_format:1962 + description: strider format + title: strider format + EDAM_format:1963: + text: EDAM_format:1963 + description: UniProtKB format + title: UniProtKB format + EDAM_format:1964: + text: EDAM_format:1964 + description: plain text format (unformatted) + title: plain text format (unformatted) + EDAM_format:1966: + text: EDAM_format:1966 + description: ASN.1 sequence format + title: ASN.1 sequence format + EDAM_format:1967: + text: EDAM_format:1967 + description: DAS format + title: DAS format + EDAM_format:1968: + text: EDAM_format:1968 + description: dasdna + title: dasdna + EDAM_format:1969: + text: EDAM_format:1969 + description: debug-seq + title: debug-seq + EDAM_format:1970: + text: EDAM_format:1970 + description: jackknifernon + title: jackknifernon + EDAM_format:1972: + text: EDAM_format:1972 + description: NCBI format + title: NCBI format + EDAM_format:1973: + text: EDAM_format:1973 + description: nexusnon + title: nexusnon + EDAM_format:1974: + text: EDAM_format:1974 + description: GFF2 + title: GFF2 + EDAM_format:1975: + text: EDAM_format:1975 + description: GFF3 + title: GFF3 + EDAM_format:1978: + text: EDAM_format:1978 + description: DASGFF + title: DASGFF + EDAM_format:1979: + text: EDAM_format:1979 + description: debug-feat + title: debug-feat + EDAM_format:1982: + text: EDAM_format:1982 + description: ClustalW format + title: ClustalW format + EDAM_format:1983: + text: EDAM_format:1983 + description: debug + title: debug + EDAM_format:1984: + text: EDAM_format:1984 + description: FASTA-aln + title: FASTA-aln + EDAM_format:1985: + text: EDAM_format:1985 + description: markx0 + title: markx0 + EDAM_format:1986: + text: EDAM_format:1986 + description: markx1 + title: markx1 + EDAM_format:1987: + text: EDAM_format:1987 + description: markx10 + title: markx10 + EDAM_format:1988: + text: EDAM_format:1988 + description: markx2 + title: markx2 + EDAM_format:1989: + text: EDAM_format:1989 + description: markx3 + title: markx3 + EDAM_format:1990: + text: EDAM_format:1990 + description: match + title: match + EDAM_format:1991: + text: EDAM_format:1991 + description: mega + title: mega + EDAM_format:1992: + text: EDAM_format:1992 + description: meganon + title: meganon + EDAM_format:1996: + text: EDAM_format:1996 + description: pair + title: pair + EDAM_format:1997: + text: EDAM_format:1997 + description: PHYLIP format + title: PHYLIP format + EDAM_format:1998: + text: EDAM_format:1998 + description: PHYLIP sequential + title: PHYLIP sequential + EDAM_format:1999: + text: EDAM_format:1999 + description: scores format + title: scores format + EDAM_format:2000: + text: EDAM_format:2000 + description: selex + title: selex + EDAM_format:2001: + text: EDAM_format:2001 + description: EMBOSS simple format + title: EMBOSS simple format + EDAM_format:2002: + text: EDAM_format:2002 + description: srs format + title: srs format + EDAM_format:2003: + text: EDAM_format:2003 + description: srspair + title: srspair + EDAM_format:2004: + text: EDAM_format:2004 + description: T-Coffee format + title: T-Coffee format + EDAM_format:2005: + text: EDAM_format:2005 + description: TreeCon-seq + title: TreeCon-seq + EDAM_format:2006: + text: EDAM_format:2006 + description: Phylogenetic tree format + title: Phylogenetic tree format + EDAM_format:2013: + text: EDAM_format:2013 + description: Biological pathway or network format + title: Biological pathway or network format + EDAM_format:2014: + text: EDAM_format:2014 + description: Sequence-profile alignment format + title: Sequence-profile alignment format + EDAM_format:2017: + text: EDAM_format:2017 + description: Amino acid index format + title: Amino acid index format + EDAM_format:2020: + text: EDAM_format:2020 + description: Article format + title: Article format + EDAM_format:2021: + text: EDAM_format:2021 + description: Text mining report format + title: Text mining report format + EDAM_format:2027: + text: EDAM_format:2027 + description: Enzyme kinetics report format + title: Enzyme kinetics report format + EDAM_format:2030: + text: EDAM_format:2030 + description: Chemical data format + title: Chemical data format + EDAM_format:2031: + text: EDAM_format:2031 + description: Gene annotation format + title: Gene annotation format + EDAM_format:2032: + text: EDAM_format:2032 + description: Workflow format + title: Workflow format + EDAM_format:2033: + text: EDAM_format:2033 + description: Tertiary structure format + title: Tertiary structure format + EDAM_format:2035: + text: EDAM_format:2035 + description: Chemical formula format + title: Chemical formula format + EDAM_format:2036: + text: EDAM_format:2036 + description: Phylogenetic character data format + title: Phylogenetic character data format + EDAM_format:2037: + text: EDAM_format:2037 + description: Phylogenetic continuous quantitative character format + title: Phylogenetic continuous quantitative character format + EDAM_format:2038: + text: EDAM_format:2038 + description: Phylogenetic discrete states format + title: Phylogenetic discrete states format + EDAM_format:2039: + text: EDAM_format:2039 + description: Phylogenetic tree report (cliques) format + title: Phylogenetic tree report (cliques) format + EDAM_format:2040: + text: EDAM_format:2040 + description: Phylogenetic tree report (invariants) format + title: Phylogenetic tree report (invariants) format + EDAM_format:2049: + text: EDAM_format:2049 + description: Phylogenetic tree report (tree distances) format + title: Phylogenetic tree report (tree distances) format + EDAM_format:2052: + text: EDAM_format:2052 + description: Protein family report format + title: Protein family report format + EDAM_format:2054: + text: EDAM_format:2054 + description: Protein interaction format + title: Protein interaction format + EDAM_format:2055: + text: EDAM_format:2055 + description: Sequence assembly format + title: Sequence assembly format + EDAM_format:2056: + text: EDAM_format:2056 + description: Microarray experiment data format + title: Microarray experiment data format + EDAM_format:2057: + text: EDAM_format:2057 + description: Sequence trace format + title: Sequence trace format + EDAM_format:2058: + text: EDAM_format:2058 + description: Gene expression report format + title: Gene expression report format + EDAM_format:2060: + text: EDAM_format:2060 + description: Map format + title: Map format + EDAM_format:2061: + text: EDAM_format:2061 + description: Nucleic acid features (primers) format + title: Nucleic acid features (primers) format + EDAM_format:2062: + text: EDAM_format:2062 + description: Protein report format + title: Protein report format + EDAM_format:2064: + text: EDAM_format:2064 + description: 3D-1D scoring matrix format + title: 3D-1D scoring matrix format + EDAM_format:2065: + text: EDAM_format:2065 + description: Protein structure report (quality evaluation) format + title: Protein structure report (quality evaluation) format + EDAM_format:2066: + text: EDAM_format:2066 + description: Database hits (sequence) format + title: Database hits (sequence) format + EDAM_format:2067: + text: EDAM_format:2067 + description: Sequence distance matrix format + title: Sequence distance matrix format + EDAM_format:2068: + text: EDAM_format:2068 + description: Sequence motif format + title: Sequence motif format + EDAM_format:2069: + text: EDAM_format:2069 + description: Sequence profile format + title: Sequence profile format + EDAM_format:2072: + text: EDAM_format:2072 + description: Hidden Markov model format + title: Hidden Markov model format + EDAM_format:2074: + text: EDAM_format:2074 + description: Dirichlet distribution format + title: Dirichlet distribution format + EDAM_format:2075: + text: EDAM_format:2075 + description: HMM emission and transition counts format + title: HMM emission and transition counts format + EDAM_format:2076: + text: EDAM_format:2076 + description: RNA secondary structure format + title: RNA secondary structure format + EDAM_format:2077: + text: EDAM_format:2077 + description: Protein secondary structure format + title: Protein secondary structure format + EDAM_format:2078: + text: EDAM_format:2078 + description: Sequence range format + title: Sequence range format + EDAM_format:2094: + text: EDAM_format:2094 + description: pure + title: pure + EDAM_format:2095: + text: EDAM_format:2095 + description: unpure + title: unpure + EDAM_format:2096: + text: EDAM_format:2096 + description: unambiguous sequence + title: unambiguous sequence + EDAM_format:2097: + text: EDAM_format:2097 + description: ambiguous + title: ambiguous + EDAM_format:2155: + text: EDAM_format:2155 + description: Sequence features (repeats) format + title: Sequence features (repeats) format + EDAM_format:2158: + text: EDAM_format:2158 + description: Nucleic acid features (restriction sites) format + title: Nucleic acid features (restriction sites) format + EDAM_format:2170: + text: EDAM_format:2170 + description: Sequence cluster format + title: Sequence cluster format + EDAM_format:2171: + text: EDAM_format:2171 + description: Sequence cluster format (protein) + title: Sequence cluster format (protein) + EDAM_format:2172: + text: EDAM_format:2172 + description: Sequence cluster format (nucleic acid) + title: Sequence cluster format (nucleic acid) + EDAM_format:2181: + text: EDAM_format:2181 + description: EMBL-like (text) + title: EMBL-like (text) + EDAM_format:2182: + text: EDAM_format:2182 + description: FASTQ-like format (text) + title: FASTQ-like format (text) + EDAM_format:2183: + text: EDAM_format:2183 + description: EMBLXML + title: EMBLXML + EDAM_format:2184: + text: EDAM_format:2184 + description: cdsxml + title: cdsxml + EDAM_format:2185: + text: EDAM_format:2185 + description: INSDSeq + title: INSDSeq + EDAM_format:2186: + text: EDAM_format:2186 + description: geneseq + title: geneseq + EDAM_format:2187: + text: EDAM_format:2187 + description: UniProt-like (text) + title: UniProt-like (text) + EDAM_format:2194: + text: EDAM_format:2194 + description: medline + title: medline + EDAM_format:2195: + text: EDAM_format:2195 + description: Ontology format + title: Ontology format + EDAM_format:2196: + text: EDAM_format:2196 + description: OBO format + title: OBO format + EDAM_format:2197: + text: EDAM_format:2197 + description: OWL format + title: OWL format + EDAM_format:2200: + text: EDAM_format:2200 + description: FASTA-like (text) + title: FASTA-like (text) + EDAM_format:2204: + text: EDAM_format:2204 + description: EMBL format (XML) + title: EMBL format (XML) + EDAM_format:2205: + text: EDAM_format:2205 + description: GenBank-like format (text) + title: GenBank-like format (text) + EDAM_format:2206: + text: EDAM_format:2206 + description: Sequence feature table format (text) + title: Sequence feature table format (text) + EDAM_format:2304: + text: EDAM_format:2304 + description: STRING entry format (XML) + title: STRING entry format (XML) + EDAM_format:2305: + text: EDAM_format:2305 + description: GFF + title: GFF + EDAM_format:2306: + text: EDAM_format:2306 + description: GTF + title: GTF + EDAM_format:2310: + text: EDAM_format:2310 + description: FASTA-HTML + title: FASTA-HTML + EDAM_format:2311: + text: EDAM_format:2311 + description: EMBL-HTML + title: EMBL-HTML + EDAM_format:2330: + text: EDAM_format:2330 + description: Textual format + title: Textual format + EDAM_format:2331: + text: EDAM_format:2331 + description: HTML + title: HTML + EDAM_format:2332: + text: EDAM_format:2332 + description: XML + title: XML + EDAM_format:2333: + text: EDAM_format:2333 + description: Binary format + title: Binary format + EDAM_format:2350: + text: EDAM_format:2350 + description: Format (by type of data) + title: Format (by type of data) + EDAM_format:2352: + text: EDAM_format:2352 + description: BioXSD (XML) + title: BioXSD (XML) + EDAM_format:2376: + text: EDAM_format:2376 + description: RDF format + title: RDF format + EDAM_format:2532: + text: EDAM_format:2532 + description: GenBank-HTML + title: GenBank-HTML + EDAM_format:2543: + text: EDAM_format:2543 + description: EMBL-like format + title: EMBL-like format + EDAM_format:2545: + text: EDAM_format:2545 + description: FASTQ-like format + title: FASTQ-like format + EDAM_format:2546: + text: EDAM_format:2546 + description: FASTA-like + title: FASTA-like + EDAM_format:2547: + text: EDAM_format:2547 + description: uniprotkb-like format + title: uniprotkb-like format + EDAM_format:2548: + text: EDAM_format:2548 + description: Sequence feature table format + title: Sequence feature table format + EDAM_format:2549: + text: EDAM_format:2549 + description: OBO + title: OBO + EDAM_format:2550: + text: EDAM_format:2550 + description: OBO-XML + title: OBO-XML + EDAM_format:2551: + text: EDAM_format:2551 + description: Sequence record format (text) + title: Sequence record format (text) + EDAM_format:2552: + text: EDAM_format:2552 + description: Sequence record format (XML) + title: Sequence record format (XML) + EDAM_format:2553: + text: EDAM_format:2553 + description: Sequence feature table format (XML) + title: Sequence feature table format (XML) + EDAM_format:2554: + text: EDAM_format:2554 + description: Alignment format (text) + title: Alignment format (text) + EDAM_format:2555: + text: EDAM_format:2555 + description: Alignment format (XML) + title: Alignment format (XML) + EDAM_format:2556: + text: EDAM_format:2556 + description: Phylogenetic tree format (text) + title: Phylogenetic tree format (text) + EDAM_format:2557: + text: EDAM_format:2557 + description: Phylogenetic tree format (XML) + title: Phylogenetic tree format (XML) + EDAM_format:2558: + text: EDAM_format:2558 + description: EMBL-like (XML) + title: EMBL-like (XML) + EDAM_format:2559: + text: EDAM_format:2559 + description: GenBank-like format + title: GenBank-like format + EDAM_format:2561: + text: EDAM_format:2561 + description: Sequence assembly format (text) + title: Sequence assembly format (text) + EDAM_format:2566: + text: EDAM_format:2566 + description: completely unambiguous + title: completely unambiguous + EDAM_format:2567: + text: EDAM_format:2567 + description: completely unambiguous pure + title: completely unambiguous pure + EDAM_format:2568: + text: EDAM_format:2568 + description: completely unambiguous pure nucleotide + title: completely unambiguous pure nucleotide + EDAM_format:2569: + text: EDAM_format:2569 + description: completely unambiguous pure dna + title: completely unambiguous pure dna + EDAM_format:2570: + text: EDAM_format:2570 + description: completely unambiguous pure rna sequence + title: completely unambiguous pure rna sequence + EDAM_format:2571: + text: EDAM_format:2571 + description: Raw sequence format + title: Raw sequence format + EDAM_format:2572: + text: EDAM_format:2572 + description: BAM + title: BAM + EDAM_format:2573: + text: EDAM_format:2573 + description: SAM + title: SAM + EDAM_format:2585: + text: EDAM_format:2585 + description: SBML + title: SBML + EDAM_format:2607: + text: EDAM_format:2607 + description: completely unambiguous pure protein + title: completely unambiguous pure protein + EDAM_format:2848: + text: EDAM_format:2848 + description: Bibliographic reference format + title: Bibliographic reference format + EDAM_format:2919: + text: EDAM_format:2919 + description: Sequence annotation track format + title: Sequence annotation track format + EDAM_format:2920: + text: EDAM_format:2920 + description: Alignment format (pair only) + title: Alignment format (pair only) + EDAM_format:2921: + text: EDAM_format:2921 + description: Sequence variation annotation format + title: Sequence variation annotation format + EDAM_format:2922: + text: EDAM_format:2922 + description: markx0 variant + title: markx0 variant + EDAM_format:2923: + text: EDAM_format:2923 + description: mega variant + title: mega variant + EDAM_format:2924: + text: EDAM_format:2924 + description: Phylip format variant + title: Phylip format variant + EDAM_format:3000: + text: EDAM_format:3000 + description: AB1 + title: AB1 + EDAM_format:3001: + text: EDAM_format:3001 + description: ACE + title: ACE + EDAM_format:3003: + text: EDAM_format:3003 + description: BED + title: BED + EDAM_format:3004: + text: EDAM_format:3004 + description: bigBed + title: bigBed + EDAM_format:3005: + text: EDAM_format:3005 + description: WIG + title: WIG + EDAM_format:3006: + text: EDAM_format:3006 + description: bigWig + title: bigWig + EDAM_format:3007: + text: EDAM_format:3007 + description: PSL + title: PSL + EDAM_format:3008: + text: EDAM_format:3008 + description: MAF + title: MAF + EDAM_format:3009: + text: EDAM_format:3009 + description: 2bit + title: 2bit + EDAM_format:3010: + text: EDAM_format:3010 + description: .nib + title: .nib + EDAM_format:3011: + text: EDAM_format:3011 + description: genePred + title: genePred + EDAM_format:3012: + text: EDAM_format:3012 + description: pgSnp + title: pgSnp + EDAM_format:3013: + text: EDAM_format:3013 + description: axt + title: axt + EDAM_format:3014: + text: EDAM_format:3014 + description: LAV + title: LAV + EDAM_format:3015: + text: EDAM_format:3015 + description: Pileup + title: Pileup + EDAM_format:3016: + text: EDAM_format:3016 + description: VCF + title: VCF + EDAM_format:3017: + text: EDAM_format:3017 + description: SRF + title: SRF + EDAM_format:3018: + text: EDAM_format:3018 + description: ZTR + title: ZTR + EDAM_format:3019: + text: EDAM_format:3019 + description: GVF + title: GVF + EDAM_format:3020: + text: EDAM_format:3020 + description: BCF + title: BCF + EDAM_format:3033: + text: EDAM_format:3033 + description: Matrix format + title: Matrix format + EDAM_format:3097: + text: EDAM_format:3097 + description: Protein domain classification format + title: Protein domain classification format + EDAM_format:3098: + text: EDAM_format:3098 + description: Raw SCOP domain classification format + title: Raw SCOP domain classification format + EDAM_format:3099: + text: EDAM_format:3099 + description: Raw CATH domain classification format + title: Raw CATH domain classification format + EDAM_format:3100: + text: EDAM_format:3100 + description: CATH domain report format + title: CATH domain report format + EDAM_format:3155: + text: EDAM_format:3155 + description: SBRML + title: SBRML + EDAM_format:3156: + text: EDAM_format:3156 + description: BioPAX + title: BioPAX + EDAM_format:3157: + text: EDAM_format:3157 + description: EBI Application Result XML + title: EBI Application Result XML + EDAM_format:3158: + text: EDAM_format:3158 + description: PSI MI XML (MIF) + title: PSI MI XML (MIF) + EDAM_format:3159: + text: EDAM_format:3159 + description: phyloXML + title: phyloXML + EDAM_format:3160: + text: EDAM_format:3160 + description: NeXML + title: NeXML + EDAM_format:3161: + text: EDAM_format:3161 + description: MAGE-ML + title: MAGE-ML + EDAM_format:3162: + text: EDAM_format:3162 + description: MAGE-TAB + title: MAGE-TAB + EDAM_format:3163: + text: EDAM_format:3163 + description: GCDML + title: GCDML + EDAM_format:3164: + text: EDAM_format:3164 + description: GTrack + title: GTrack + EDAM_format:3166: + text: EDAM_format:3166 + description: Biological pathway or network report format + title: Biological pathway or network report format + EDAM_format:3167: + text: EDAM_format:3167 + description: Experiment annotation format + title: Experiment annotation format + EDAM_format:3235: + text: EDAM_format:3235 + description: Cytoband format + title: Cytoband format + EDAM_format:3239: + text: EDAM_format:3239 + description: CopasiML + title: CopasiML + EDAM_format:3240: + text: EDAM_format:3240 + description: CellML + title: CellML + EDAM_format:3242: + text: EDAM_format:3242 + description: PSI MI TAB (MITAB) + title: PSI MI TAB (MITAB) + EDAM_format:3243: + text: EDAM_format:3243 + description: PSI-PAR + title: PSI-PAR + EDAM_format:3244: + text: EDAM_format:3244 + description: mzML + title: mzML + EDAM_format:3245: + text: EDAM_format:3245 + description: Mass spectrometry data format + title: Mass spectrometry data format + EDAM_format:3246: + text: EDAM_format:3246 + description: TraML + title: TraML + EDAM_format:3247: + text: EDAM_format:3247 + description: mzIdentML + title: mzIdentML + EDAM_format:3248: + text: EDAM_format:3248 + description: mzQuantML + title: mzQuantML + EDAM_format:3249: + text: EDAM_format:3249 + description: GelML + title: GelML + EDAM_format:3250: + text: EDAM_format:3250 + description: spML + title: spML + EDAM_format:3252: + text: EDAM_format:3252 + description: OWL Functional Syntax + title: OWL Functional Syntax + EDAM_format:3253: + text: EDAM_format:3253 + description: Manchester OWL Syntax + title: Manchester OWL Syntax + EDAM_format:3254: + text: EDAM_format:3254 + description: KRSS2 Syntax + title: KRSS2 Syntax + EDAM_format:3255: + text: EDAM_format:3255 + description: Turtle + title: Turtle + EDAM_format:3256: + text: EDAM_format:3256 + description: N-Triples + title: N-Triples + EDAM_format:3257: + text: EDAM_format:3257 + description: Notation3 + title: Notation3 + EDAM_format:3261: + text: EDAM_format:3261 + description: RDF/XML + title: RDF/XML + EDAM_format:3262: + text: EDAM_format:3262 + description: OWL/XML + title: OWL/XML + EDAM_format:3281: + text: EDAM_format:3281 + description: A2M + title: A2M + EDAM_format:3284: + text: EDAM_format:3284 + description: SFF + title: SFF + EDAM_format:3285: + text: EDAM_format:3285 + description: MAP + title: MAP + EDAM_format:3286: + text: EDAM_format:3286 + description: PED + title: PED + EDAM_format:3287: + text: EDAM_format:3287 + description: Individual genetic data format + title: Individual genetic data format + EDAM_format:3288: + text: EDAM_format:3288 + description: PED/MAP + title: PED/MAP + EDAM_format:3309: + text: EDAM_format:3309 + description: CT + title: CT + EDAM_format:3310: + text: EDAM_format:3310 + description: SS + title: SS + EDAM_format:3311: + text: EDAM_format:3311 + description: RNAML + title: RNAML + EDAM_format:3312: + text: EDAM_format:3312 + description: GDE + title: GDE + EDAM_format:3313: + text: EDAM_format:3313 + description: BLC + title: BLC + EDAM_format:3326: + text: EDAM_format:3326 + description: Data index format + title: Data index format + EDAM_format:3327: + text: EDAM_format:3327 + description: BAI + title: BAI + EDAM_format:3328: + text: EDAM_format:3328 + description: HMMER2 + title: HMMER2 + EDAM_format:3329: + text: EDAM_format:3329 + description: HMMER3 + title: HMMER3 + EDAM_format:3330: + text: EDAM_format:3330 + description: PO + title: PO + EDAM_format:3331: + text: EDAM_format:3331 + description: BLAST XML results format + title: BLAST XML results format + EDAM_format:3462: + text: EDAM_format:3462 + description: CRAM + title: CRAM + EDAM_format:3464: + text: EDAM_format:3464 + description: JSON + title: JSON + EDAM_format:3466: + text: EDAM_format:3466 + description: EPS + title: EPS + EDAM_format:3467: + text: EDAM_format:3467 + description: GIF + title: GIF + EDAM_format:3468: + text: EDAM_format:3468 + description: xls + title: xls + EDAM_format:3475: + text: EDAM_format:3475 + description: TSV + title: TSV + EDAM_format:3477: + text: EDAM_format:3477 + description: Cytoscape input file format + title: Cytoscape input file format + EDAM_format:3484: + text: EDAM_format:3484 + description: ebwt + title: ebwt + EDAM_format:3485: + text: EDAM_format:3485 + description: RSF + title: RSF + EDAM_format:3486: + text: EDAM_format:3486 + description: GCG format variant + title: GCG format variant + EDAM_format:3487: + text: EDAM_format:3487 + description: BSML + title: BSML + EDAM_format:3491: + text: EDAM_format:3491 + description: ebwtl + title: ebwtl + EDAM_format:3499: + text: EDAM_format:3499 + description: Ensembl variation file format + title: Ensembl variation file format + EDAM_format:3506: + text: EDAM_format:3506 + description: docx + title: docx + EDAM_format:3507: + text: EDAM_format:3507 + description: Document format + title: Document format + EDAM_format:3508: + text: EDAM_format:3508 + description: PDF + title: PDF + EDAM_format:3547: + text: EDAM_format:3547 + description: Image format + title: Image format + EDAM_format:3548: + text: EDAM_format:3548 + description: DICOM format + title: DICOM format + EDAM_format:3549: + text: EDAM_format:3549 + description: nii + title: nii + EDAM_format:3550: + text: EDAM_format:3550 + description: mhd + title: mhd + EDAM_format:3551: + text: EDAM_format:3551 + description: nrrd + title: nrrd + EDAM_format:3554: + text: EDAM_format:3554 + description: R file format + title: R file format + EDAM_format:3555: + text: EDAM_format:3555 + description: SPSS + title: SPSS + EDAM_format:3556: + text: EDAM_format:3556 + description: MHTML + title: MHTML + EDAM_format:3578: + text: EDAM_format:3578 + description: IDAT + title: IDAT + EDAM_format:3579: + text: EDAM_format:3579 + description: JPG + title: JPG + EDAM_format:3580: + text: EDAM_format:3580 + description: rcc + title: rcc + EDAM_format:3581: + text: EDAM_format:3581 + description: arff + title: arff + EDAM_format:3582: + text: EDAM_format:3582 + description: afg + title: afg + EDAM_format:3583: + text: EDAM_format:3583 + description: bedgraph + title: bedgraph + EDAM_format:3584: + text: EDAM_format:3584 + description: bedstrict + title: bedstrict + EDAM_format:3585: + text: EDAM_format:3585 + description: bed6 + title: bed6 + EDAM_format:3586: + text: EDAM_format:3586 + description: bed12 + title: bed12 + EDAM_format:3587: + text: EDAM_format:3587 + description: chrominfo + title: chrominfo + EDAM_format:3588: + text: EDAM_format:3588 + description: customtrack + title: customtrack + EDAM_format:3589: + text: EDAM_format:3589 + description: csfasta + title: csfasta + EDAM_format:3590: + text: EDAM_format:3590 + description: HDF5 + title: HDF5 + EDAM_format:3591: + text: EDAM_format:3591 + description: TIFF + title: TIFF + EDAM_format:3592: + text: EDAM_format:3592 + description: BMP + title: BMP + EDAM_format:3593: + text: EDAM_format:3593 + description: im + title: im + EDAM_format:3594: + text: EDAM_format:3594 + description: pcd + title: pcd + EDAM_format:3595: + text: EDAM_format:3595 + description: pcx + title: pcx + EDAM_format:3596: + text: EDAM_format:3596 + description: ppm + title: ppm + EDAM_format:3597: + text: EDAM_format:3597 + description: psd + title: psd + EDAM_format:3598: + text: EDAM_format:3598 + description: xbm + title: xbm + EDAM_format:3599: + text: EDAM_format:3599 + description: xpm + title: xpm + EDAM_format:3600: + text: EDAM_format:3600 + description: rgb + title: rgb + EDAM_format:3601: + text: EDAM_format:3601 + description: pbm + title: pbm + EDAM_format:3602: + text: EDAM_format:3602 + description: pgm + title: pgm + EDAM_format:3603: + text: EDAM_format:3603 + description: PNG + title: PNG + EDAM_format:3604: + text: EDAM_format:3604 + description: SVG + title: SVG + EDAM_format:3605: + text: EDAM_format:3605 + description: rast + title: rast + EDAM_format:3606: + text: EDAM_format:3606 + description: Sequence quality report format (text) + title: Sequence quality report format (text) + EDAM_format:3607: + text: EDAM_format:3607 + description: qual + title: qual + EDAM_format:3608: + text: EDAM_format:3608 + description: qualsolexa + title: qualsolexa + EDAM_format:3609: + text: EDAM_format:3609 + description: qualillumina + title: qualillumina + EDAM_format:3610: + text: EDAM_format:3610 + description: qualsolid + title: qualsolid + EDAM_format:3611: + text: EDAM_format:3611 + description: qual454 + title: qual454 + EDAM_format:3612: + text: EDAM_format:3612 + description: ENCODE peak format + title: ENCODE peak format + EDAM_format:3613: + text: EDAM_format:3613 + description: ENCODE narrow peak format + title: ENCODE narrow peak format + EDAM_format:3614: + text: EDAM_format:3614 + description: ENCODE broad peak format + title: ENCODE broad peak format + EDAM_format:3615: + text: EDAM_format:3615 + description: bgzip + title: bgzip + EDAM_format:3616: + text: EDAM_format:3616 + description: tabix + title: tabix + EDAM_format:3617: + text: EDAM_format:3617 + description: Graph format + title: Graph format + EDAM_format:3618: + text: EDAM_format:3618 + description: xgmml + title: xgmml + EDAM_format:3619: + text: EDAM_format:3619 + description: sif + title: sif + EDAM_format:3620: + text: EDAM_format:3620 + description: xlsx + title: xlsx + EDAM_format:3621: + text: EDAM_format:3621 + description: SQLite format + title: SQLite format + EDAM_format:3622: + text: EDAM_format:3622 + description: Gemini SQLite format + title: Gemini SQLite format + EDAM_format:3624: + text: EDAM_format:3624 + description: snpeffdb + title: snpeffdb + EDAM_format:3626: + text: EDAM_format:3626 + description: MAT + title: MAT + EDAM_format:3650: + text: EDAM_format:3650 + description: NetCDF + title: NetCDF + EDAM_format:3651: + text: EDAM_format:3651 + description: MGF + title: MGF + EDAM_format:3652: + text: EDAM_format:3652 + description: dta + title: dta + EDAM_format:3653: + text: EDAM_format:3653 + description: pkl + title: pkl + EDAM_format:3654: + text: EDAM_format:3654 + description: mzXML + title: mzXML + EDAM_format:3655: + text: EDAM_format:3655 + description: pepXML + title: pepXML + EDAM_format:3657: + text: EDAM_format:3657 + description: GPML + title: GPML + EDAM_format:3665: + text: EDAM_format:3665 + description: K-mer countgraph + title: K-mer countgraph + EDAM_format:3681: + text: EDAM_format:3681 + description: mzTab + title: mzTab + EDAM_format:3682: + text: EDAM_format:3682 + description: imzML metadata file + title: imzML metadata file + EDAM_format:3683: + text: EDAM_format:3683 + description: qcML + title: qcML + EDAM_format:3684: + text: EDAM_format:3684 + description: PRIDE XML + title: PRIDE XML + EDAM_format:3685: + text: EDAM_format:3685 + description: SED-ML + title: SED-ML + EDAM_format:3686: + text: EDAM_format:3686 + description: COMBINE OMEX + title: COMBINE OMEX + EDAM_format:3687: + text: EDAM_format:3687 + description: ISA-TAB + title: ISA-TAB + EDAM_format:3688: + text: EDAM_format:3688 + description: SBtab + title: SBtab + EDAM_format:3689: + text: EDAM_format:3689 + description: BCML + title: BCML + EDAM_format:3690: + text: EDAM_format:3690 + description: BDML + title: BDML + EDAM_format:3691: + text: EDAM_format:3691 + description: BEL + title: BEL + EDAM_format:3692: + text: EDAM_format:3692 + description: SBGN-ML + title: SBGN-ML + EDAM_format:3693: + text: EDAM_format:3693 + description: AGP + title: AGP + EDAM_format:3696: + text: EDAM_format:3696 + description: PS + title: PS + EDAM_format:3698: + text: EDAM_format:3698 + description: SRA format + title: SRA format + EDAM_format:3699: + text: EDAM_format:3699 + description: VDB + title: VDB + EDAM_format:3701: + text: EDAM_format:3701 + description: Sequin format + title: Sequin format + EDAM_format:3702: + text: EDAM_format:3702 + description: MSF + title: MSF + EDAM_format:3706: + text: EDAM_format:3706 + description: Biodiversity data format + title: Biodiversity data format + EDAM_format:3708: + text: EDAM_format:3708 + description: ABCD format + title: ABCD format + EDAM_format:3709: + text: EDAM_format:3709 + description: GCT/Res format + title: GCT/Res format + EDAM_format:3710: + text: EDAM_format:3710 + description: WIFF format + title: WIFF format + EDAM_format:3711: + text: EDAM_format:3711 + description: X!Tandem XML + title: X!Tandem XML + EDAM_format:3712: + text: EDAM_format:3712 + description: Thermo RAW + title: Thermo RAW + EDAM_format:3713: + text: EDAM_format:3713 + description: Mascot .dat file + title: Mascot .dat file + EDAM_format:3714: + text: EDAM_format:3714 + description: MaxQuant APL peaklist format + title: MaxQuant APL peaklist format + EDAM_format:3725: + text: EDAM_format:3725 + description: SBOL + title: SBOL + EDAM_format:3726: + text: EDAM_format:3726 + description: PMML + title: PMML + EDAM_format:3727: + text: EDAM_format:3727 + description: OME-TIFF + title: OME-TIFF + EDAM_format:3728: + text: EDAM_format:3728 + description: LocARNA PP + title: LocARNA PP + EDAM_format:3729: + text: EDAM_format:3729 + description: dbGaP format + title: dbGaP format + EDAM_format:3746: + text: EDAM_format:3746 + description: BIOM format + title: BIOM format + EDAM_format:3747: + text: EDAM_format:3747 + description: protXML + title: protXML + EDAM_format:3748: + text: EDAM_format:3748 + description: Linked data format + title: Linked data format + EDAM_format:3749: + text: EDAM_format:3749 + description: JSON-LD + title: JSON-LD + EDAM_format:3750: + text: EDAM_format:3750 + description: YAML + title: YAML + EDAM_format:3751: + text: EDAM_format:3751 + description: DSV + title: DSV + EDAM_format:3752: + text: EDAM_format:3752 + description: CSV + title: CSV + EDAM_format:3758: + text: EDAM_format:3758 + description: SEQUEST .out file + title: SEQUEST .out file + EDAM_format:3764: + text: EDAM_format:3764 + description: idXML + title: idXML + EDAM_format:3765: + text: EDAM_format:3765 + description: KNIME datatable format + title: KNIME datatable format + EDAM_format:3770: + text: EDAM_format:3770 + description: UniProtKB XML + title: UniProtKB XML + EDAM_format:3771: + text: EDAM_format:3771 + description: UniProtKB RDF + title: UniProtKB RDF + EDAM_format:3772: + text: EDAM_format:3772 + description: BioJSON (BioXSD) + title: BioJSON (BioXSD) + EDAM_format:3773: + text: EDAM_format:3773 + description: BioYAML + title: BioYAML + EDAM_format:3774: + text: EDAM_format:3774 + description: BioJSON (Jalview) + title: BioJSON (Jalview) + EDAM_format:3775: + text: EDAM_format:3775 + description: GSuite + title: GSuite + EDAM_format:3776: + text: EDAM_format:3776 + description: BTrack + title: BTrack + EDAM_format:3777: + text: EDAM_format:3777 + description: MCPD + title: MCPD + EDAM_format:3780: + text: EDAM_format:3780 + description: Annotated text format + title: Annotated text format + EDAM_format:3781: + text: EDAM_format:3781 + description: PubAnnotation format + title: PubAnnotation format + EDAM_format:3782: + text: EDAM_format:3782 + description: BioC + title: BioC + EDAM_format:3783: + text: EDAM_format:3783 + description: PubTator format + title: PubTator format + EDAM_format:3784: + text: EDAM_format:3784 + description: Open Annotation format + title: Open Annotation format + EDAM_format:3785: + text: EDAM_format:3785 + description: BioNLP Shared Task format + title: BioNLP Shared Task format + EDAM_format:3787: + text: EDAM_format:3787 + description: Query language + title: Query language + EDAM_format:3788: + text: EDAM_format:3788 + description: SQL + title: SQL + EDAM_format:3789: + text: EDAM_format:3789 + description: XQuery + title: XQuery + EDAM_format:3790: + text: EDAM_format:3790 + description: SPARQL + title: SPARQL + EDAM_format:3804: + text: EDAM_format:3804 + description: xsd + title: xsd + EDAM_format:3811: + text: EDAM_format:3811 + description: XMFA + title: XMFA + EDAM_format:3812: + text: EDAM_format:3812 + description: GEN + title: GEN + EDAM_format:3813: + text: EDAM_format:3813 + description: SAMPLE file format + title: SAMPLE file format + EDAM_format:3814: + text: EDAM_format:3814 + description: SDF + title: SDF + EDAM_format:3815: + text: EDAM_format:3815 + description: Molfile + title: Molfile + EDAM_format:3816: + text: EDAM_format:3816 + description: Mol2 + title: Mol2 + EDAM_format:3817: + text: EDAM_format:3817 + description: latex + title: latex + EDAM_format:3818: + text: EDAM_format:3818 + description: ELAND format + title: ELAND format + EDAM_format:3819: + text: EDAM_format:3819 + description: Relaxed PHYLIP Interleaved + title: Relaxed PHYLIP Interleaved + EDAM_format:3820: + text: EDAM_format:3820 + description: Relaxed PHYLIP Sequential + title: Relaxed PHYLIP Sequential + EDAM_format:3821: + text: EDAM_format:3821 + description: VisML + title: VisML + EDAM_format:3822: + text: EDAM_format:3822 + description: GML + title: GML + EDAM_format:3823: + text: EDAM_format:3823 + description: FASTG + title: FASTG + EDAM_format:3824: + text: EDAM_format:3824 + description: NMR data format + title: NMR data format + EDAM_format:3825: + text: EDAM_format:3825 + description: nmrML + title: nmrML + EDAM_format:3826: + text: EDAM_format:3826 + description: proBAM + title: proBAM + EDAM_format:3827: + text: EDAM_format:3827 + description: proBED + title: proBED + EDAM_format:3828: + text: EDAM_format:3828 + description: Raw microarray data format + title: Raw microarray data format + EDAM_format:3829: + text: EDAM_format:3829 + description: GPR + title: GPR + EDAM_format:3830: + text: EDAM_format:3830 + description: ARB + title: ARB + EDAM_format:3832: + text: EDAM_format:3832 + description: consensusXML + title: consensusXML + EDAM_format:3833: + text: EDAM_format:3833 + description: featureXML + title: featureXML + EDAM_format:3834: + text: EDAM_format:3834 + description: mzData + title: mzData + EDAM_format:3835: + text: EDAM_format:3835 + description: TIDE TXT + title: TIDE TXT + EDAM_format:3836: + text: EDAM_format:3836 + description: BLAST XML v2 results format + title: BLAST XML v2 results format + EDAM_format:3838: + text: EDAM_format:3838 + description: pptx + title: pptx + EDAM_format:3839: + text: EDAM_format:3839 + description: ibd + title: ibd + EDAM_format:3841: + text: EDAM_format:3841 + description: NLP format + title: NLP format + EDAM_format:3843: + text: EDAM_format:3843 + description: BEAST + title: BEAST + EDAM_format:3844: + text: EDAM_format:3844 + description: Chado-XML + title: Chado-XML + EDAM_format:3845: + text: EDAM_format:3845 + description: HSAML + title: HSAML + EDAM_format:3846: + text: EDAM_format:3846 + description: InterProScan XML + title: InterProScan XML + EDAM_format:3847: + text: EDAM_format:3847 + description: KGML + title: KGML + EDAM_format:3848: + text: EDAM_format:3848 + description: PubMed XML + title: PubMed XML + EDAM_format:3849: + text: EDAM_format:3849 + description: MSAML + title: MSAML + EDAM_format:3850: + text: EDAM_format:3850 + description: OrthoXML + title: OrthoXML + EDAM_format:3851: + text: EDAM_format:3851 + description: PSDML + title: PSDML + EDAM_format:3852: + text: EDAM_format:3852 + description: SeqXML + title: SeqXML + EDAM_format:3853: + text: EDAM_format:3853 + description: UniParc XML + title: UniParc XML + EDAM_format:3854: + text: EDAM_format:3854 + description: UniRef XML + title: UniRef XML + EDAM_format:3857: + text: EDAM_format:3857 + description: CWL + title: CWL + EDAM_format:3858: + text: EDAM_format:3858 + description: Waters RAW + title: Waters RAW + EDAM_format:3859: + text: EDAM_format:3859 + description: JCAMP-DX + title: JCAMP-DX + EDAM_format:3862: + text: EDAM_format:3862 + description: NLP annotation format + title: NLP annotation format + EDAM_format:3863: + text: EDAM_format:3863 + description: NLP corpus format + title: NLP corpus format + EDAM_format:3864: + text: EDAM_format:3864 + description: mirGFF3 + title: mirGFF3 + EDAM_format:3865: + text: EDAM_format:3865 + description: RNA annotation format + title: RNA annotation format + EDAM_format:3866: + text: EDAM_format:3866 + description: Trajectory format + title: Trajectory format + EDAM_format:3867: + text: EDAM_format:3867 + description: Trajectory format (binary) + title: Trajectory format (binary) + EDAM_format:3868: + text: EDAM_format:3868 + description: Trajectory format (text) + title: Trajectory format (text) + EDAM_format:3873: + text: EDAM_format:3873 + description: HDF + title: HDF + EDAM_format:3874: + text: EDAM_format:3874 + description: PCAzip + title: PCAzip + EDAM_format:3875: + text: EDAM_format:3875 + description: XTC + title: XTC + EDAM_format:3876: + text: EDAM_format:3876 + description: TNG + title: TNG + EDAM_format:3877: + text: EDAM_format:3877 + description: XYZ + title: XYZ + EDAM_format:3878: + text: EDAM_format:3878 + description: mdcrd + title: mdcrd + EDAM_format:3879: + text: EDAM_format:3879 + description: Topology format + title: Topology format + EDAM_format:3880: + text: EDAM_format:3880 + description: GROMACS top + title: GROMACS top + EDAM_format:3881: + text: EDAM_format:3881 + description: AMBER top + title: AMBER top + EDAM_format:3882: + text: EDAM_format:3882 + description: PSF + title: PSF + EDAM_format:3883: + text: EDAM_format:3883 + description: GROMACS itp + title: GROMACS itp + EDAM_format:3884: + text: EDAM_format:3884 + description: FF parameter format + title: FF parameter format + EDAM_format:3885: + text: EDAM_format:3885 + description: BinPos + title: BinPos + EDAM_format:3886: + text: EDAM_format:3886 + description: RST + title: RST + EDAM_format:3887: + text: EDAM_format:3887 + description: CHARMM rtf + title: CHARMM rtf + EDAM_format:3888: + text: EDAM_format:3888 + description: AMBER frcmod + title: AMBER frcmod + EDAM_format:3889: + text: EDAM_format:3889 + description: AMBER off + title: AMBER off + EDAM_format:3906: + text: EDAM_format:3906 + description: NMReDATA + title: NMReDATA + EDAM_format:3909: + text: EDAM_format:3909 + description: BpForms + title: BpForms + EDAM_format:3910: + text: EDAM_format:3910 + description: trr + title: trr + EDAM_format:3911: + text: EDAM_format:3911 + description: msh + title: msh + EDAM_format:3913: + text: EDAM_format:3913 + description: Loom + title: Loom + EDAM_format:3915: + text: EDAM_format:3915 + description: Zarr + title: Zarr + EDAM_format:3916: + text: EDAM_format:3916 + description: MTX + title: MTX + EDAM_format:3951: + text: EDAM_format:3951 + description: BcForms + title: BcForms + EDAM_format:3956: + text: EDAM_format:3956 + description: N-Quads + title: N-Quads + EDAM_format:3969: + text: EDAM_format:3969 + description: Vega + title: Vega + EDAM_format:3970: + text: EDAM_format:3970 + description: Vega-lite + title: Vega-lite + EDAM_format:3971: + text: EDAM_format:3971 + description: NeuroML + title: NeuroML + EDAM_format:3972: + text: EDAM_format:3972 + description: BNGL + title: BNGL + EDAM_format:3973: + text: EDAM_format:3973 + description: Docker image + title: Docker image + EDAM_format:3975: + text: EDAM_format:3975 + description: GFA 1 + title: GFA 1 + EDAM_format:3976: + text: EDAM_format:3976 + description: GFA 2 + title: GFA 2 + EDAM_format:3977: + text: EDAM_format:3977 + description: ObjTables + title: ObjTables + EDAM_format:3978: + text: EDAM_format:3978 + description: CONTIG + title: CONTIG + EDAM_format:3979: + text: EDAM_format:3979 + description: WEGO + title: WEGO + EDAM_format:3980: + text: EDAM_format:3980 + description: RPKM + title: RPKM + EDAM_format:3981: + text: EDAM_format:3981 + description: TAR format + title: TAR format + EDAM_format:3982: + text: EDAM_format:3982 + description: CHAIN + title: CHAIN + EDAM_format:3983: + text: EDAM_format:3983 + description: NET + title: NET + EDAM_format:3984: + text: EDAM_format:3984 + description: QMAP + title: QMAP + EDAM_format:3985: + text: EDAM_format:3985 + description: gxformat2 + title: gxformat2 + EDAM_format:3986: + text: EDAM_format:3986 + description: WMV + title: WMV + EDAM_format:3987: + text: EDAM_format:3987 + description: ZIP format + title: ZIP format + EDAM_format:3988: + text: EDAM_format:3988 + description: LSM + title: LSM + EDAM_format:3989: + text: EDAM_format:3989 + description: GZIP format + title: GZIP format + EDAM_format:3990: + text: EDAM_format:3990 + description: AVI + title: AVI + EDAM_format:3991: + text: EDAM_format:3991 + description: TrackDB + title: TrackDB + EDAM_format:3992: + text: EDAM_format:3992 + description: CIGAR format + title: CIGAR format + EDAM_format:3993: + text: EDAM_format:3993 + description: Stereolithography format + title: Stereolithography format + EDAM_format:3994: + text: EDAM_format:3994 + description: U3D + title: U3D + EDAM_format:3995: + text: EDAM_format:3995 + description: Texture file format + title: Texture file format + EDAM_format:3996: + text: EDAM_format:3996 + description: Python script + title: Python script + EDAM_format:3997: + text: EDAM_format:3997 + description: MPEG-4 + title: MPEG-4 + EDAM_format:3998: + text: EDAM_format:3998 + description: Perl script + title: Perl script + EDAM_format:3999: + text: EDAM_format:3999 + description: R script + title: R script + EDAM_format:4000: + text: EDAM_format:4000 + description: R markdown + title: R markdown + EDAM_format:4002: + text: EDAM_format:4002 + description: pickle + title: pickle + EDAM_format:4003: + text: EDAM_format:4003 + description: NumPy format + title: NumPy format + EDAM_format:4004: + text: EDAM_format:4004 + description: SimTools repertoire file format + title: SimTools repertoire file format + EDAM_format:4005: + text: EDAM_format:4005 + description: Configuration file format + title: Configuration file format + EDAM_format:4006: + text: EDAM_format:4006 + description: Zstandard format + title: Zstandard format + EDAM_format:4007: + text: EDAM_format:4007 + description: MATLAB script + title: MATLAB script + EDAM_format:4015: + text: EDAM_format:4015 + description: PEtab + title: PEtab + EDAM_format:4018: + text: EDAM_format:4018 + description: gVCF + title: gVCF + EDAM_format:4023: + text: EDAM_format:4023 + description: cml + title: cml + EDAM_format:4024: + text: EDAM_format:4024 + description: cif + title: cif + EDAM_format:4025: + text: EDAM_format:4025 + description: BioSimulators format for the specifications of biosimulation + tools + title: BioSimulators format for the specifications of biosimulation tools + EDAM_format:4026: + text: EDAM_format:4026 + description: BioSimulators standard for command-line interfaces for biosimulation + tools + title: BioSimulators standard for command-line interfaces for biosimulation + tools + EDAM_format:4035: + text: EDAM_format:4035 + description: PQR + title: PQR + EDAM_format:4036: + text: EDAM_format:4036 + description: PDBQT + title: PDBQT + EDAM_format:4039: + text: EDAM_format:4039 + description: MSP + title: MSP + EDAM_format:4041: + text: EDAM_format:4041 + description: maDMP + title: maDMP + EDAM_format:4048: + text: EDAM_format:4048 + description: Nextflow + title: Nextflow + EDAM_format:4049: + text: EDAM_format:4049 + description: Snakemake + title: Snakemake + EDAM_format:4050: + text: EDAM_format:4050 + description: SDRF + title: SDRF + EDAM_format:4058: + text: EDAM_format:4058 + description: mzTab-M + title: mzTab-M + EDAM_format:4059: + text: EDAM_format:4059 + description: mzTab-L + title: mzTab-L diff --git a/output/EnumEthnicity.yaml b/output/EnumEthnicity.yaml new file mode 100644 index 0000000..4dca250 --- /dev/null +++ b/output/EnumEthnicity.yaml @@ -0,0 +1,19 @@ +--- +id: https://includedcc.org/common-access-model/EnumEthnicity +name: EnumEthnicity +enums: + EnumEthnicity: + description: Participant ethnicity, specific to Hispanic or Latino. + permissible_values: + hispanic_or_latino: + title: Hispanic or Latino + meaning: NCIT:C17459 + not_hispanic_or_latino: + title: Not Hispanic or Latino + meaning: NCIT:C41222 + prefer_not_to_answer: + title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + title: Unknown + meaning: NCIT:C17998 diff --git a/output/EnumFamilyType.yaml b/output/EnumFamilyType.yaml new file mode 100644 index 0000000..38575bf --- /dev/null +++ b/output/EnumFamilyType.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumFamilyType +name: EnumFamilyType +enums: + EnumFamilyType: + description: Enumerations describing research family type + is_a: EnumNull + permissible_values: + control_only: + title: Control-only + description: Control Only + duo: + title: Duo + description: Duo + proband_only: + title: Proband-only + description: Proband Only + trio: + title: Trio + description: Trio (2 parents and affected child) + trio_plus: + title: Trio+ + description: 2 Parents and 2 or more children diff --git a/output/EnumFileHashType.yaml b/output/EnumFileHashType.yaml new file mode 100644 index 0000000..d0950ed --- /dev/null +++ b/output/EnumFileHashType.yaml @@ -0,0 +1,13 @@ +--- +id: https://includedcc.org/common-access-model/EnumFileHashType +name: EnumFileHashType +enums: + EnumFileHashType: + description: Types of file hashes supported. + permissible_values: + md5: + title: MD5 + etag: + title: ETag + sha1: + title: SHA-1 diff --git a/output/EnumNull.yaml b/output/EnumNull.yaml new file mode 100644 index 0000000..c6582e6 --- /dev/null +++ b/output/EnumNull.yaml @@ -0,0 +1,10 @@ +--- +id: https://includedcc.org/common-access-model/EnumNull +name: EnumNull +enums: + EnumNull: + description: Base enumeration providing null options. + permissible_values: + unknown: + title: Unknown + meaning: NCIT:C17998 diff --git a/output/EnumParticipantLifespanStage.yaml b/output/EnumParticipantLifespanStage.yaml new file mode 100644 index 0000000..b134d03 --- /dev/null +++ b/output/EnumParticipantLifespanStage.yaml @@ -0,0 +1,20 @@ +--- +id: https://includedcc.org/common-access-model/EnumParticipantLifespanStage +name: EnumParticipantLifespanStage +enums: + EnumParticipantLifespanStage: + title: Participant Lifespan Stage + description: Stages of life during which participants may be recruited. + permissible_values: + fetal: + title: Fetal + description: Before birth + neonatal: + title: Neonatal + description: 0-28 days old + pediatric: + title: Pediatric + description: Birth-17 years old + adult: + title: Adult + description: 18+ years old diff --git a/output/EnumProgram.yaml b/output/EnumProgram.yaml new file mode 100644 index 0000000..de6b598 --- /dev/null +++ b/output/EnumProgram.yaml @@ -0,0 +1,14 @@ +--- +id: https://includedcc.org/common-access-model/EnumProgram +name: EnumProgram +enums: + EnumProgram: + title: Funding Programs + description: Funding programs relevant to inform operations. + permissible_values: + include: + title: INCLUDE + kf: + title: KF + other: + title: Other diff --git a/output/EnumRace.yaml b/output/EnumRace.yaml new file mode 100644 index 0000000..3d89953 --- /dev/null +++ b/output/EnumRace.yaml @@ -0,0 +1,50 @@ +--- +id: https://includedcc.org/common-access-model/EnumRace +name: EnumRace +enums: + EnumRace: + description: Participant Race + permissible_values: + american_indian_or_alaska_native: + title: American Indian or Alaska Native + meaning: NCIT:C41259 + asian: + title: Asian + meaning: NCIT:C41260 + black_or_african_american: + title: Black or African American + meaning: NCIT:C16352 + more_than_one_race: + title: More than one race + meaning: NCIT:C67109 + native_hawaiian_or_other_pacific_islander: + title: Native Hawaiian or Other Pacific Islander + meaning: NCIT:C41219 + other: + title: Other + meaning: NCIT:C17649 + white: + title: White + meaning: NCIT:C41261 + prefer_not_to_answer: + title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + title: Unknown + meaning: NCIT:C17998 + east_asian: + title: East Asian + description: UK only; do not use for US data + meaning: NCIT:C161419 + latin_american: + title: Latin American + description: UK only; do not use for US data + meaning: NCIT:C126531 + middle_eastern_or_north_african: + title: Middle Eastern or North African + description: UK only; do not use for US data + meaning: NCIT:C43866 + south_asian: + title: South Asian + description: UK only; do not use for US data + meaning: NCIT:C41263 diff --git a/output/EnumResearchDomain.yaml b/output/EnumResearchDomain.yaml new file mode 100644 index 0000000..b4aba2c --- /dev/null +++ b/output/EnumResearchDomain.yaml @@ -0,0 +1,34 @@ +--- +id: https://includedcc.org/common-access-model/EnumResearchDomain +name: EnumResearchDomain +enums: + EnumResearchDomain: + title: Research Domain + description: Domains of Research used to find studies. + permissible_values: + behavior_and_behavior_mechanisms: + title: Behavior and Behavior Mechanisms + meaning: mesh:D001520 + congenital_heart_defects: + title: Congenital Heart Defects + meaning: mesh:D006330 + immune_system_diseases: + title: Immune System Diseases + meaning: mesh:D007154 + hematologic_diseases: + title: Hematologic Diseases + meaning: mesh:D006402 + neurodevelopment: + title: Neurodevelopment + meaning: mesh:D065886 + sleep_wake_disorders: + title: Sleep Wake Disorders + meaning: mesh:D012893 + all_co_occurring_conditions: + title: All Co-occurring Conditions + meaning: mesh:D013568 + physical_fitness: + title: Physical Fitness + meaning: mesh:D010809 + other: + title: Other diff --git a/output/EnumSex.yaml b/output/EnumSex.yaml new file mode 100644 index 0000000..585b6aa --- /dev/null +++ b/output/EnumSex.yaml @@ -0,0 +1,19 @@ +--- +id: https://includedcc.org/common-access-model/EnumSex +name: EnumSex +enums: + EnumSex: + description: Subject Sex + permissible_values: + female: + title: Female + meaning: NCIT:C16576 + male: + title: Male + meaning: NCIT:C20197 + other: + title: Other + meaning: NCIT:C17649 + unknown: + title: Unknown + meaning: NCIT:C17998 diff --git a/output/EnumSpatialQualifiers.yaml b/output/EnumSpatialQualifiers.yaml new file mode 100644 index 0000000..91e5168 --- /dev/null +++ b/output/EnumSpatialQualifiers.yaml @@ -0,0 +1,23 @@ +id: https://includedcc.org/common-access-model/EnumSpatialQualifiers +name: EnumSpatialQualifiers +enums: + EnumSpatialQualifiers: + description: Any spatial/location qualifiers. + enum_uri: http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs + reachable_from: + source_ontology: bioregistry:snomedct + source_nodes: + - snomedct:106233006 + - snomedct:272424004 + - snomedct:51440002 + - snomedct:399488007 + - snomedct:24028007 + - snomedct:7771000 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + SNOMED:51440002: + text: SNOMED:51440002 + description: Right and left + title: Right and left diff --git a/output/EnumStudyDesign.yaml b/output/EnumStudyDesign.yaml new file mode 100644 index 0000000..6941216 --- /dev/null +++ b/output/EnumStudyDesign.yaml @@ -0,0 +1,29 @@ +--- +id: https://includedcc.org/common-access-model/EnumStudyDesign +name: EnumStudyDesign +enums: + EnumStudyDesign: + title: Study Design + description: Approaches for collecting data, investigating interventions, and/or + analyzing data. + permissible_values: + case_control: + title: Case-Control + case_set: + title: Case Set + control_set: + title: Control Set + clinical_trial: + title: Clinical Trial + cross_sectional: + title: Cross-Sectional + family_twins_trios: + title: Family/Twins/Trios + interventional: + title: Interventional + longitudinal: + title: Longitudinal + trial_readiness_study: + title: Trial Readiness Study + tumor_vs_matched_normal: + title: Tumor vs Matched Normal diff --git a/output/EnumSubjectType.yaml b/output/EnumSubjectType.yaml new file mode 100644 index 0000000..f3aa2da --- /dev/null +++ b/output/EnumSubjectType.yaml @@ -0,0 +1,20 @@ +--- +id: https://includedcc.org/common-access-model/EnumSubjectType +name: EnumSubjectType +enums: + EnumSubjectType: + description: Types of Subject entities + permissible_values: + participant: + description: Study participant with consent, assent, or waiver of consent. + non_participant: + description: An individual associated with a study who was not explictly consented, + eg, the subject of a reported family history. + cell_line: + description: Cell Line + animal_model: + description: Animal model + group: + description: A group of individuals or entities. + other: + description: A different entity type- ideally this will be resolved! diff --git a/output/EnumVitalStatus.yaml b/output/EnumVitalStatus.yaml new file mode 100644 index 0000000..3e6ba19 --- /dev/null +++ b/output/EnumVitalStatus.yaml @@ -0,0 +1,14 @@ +--- +id: https://includedcc.org/common-access-model/EnumVitalStatus +name: EnumVitalStatus +enums: + EnumVitalStatus: + description: Descriptions of a Subject's vital status + is_a: EnumNull + permissible_values: + dead: + title: Dead + meaning: NCIT:C28554 + alive: + title: Alive + meaning: NCIT:C37987 diff --git a/project.justfile b/project.justfile new file mode 100644 index 0000000..6e7192f --- /dev/null +++ b/project.justfile @@ -0,0 +1,5 @@ +## Add your own just recipes here. This is imported by the main justfile. + +# Overriding recipes from the root justfile by adding a recipe with the same +# name in this file is not possible until a known issue in just is fixed, +# https://github.com/casey/just/issues/2540 diff --git a/pyproject.toml b/pyproject.toml index e3df151..ab2f97c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,23 +1,27 @@ [build-system] -requires = ["setuptools>=61.0", "setuptools-scm"] -build-backend = "setuptools.build_meta" +requires = ["hatchling", "uv-dynamic-versioning"] +build-backend = "hatchling.build" [project] -name = "term-weaver" -description = "Enumeration Materialization" -readme = "README.md" -requires-python = ">=3.10" -classifiers = [ - "Programming Language :: Python :: 3", +name = "cam_expanded_enums" +description = "This project is a LinkML model containing expanded enumerations from the Common Access Model." +authors = [ + {name = "Yelena Cox", email = "yelena.cox@vumc.org"}, ] +license = "MIT" +license-files = ["LICENSE"] +readme = "README.md" +requires-python = ">=3.12" +dynamic = ["version"] dependencies = [ - "requests", - "linkml", - "PyYAML", - "jinja2", - "search-dragon@git+https://github.com/NIH-NCPI/search-dragon.git@yc/fd-3693"] -dynamic = ["version"] + "linkml-runtime >=1.9.4", + "requests", + "linkml", + "PyYAML", + "jinja2", + "search-dragon@git+https://github.com/NIH-NCPI/search-dragon.git@yc/fd-3693" +] [project.optional-dependencies] dev = [ @@ -26,6 +30,73 @@ dev = [ "rich_argparse", ] + +[dependency-groups] +dev = [ + "linkml>=1.9.3", + "mkdocs-material>=8.2.8", + "mkdocs-mermaid2-plugin>=1.1.1", + "mkdocs-pymdownx-material-extras>=2.5.6", + "jupyter>=1.0.0", + "mknotebooks>= 0.8.0", +] + +# See https://hatch.pypa.io/latest/config/build/#file-selection for how to +# explicitly include files other than default into the build distributions. + +[tool.hatch.version] +source = "uv-dynamic-versioning" + +[tool.hatch.metadata] +allow-direct-references = true + +# Ref.: https://github.com/ninoseki/uv-dynamic-versioning/ +[tool.uv-dynamic-versioning] +vcs = "git" +style = "pep440" +fallback-version = "0.0.0" + +# Ref.: https://docs.pytest.org/en/stable/reference/reference.html#configuration-options +[tool.pytest.ini_options] +testpaths = ["tests"] + +# https://docs.astral.sh/ruff/configuration/ +[tool.ruff] +exclude = [ + "src/cam_expanded_enums/_version.py", +] +# Set oldest supported Python version +target-version = "py310" + +# Ref.: https://github.com/codespell-project/codespell +[tool.codespell] +skip = [ + "LICENSE", + "pyproject.toml", + "uv.lock", + "project/*", + "src/cam_expanded_enums/datamodel/cam_expanded_enums_pydantic.py", + "src/cam_expanded_enums/datamodel/cam_expanded_enums.py", +] + +# Reminder: words have to be lowercased for the ignore-words-list +ignore-words-list = "linke" +quiet-level = 3 + +# Ref.: https://github.com/crate-ci/typos (spell checker) +[tool.typos.default.extend-words] +linke = "linke" + +[tool.typos.files] +extend-exclude = [ + "LICENSE", + "uv.lock", + "pyproject.toml", + "project/*", + "src/cam_expanded_enums/datamodel/cam_expanded_enums_pydantic.py", + "src/cam_expanded_enums/datamodel/cam_expanded_enums.py", +] + [tool.setuptools_scm] version_file = "src/tweaver/_version.py" diff --git a/source b/source new file mode 120000 index 0000000..c3099d9 --- /dev/null +++ b/source @@ -0,0 +1 @@ +../cam-source-enums/src/cam_source_enums/schema/ \ No newline at end of file diff --git a/src/README.md b/src/README.md new file mode 100644 index 0000000..e006d1c --- /dev/null +++ b/src/README.md @@ -0,0 +1,4 @@ +# The linkML model and its Python representations + +This directory holds the schema, its Python representations +and optionally also additional Python code for the project. diff --git a/src/cam-expanded-enums/EnumAvailabilityStatus.yaml b/src/cam-expanded-enums/EnumAvailabilityStatus.yaml new file mode 100644 index 0000000..f748345 --- /dev/null +++ b/src/cam-expanded-enums/EnumAvailabilityStatus.yaml @@ -0,0 +1,16 @@ +id: https://includedcc.org/common-access-model/EnumAvailabilityStatus +name: EnumAvailabilityStatus +enums: + EnumAvailabilityStatus: + description: Is the biospecimen available for use? + permissible_values: + available: + text: available + description: Biospecimen is Available + meaning: ig2_biospecimen_availability:available + title: Available + unavailable: + text: unavailable + description: Biospecimen is Unavailable + meaning: ig2_biospecimen_availability:unavailable + title: Unavailable diff --git a/src/cam-expanded-enums/EnumClinicalDataSourceType.yaml b/src/cam-expanded-enums/EnumClinicalDataSourceType.yaml new file mode 100644 index 0000000..76d38ee --- /dev/null +++ b/src/cam-expanded-enums/EnumClinicalDataSourceType.yaml @@ -0,0 +1,29 @@ +id: https://includedcc.org/common-access-model/EnumClinicalDataSourceType +name: EnumClinicalDataSourceType +enums: + EnumClinicalDataSourceType: + title: Clinical Data Source Type + description: Approaches to ascertain clinical information about a + participant. + permissible_values: + medical_record: + text: medical_record + description: Data obtained directly from medical record + title: Medical Record + investigator_assessment: + text: investigator_assessment + description: Data obtained by examination, interview, etc. with + investigator + title: Investigator Assessment + participant_or_caregiver_report: + text: participant_or_caregiver_report + description: Data obtained from survey, questionnaire, etc. filled out + by participant or caregiver + title: Participant or Caregiver Report + other: + text: other + description: Data obtained from other source, such as tissue bank + title: Other + unknown: + text: unknown + title: Unknown diff --git a/src/cam-expanded-enums/EnumConsanguinityAssertion.yaml b/src/cam-expanded-enums/EnumConsanguinityAssertion.yaml new file mode 100644 index 0000000..a75cfa7 --- /dev/null +++ b/src/cam-expanded-enums/EnumConsanguinityAssertion.yaml @@ -0,0 +1,26 @@ +id: https://includedcc.org/common-access-model/EnumConsanguinityAssertion +name: EnumConsanguinityAssertion +enums: + EnumConsanguinityAssertion: + description: Asserts known or suspected consanguinity in this study family + permissible_values: + not_suspected: + text: not_suspected + description: Not suspected + meaning: snomed_ct:428263003 + title: not-suspected + suspected: + text: suspected + description: Suspected + meaning: snomed_ct:415684004 + title: suspected + known_present: + text: known_present + description: Known Present + meaning: snomed_ct:410515003 + title: known-present + unknown: + text: unknown + description: Unknown + meaning: snomed_ct:261665006 + title: unknown diff --git a/src/cam-expanded-enums/EnumDataCategory.yaml b/src/cam-expanded-enums/EnumDataCategory.yaml new file mode 100644 index 0000000..238181b --- /dev/null +++ b/src/cam-expanded-enums/EnumDataCategory.yaml @@ -0,0 +1,52 @@ +id: https://includedcc.org/common-access-model/EnumDataCategory +name: EnumDataCategory +enums: + EnumDataCategory: + title: Data Category + description: Categories of data which may be collected about participants. + permissible_values: + unharmonized_demographic_clinical_data: + text: unharmonized_demographic_clinical_data + title: Unharmonized Demographic/Clinical Data + harmonized_demographic_clinical_data: + text: harmonized_demographic_clinical_data + title: Harmonized Demographic/Clinical Data + genomics: + text: genomics + title: Genomics + transcriptomics: + text: transcriptomics + title: Transcriptomics + epigenomics: + text: epigenomics + title: Epigenomics + proteomics: + text: proteomics + title: Proteomics + metabolomics: + text: metabolomics + title: Metabolomics + cognitive_behavioral: + text: cognitive_behavioral + title: Cognitive/Behavioral + immune_profiling: + text: immune_profiling + title: Immune Profiling + imaging: + text: imaging + title: Imaging + microbiome: + text: microbiome + title: Microbiome + fitness: + text: fitness + title: Fitness + physical_activity: + text: physical_activity + title: Physical Activity + other: + text: other + title: Other + sleep_study: + text: sleep_study + title: Sleep Study diff --git a/src/cam-expanded-enums/EnumDataUseModifier.yaml b/src/cam-expanded-enums/EnumDataUseModifier.yaml new file mode 100644 index 0000000..455d629 --- /dev/null +++ b/src/cam-expanded-enums/EnumDataUseModifier.yaml @@ -0,0 +1,127 @@ +id: https://includedcc.org/common-access-model/EnumDataUseModifier +name: EnumDataUseModifier +enums: + EnumDataUseModifier: + title: Data Use Modifier + description: Data Use Ontology (DUO) terms for data use modifiers. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000017 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + DUO:0000026: + text: DUO:0000026 + description: This data use modifier indicates that use is limited to use + by approved users. + meaning: DUO:0000026 + title: user specific restriction + DUO:0000015: + text: DUO:0000015 + description: This data use modifier indicates that use does not allow + methods development research (e.g., development of software or + algorithms). + meaning: DUO:0000015 + title: no general methods research + DUO:0000012: + text: DUO:0000012 + description: This data use modifier indicates that use is limited to + studies of a certain research type. + meaning: DUO:0000012 + title: research specific restrictions + DUO:0000043: + text: DUO:0000043 + description: This data use modifier indicates that use is allowed for + clinical use and care. + meaning: DUO:0000043 + title: clinical care use + DUO:0000029: + text: DUO:0000029 + description: This data use modifier indicates that the requestor must + return derived/enriched data to the database/resource. + meaning: DUO:0000029 + title: return to database or resource + DUO:0000024: + text: DUO:0000024 + description: This data use modifier indicates that requestor agrees not + to publish results of studies until a specific date. + meaning: DUO:0000024 + title: publication moratorium + DUO:0000045: + text: DUO:0000045 + description: This data use modifier indicates that use of the data is + limited to not-for-profit organizations. + meaning: DUO:0000045 + title: not for profit organisation use only + DUO:0000018: + text: DUO:0000018 + description: This data use modifier indicates that use of the data is + limited to not-for-profit organizations and not-for-profit use, + non-commercial use. + meaning: DUO:0000018 + title: not for profit, non commercial use only + DUO:0000028: + text: DUO:0000028 + description: This data use modifier indicates that use is limited to use + within an approved institution. + meaning: DUO:0000028 + title: institution specific restriction + DUO:0000019: + text: DUO:0000019 + description: This data use modifier indicates that requestor agrees to + make results of studies using the data available to the larger + scientific community. + meaning: DUO:0000019 + title: publication required + DUO:0000016: + text: DUO:0000016 + description: This data use modifier indicates that use is limited to + genetic studies only (i.e., studies that include genotype research + alone or both genotype and phenotype research, but not phenotype + research exclusively) + meaning: DUO:0000016 + title: genetic studies only + DUO:0000021: + text: DUO:0000021 + description: This data use modifier indicates that the requestor must + provide documentation of local IRB/ERB approval. + meaning: DUO:0000021 + title: ethics approval required + DUO:0000022: + text: DUO:0000022 + description: This data use modifier indicates that use is limited to + within a specific geographic region. + meaning: DUO:0000022 + title: geographical restriction + DUO:0000020: + text: DUO:0000020 + description: This data use modifier indicates that the requestor must + agree to collaboration with the primary study investigator(s). + meaning: DUO:0000020 + title: collaboration required + DUO:0000027: + text: DUO:0000027 + description: This data use modifier indicates that use is limited to use + within an approved project. + meaning: DUO:0000027 + title: project specific restriction + DUO:0000046: + text: DUO:0000046 + description: This data use modifier indicates that use of the data is + limited to not-for-profit use. + meaning: DUO:0000046 + title: non-commercial use only + DUO:00000044: + text: DUO:00000044 + description: This data use modifier indicates use for purposes of + population, origin, or ancestry research is prohibited. + meaning: DUO:00000044 + title: population origins or ancestry research prohibited + DUO:0000025: + text: DUO:0000025 + description: This data use modifier indicates that use is approved for a + specific number of months. + meaning: DUO:0000025 + title: time limit on use diff --git a/src/cam-expanded-enums/EnumDataUsePermission.yaml b/src/cam-expanded-enums/EnumDataUsePermission.yaml new file mode 100644 index 0000000..b7a1535 --- /dev/null +++ b/src/cam-expanded-enums/EnumDataUsePermission.yaml @@ -0,0 +1,45 @@ +id: https://includedcc.org/common-access-model/EnumDataUsePermission +name: EnumDataUsePermission +enums: + EnumDataUsePermission: + title: Data Use Permission + description: Data Use Ontology (DUO) terms for data use permissions. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000001 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + DUO:0000042: + text: DUO:0000042 + description: This data use permission indicates that use is allowed for + general research use for any research purpose. + meaning: DUO:0000042 + title: general research use + DUO:0000006: + text: DUO:0000006 + description: This data use permission indicates that use is allowed for + health/medical/biomedical purposes; does not include the study of + population origins or ancestry. + meaning: DUO:0000006 + title: health or medical or biomedical research + DUO:0000007: + text: DUO:0000007 + description: This data use permission indicates that use is allowed + provided it is related to the specified disease. + meaning: DUO:0000007 + title: disease specific research + DUO:0000011: + text: DUO:0000011 + description: This data use permission indicates that use of the data is + limited to the study of population origins or ancestry. + meaning: DUO:0000011 + title: population origins or ancestry research only + DUO:0000004: + text: DUO:0000004 + description: This data use permission indicates there is no restriction + on use. + meaning: DUO:0000004 + title: no restriction diff --git a/src/cam-expanded-enums/EnumEDAMDataTypes.yaml b/src/cam-expanded-enums/EnumEDAMDataTypes.yaml new file mode 100644 index 0000000..aef2d7e --- /dev/null +++ b/src/cam-expanded-enums/EnumEDAMDataTypes.yaml @@ -0,0 +1,14 @@ +id: https://includedcc.org/common-access-model/EnumEDAMDataTypes +name: EnumEDAMDataTypes +enums: + EnumEDAMDataTypes: + description: Data types from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:data_0006 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: {} diff --git a/src/cam-expanded-enums/EnumEDAMFormats.yaml b/src/cam-expanded-enums/EnumEDAMFormats.yaml new file mode 100644 index 0000000..bc82c6b --- /dev/null +++ b/src/cam-expanded-enums/EnumEDAMFormats.yaml @@ -0,0 +1,14 @@ +id: https://includedcc.org/common-access-model/EnumEDAMFormats +name: EnumEDAMFormats +enums: + EnumEDAMFormats: + description: Data formats from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:format_1915 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: {} diff --git a/src/cam-expanded-enums/EnumEthnicity.yaml b/src/cam-expanded-enums/EnumEthnicity.yaml new file mode 100644 index 0000000..b8ee2ca --- /dev/null +++ b/src/cam-expanded-enums/EnumEthnicity.yaml @@ -0,0 +1,22 @@ +id: https://includedcc.org/common-access-model/EnumEthnicity +name: EnumEthnicity +enums: + EnumEthnicity: + description: Participant ethnicity, specific to Hispanic or Latino. + permissible_values: + hispanic_or_latino: + text: hispanic_or_latino + meaning: NCIT:C17459 + title: Hispanic or Latino + not_hispanic_or_latino: + text: not_hispanic_or_latino + meaning: NCIT:C41222 + title: Not Hispanic or Latino + prefer_not_to_answer: + text: prefer_not_to_answer + meaning: NCIT:C132222 + title: Prefer not to answer + unknown: + text: unknown + meaning: NCIT:C17998 + title: Unknown diff --git a/src/cam-expanded-enums/EnumFamilyType.yaml b/src/cam-expanded-enums/EnumFamilyType.yaml new file mode 100644 index 0000000..58f1c06 --- /dev/null +++ b/src/cam-expanded-enums/EnumFamilyType.yaml @@ -0,0 +1,27 @@ +id: https://includedcc.org/common-access-model/EnumFamilyType +name: EnumFamilyType +enums: + EnumFamilyType: + description: Enumerations describing research family type + is_a: EnumNull + permissible_values: + control_only: + text: control_only + description: Control Only + title: Control-only + duo: + text: duo + description: Duo + title: Duo + proband_only: + text: proband_only + description: Proband Only + title: Proband-only + trio: + text: trio + description: Trio (2 parents and affected child) + title: Trio + trio_plus: + text: trio_plus + description: 2 Parents and 2 or more children + title: Trio+ diff --git a/src/cam-expanded-enums/EnumFileHashType.yaml b/src/cam-expanded-enums/EnumFileHashType.yaml new file mode 100644 index 0000000..bf3026d --- /dev/null +++ b/src/cam-expanded-enums/EnumFileHashType.yaml @@ -0,0 +1,15 @@ +id: https://includedcc.org/common-access-model/EnumFileHashType +name: EnumFileHashType +enums: + EnumFileHashType: + description: Types of file hashes supported. + permissible_values: + md5: + text: md5 + title: MD5 + etag: + text: etag + title: ETag + sha1: + text: sha1 + title: SHA-1 diff --git a/src/cam-expanded-enums/EnumLaterality.yaml b/src/cam-expanded-enums/EnumLaterality.yaml new file mode 100644 index 0000000..704adea --- /dev/null +++ b/src/cam-expanded-enums/EnumLaterality.yaml @@ -0,0 +1,6 @@ +id: https://includedcc.org/common-access-model/EnumLaterality +name: EnumLaterality +enums: + EnumLaterality: + description: Laterality information for the site + permissible_values: {} diff --git a/src/cam-expanded-enums/EnumNull.yaml b/src/cam-expanded-enums/EnumNull.yaml new file mode 100644 index 0000000..4ef0a10 --- /dev/null +++ b/src/cam-expanded-enums/EnumNull.yaml @@ -0,0 +1,10 @@ +id: https://includedcc.org/common-access-model/EnumNull +name: EnumNull +enums: + EnumNull: + description: Base enumeration providing null options. + permissible_values: + unknown: + text: unknown + meaning: NCIT:C17998 + title: Unknown diff --git a/src/cam-expanded-enums/EnumParticipantLifespanStage.yaml b/src/cam-expanded-enums/EnumParticipantLifespanStage.yaml new file mode 100644 index 0000000..0bba6d5 --- /dev/null +++ b/src/cam-expanded-enums/EnumParticipantLifespanStage.yaml @@ -0,0 +1,23 @@ +id: https://includedcc.org/common-access-model/EnumParticipantLifespanStage +name: EnumParticipantLifespanStage +enums: + EnumParticipantLifespanStage: + title: Participant Lifespan Stage + description: Stages of life during which participants may be recruited. + permissible_values: + fetal: + text: fetal + description: Before birth + title: Fetal + neonatal: + text: neonatal + description: 0-28 days old + title: Neonatal + pediatric: + text: pediatric + description: Birth-17 years old + title: Pediatric + adult: + text: adult + description: 18+ years old + title: Adult diff --git a/src/cam-expanded-enums/EnumProgram.yaml b/src/cam-expanded-enums/EnumProgram.yaml new file mode 100644 index 0000000..8fe8f23 --- /dev/null +++ b/src/cam-expanded-enums/EnumProgram.yaml @@ -0,0 +1,16 @@ +id: https://includedcc.org/common-access-model/EnumProgram +name: EnumProgram +enums: + EnumProgram: + title: Funding Programs + description: Funding programs relevant to inform operations. + permissible_values: + include: + text: include + title: INCLUDE + kf: + text: kf + title: KF + other: + text: other + title: Other diff --git a/src/cam-expanded-enums/EnumRace.yaml b/src/cam-expanded-enums/EnumRace.yaml new file mode 100644 index 0000000..2c7c06b --- /dev/null +++ b/src/cam-expanded-enums/EnumRace.yaml @@ -0,0 +1,62 @@ +id: https://includedcc.org/common-access-model/EnumRace +name: EnumRace +enums: + EnumRace: + description: Participant Race + permissible_values: + american_indian_or_alaska_native: + text: american_indian_or_alaska_native + meaning: NCIT:C41259 + title: American Indian or Alaska Native + asian: + text: asian + meaning: NCIT:C41260 + title: Asian + black_or_african_american: + text: black_or_african_american + meaning: NCIT:C16352 + title: Black or African American + more_than_one_race: + text: more_than_one_race + meaning: NCIT:C67109 + title: More than one race + native_hawaiian_or_other_pacific_islander: + text: native_hawaiian_or_other_pacific_islander + meaning: NCIT:C41219 + title: Native Hawaiian or Other Pacific Islander + other: + text: other + meaning: NCIT:C17649 + title: Other + white: + text: white + meaning: NCIT:C41261 + title: White + prefer_not_to_answer: + text: prefer_not_to_answer + meaning: NCIT:C132222 + title: Prefer not to answer + unknown: + text: unknown + meaning: NCIT:C17998 + title: Unknown + east_asian: + text: east_asian + description: UK only; do not use for US data + meaning: NCIT:C161419 + title: East Asian + latin_american: + text: latin_american + description: UK only; do not use for US data + meaning: NCIT:C126531 + title: Latin American + middle_eastern_or_north_african: + text: middle_eastern_or_north_african + description: UK only; do not use for US data + meaning: NCIT:C43866 + title: Middle Eastern or North African + south_asian: + text: south_asian + description: UK only; do not use for US data + meaning: NCIT:C41263 + title: South Asian diff --git a/src/cam-expanded-enums/EnumResearchDomain.yaml b/src/cam-expanded-enums/EnumResearchDomain.yaml new file mode 100644 index 0000000..eef2dcf --- /dev/null +++ b/src/cam-expanded-enums/EnumResearchDomain.yaml @@ -0,0 +1,42 @@ +id: https://includedcc.org/common-access-model/EnumResearchDomain +name: EnumResearchDomain +enums: + EnumResearchDomain: + title: Research Domain + description: Domains of Research used to find studies. + permissible_values: + behavior_and_behavior_mechanisms: + text: behavior_and_behavior_mechanisms + meaning: mesh:D001520 + title: Behavior and Behavior Mechanisms + congenital_heart_defects: + text: congenital_heart_defects + meaning: mesh:D006330 + title: Congenital Heart Defects + immune_system_diseases: + text: immune_system_diseases + meaning: mesh:D007154 + title: Immune System Diseases + hematologic_diseases: + text: hematologic_diseases + meaning: mesh:D006402 + title: Hematologic Diseases + neurodevelopment: + text: neurodevelopment + meaning: mesh:D065886 + title: Neurodevelopment + sleep_wake_disorders: + text: sleep_wake_disorders + meaning: mesh:D012893 + title: Sleep Wake Disorders + all_co_occurring_conditions: + text: all_co_occurring_conditions + meaning: mesh:D013568 + title: All Co-occurring Conditions + physical_fitness: + text: physical_fitness + meaning: mesh:D010809 + title: Physical Fitness + other: + text: other + title: Other diff --git a/src/cam-expanded-enums/EnumSampleCollectionMethod.yaml b/src/cam-expanded-enums/EnumSampleCollectionMethod.yaml new file mode 100644 index 0000000..58643c5 --- /dev/null +++ b/src/cam-expanded-enums/EnumSampleCollectionMethod.yaml @@ -0,0 +1,7 @@ +id: https://includedcc.org/common-access-model/EnumSampleCollectionMethod +name: EnumSampleCollectionMethod +enums: + EnumSampleCollectionMethod: + description: The approach used to collect the biospecimen. + [LOINC](https://loinc.org) is recommended. + permissible_values: {} diff --git a/src/cam-expanded-enums/EnumSex.yaml b/src/cam-expanded-enums/EnumSex.yaml new file mode 100644 index 0000000..f7db330 --- /dev/null +++ b/src/cam-expanded-enums/EnumSex.yaml @@ -0,0 +1,22 @@ +id: https://includedcc.org/common-access-model/EnumSex +name: EnumSex +enums: + EnumSex: + description: Subject Sex + permissible_values: + female: + text: female + meaning: NCIT:C16576 + title: Female + male: + text: male + meaning: NCIT:C20197 + title: Male + other: + text: other + meaning: NCIT:C17649 + title: Other + unknown: + text: unknown + meaning: NCIT:C17998 + title: Unknown diff --git a/src/cam-expanded-enums/EnumSite.yaml b/src/cam-expanded-enums/EnumSite.yaml new file mode 100644 index 0000000..eedbfbf --- /dev/null +++ b/src/cam-expanded-enums/EnumSite.yaml @@ -0,0 +1,7 @@ +id: https://includedcc.org/common-access-model/EnumSite +name: EnumSite +enums: + EnumSite: + description: The location of the specimen collection. [SNOMED Body + Site](https://hl7.org/fhir/R4B/valueset-body-site.html) is recommended. + permissible_values: {} diff --git a/src/cam-expanded-enums/EnumStudyDesign.yaml b/src/cam-expanded-enums/EnumStudyDesign.yaml new file mode 100644 index 0000000..2d0e736 --- /dev/null +++ b/src/cam-expanded-enums/EnumStudyDesign.yaml @@ -0,0 +1,38 @@ +id: https://includedcc.org/common-access-model/EnumStudyDesign +name: EnumStudyDesign +enums: + EnumStudyDesign: + title: Study Design + description: Approaches for collecting data, investigating interventions, + and/or analyzing data. + permissible_values: + case_control: + text: case_control + title: Case-Control + case_set: + text: case_set + title: Case Set + control_set: + text: control_set + title: Control Set + clinical_trial: + text: clinical_trial + title: Clinical Trial + cross_sectional: + text: cross_sectional + title: Cross-Sectional + family_twins_trios: + text: family_twins_trios + title: Family/Twins/Trios + interventional: + text: interventional + title: Interventional + longitudinal: + text: longitudinal + title: Longitudinal + trial_readiness_study: + text: trial_readiness_study + title: Trial Readiness Study + tumor_vs_matched_normal: + text: tumor_vs_matched_normal + title: Tumor vs Matched Normal diff --git a/src/cam-expanded-enums/EnumSubjectType.yaml b/src/cam-expanded-enums/EnumSubjectType.yaml new file mode 100644 index 0000000..df0fe1c --- /dev/null +++ b/src/cam-expanded-enums/EnumSubjectType.yaml @@ -0,0 +1,26 @@ +id: https://includedcc.org/common-access-model/EnumSubjectType +name: EnumSubjectType +enums: + EnumSubjectType: + description: Types of Subject entities + permissible_values: + participant: + text: participant + description: Study participant with consent, assent, or waiver of + consent. + non_participant: + text: non_participant + description: An individual associated with a study who was not explictly + consented, eg, the subject of a reported family history. + cell_line: + text: cell_line + description: Cell Line + animal_model: + text: animal_model + description: Animal model + group: + text: group + description: A group of individuals or entities. + other: + text: other + description: A different entity type- ideally this will be resolved! diff --git a/src/cam-expanded-enums/EnumVitalStatus.yaml b/src/cam-expanded-enums/EnumVitalStatus.yaml new file mode 100644 index 0000000..8407efa --- /dev/null +++ b/src/cam-expanded-enums/EnumVitalStatus.yaml @@ -0,0 +1,15 @@ +id: https://includedcc.org/common-access-model/EnumVitalStatus +name: EnumVitalStatus +enums: + EnumVitalStatus: + description: Descriptions of a Subject's vital status + is_a: EnumNull + permissible_values: + dead: + text: dead + meaning: NCIT:C28554 + title: Dead + alive: + text: alive + meaning: NCIT:C37987 + title: Alive diff --git a/src/cam_expanded_enums/__init__.py b/src/cam_expanded_enums/__init__.py new file mode 100644 index 0000000..2331202 --- /dev/null +++ b/src/cam_expanded_enums/__init__.py @@ -0,0 +1,10 @@ +"""cam-expanded-enums. + +This project is a LinkML model containing expanded enumerations from the Common Access Model. +""" + +try: + from cam_expanded_enums._version import __version__, __version_tuple__ +except ImportError: # pragma: no cover + __version__ = "0.0.0" + __version_tuple__ = (0, 0, 0) diff --git a/src/cam_expanded_enums/_version.py b/src/cam_expanded_enums/_version.py new file mode 100644 index 0000000..786f3aa --- /dev/null +++ b/src/cam_expanded_enums/_version.py @@ -0,0 +1,8 @@ +from importlib.metadata import version, PackageNotFoundError + +try: + __version__ = version(__name__) +except PackageNotFoundError: + # package not installed + __version__ = "0.0.0" + __version_tuple__ = (0, 0, 0) diff --git a/src/cam_expanded_enums/datamodel/__init__.py b/src/cam_expanded_enums/datamodel/__init__.py new file mode 100644 index 0000000..e6e2cef --- /dev/null +++ b/src/cam_expanded_enums/datamodel/__init__.py @@ -0,0 +1,9 @@ +"""Data model package for cam-expanded-enums.""" + +from pathlib import Path +from .cam_expanded_enums import * # noqa: F403 + +THIS_PATH = Path(__file__).parent + +SCHEMA_DIRECTORY = THIS_PATH.parent / "schema" +MAIN_SCHEMA_PATH = SCHEMA_DIRECTORY / "cam_expanded_enums.yaml" diff --git a/src/cam_expanded_enums/schema/EnumAssertionProvenance.yaml b/src/cam_expanded_enums/schema/EnumAssertionProvenance.yaml new file mode 100644 index 0000000..1f1e5fb --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumAssertionProvenance.yaml @@ -0,0 +1,21 @@ +--- +id: https://includedcc.org/common-access-model/EnumAssertionProvenance +name: EnumAssertionProvenance +enums: + EnumAssertionProvenance: + description: Possible data sources for assertions. + is_a: EnumNull + permissible_values: + medical_record: + title: Medical Record + description: Data obtained from a medical record + investigator_assessment: + title: Investigator Assessment + description: Data obtained by examination, interview, etc. with investigator + participant_or_caregiver_report: + title: Participant or Caregiver Report + description: Data obtained from survey, questionnaire, etc. filled out by + participant or caregiver + other: + title: Other + description: Data obtained from other source, such as tissue bank diff --git a/src/cam_expanded_enums/schema/EnumAvailabilityStatus.yaml b/src/cam_expanded_enums/schema/EnumAvailabilityStatus.yaml new file mode 100644 index 0000000..2bd4d68 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumAvailabilityStatus.yaml @@ -0,0 +1,15 @@ +--- +id: https://includedcc.org/common-access-model/EnumAvailabilityStatus +name: EnumAvailabilityStatus +enums: + EnumAvailabilityStatus: + description: Is the biospecimen available for use? + permissible_values: + available: + title: Available + meaning: ig2_biospecimen_availability:available + description: Biospecimen is Available + unavailable: + title: Unavailable + meaning: ig2_biospecimen_availability:unavailable + description: Biospecimen is Unavailable diff --git a/src/cam_expanded_enums/schema/EnumClinicalDataSourceType.yaml b/src/cam_expanded_enums/schema/EnumClinicalDataSourceType.yaml new file mode 100644 index 0000000..af096af --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumClinicalDataSourceType.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumClinicalDataSourceType +name: EnumClinicalDataSourceType +enums: + EnumClinicalDataSourceType: + title: Clinical Data Source Type + description: Approaches to ascertain clinical information about a participant. + permissible_values: + medical_record: + title: Medical Record + description: Data obtained directly from medical record + investigator_assessment: + title: Investigator Assessment + description: Data obtained by examination, interview, etc. with investigator + participant_or_caregiver_report: + title: Participant or Caregiver Report + description: Data obtained from survey, questionnaire, etc. filled out by + participant or caregiver + other: + title: Other + description: Data obtained from other source, such as tissue bank + unknown: + title: Unknown diff --git a/src/cam_expanded_enums/schema/EnumConsanguinityAssertion.yaml b/src/cam_expanded_enums/schema/EnumConsanguinityAssertion.yaml new file mode 100644 index 0000000..0a47e27 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumConsanguinityAssertion.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumConsanguinityAssertion +name: EnumConsanguinityAssertion +enums: + EnumConsanguinityAssertion: + description: Asserts known or suspected consanguinity in this study family + permissible_values: + not_suspected: + title: not-suspected + description: Not suspected + meaning: snomed_ct:428263003 + suspected: + title: suspected + description: Suspected + meaning: snomed_ct:415684004 + known_present: + title: known-present + description: Known Present + meaning: snomed_ct:410515003 + unknown: + title: unknown + description: Unknown + meaning: snomed_ct:261665006 diff --git a/src/cam_expanded_enums/schema/EnumDataCategory.yaml b/src/cam_expanded_enums/schema/EnumDataCategory.yaml new file mode 100644 index 0000000..f223487 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumDataCategory.yaml @@ -0,0 +1,38 @@ +--- +id: https://includedcc.org/common-access-model/EnumDataCategory +name: EnumDataCategory +enums: + EnumDataCategory: + title: Data Category + description: Categories of data which may be collected about participants. + permissible_values: + unharmonized_demographic_clinical_data: + title: Unharmonized Demographic/Clinical Data + harmonized_demographic_clinical_data: + title: Harmonized Demographic/Clinical Data + genomics: + title: Genomics + transcriptomics: + title: Transcriptomics + epigenomics: + title: Epigenomics + proteomics: + title: Proteomics + metabolomics: + title: Metabolomics + cognitive_behavioral: + title: Cognitive/Behavioral + immune_profiling: + title: Immune Profiling + imaging: + title: Imaging + microbiome: + title: Microbiome + fitness: + title: Fitness + physical_activity: + title: Physical Activity + other: + title: Other + sleep_study: + title: Sleep Study diff --git a/src/cam_expanded_enums/schema/EnumDataUseModifier.yaml b/src/cam_expanded_enums/schema/EnumDataUseModifier.yaml new file mode 100644 index 0000000..4552ffc --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumDataUseModifier.yaml @@ -0,0 +1,86 @@ +id: https://includedcc.org/common-access-model/EnumDataUseModifier +name: EnumDataUseModifier +enums: + EnumDataUseModifier: + title: Data Use Modifier + description: Data Use Ontology (DUO) terms for data use modifiers. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000017 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + DUO:00000044: + text: DUO:00000044 + description: population origins or ancestry research prohibited + title: population origins or ancestry research prohibited + DUO:0000012: + text: DUO:0000012 + description: research specific restrictions + title: research specific restrictions + DUO:0000015: + text: DUO:0000015 + description: no general methods research + title: no general methods research + DUO:0000016: + text: DUO:0000016 + description: genetic studies only + title: genetic studies only + DUO:0000018: + text: DUO:0000018 + description: not for profit, non commercial use only + title: not for profit, non commercial use only + DUO:0000019: + text: DUO:0000019 + description: publication required + title: publication required + DUO:0000020: + text: DUO:0000020 + description: collaboration required + title: collaboration required + DUO:0000021: + text: DUO:0000021 + description: ethics approval required + title: ethics approval required + DUO:0000022: + text: DUO:0000022 + description: geographical restriction + title: geographical restriction + DUO:0000024: + text: DUO:0000024 + description: publication moratorium + title: publication moratorium + DUO:0000025: + text: DUO:0000025 + description: time limit on use + title: time limit on use + DUO:0000026: + text: DUO:0000026 + description: user specific restriction + title: user specific restriction + DUO:0000027: + text: DUO:0000027 + description: project specific restriction + title: project specific restriction + DUO:0000028: + text: DUO:0000028 + description: institution specific restriction + title: institution specific restriction + DUO:0000029: + text: DUO:0000029 + description: return to database or resource + title: return to database or resource + DUO:0000043: + text: DUO:0000043 + description: clinical care use + title: clinical care use + DUO:0000045: + text: DUO:0000045 + description: not for profit organisation use only + title: not for profit organisation use only + DUO:0000046: + text: DUO:0000046 + description: non-commercial use only + title: non-commercial use only diff --git a/src/cam_expanded_enums/schema/EnumDataUsePermission.yaml b/src/cam_expanded_enums/schema/EnumDataUsePermission.yaml new file mode 100644 index 0000000..74a70dc --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumDataUsePermission.yaml @@ -0,0 +1,34 @@ +id: https://includedcc.org/common-access-model/EnumDataUsePermission +name: EnumDataUsePermission +enums: + EnumDataUsePermission: + title: Data Use Permission + description: Data Use Ontology (DUO) terms for data use permissions. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000001 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + DUO:0000004: + text: DUO:0000004 + description: no restriction + title: no restriction + DUO:0000006: + text: DUO:0000006 + description: health or medical or biomedical research + title: health or medical or biomedical research + DUO:0000007: + text: DUO:0000007 + description: disease specific research + title: disease specific research + DUO:0000011: + text: DUO:0000011 + description: population origins or ancestry research only + title: population origins or ancestry research only + DUO:0000042: + text: DUO:0000042 + description: general research use + title: general research use diff --git a/src/cam_expanded_enums/schema/EnumEDAMDataTypes.yaml b/src/cam_expanded_enums/schema/EnumEDAMDataTypes.yaml new file mode 100644 index 0000000..62f72fe --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumEDAMDataTypes.yaml @@ -0,0 +1,3806 @@ +id: https://includedcc.org/common-access-model/EnumEDAMDataTypes +name: EnumEDAMDataTypes +enums: + EnumEDAMDataTypes: + description: Data types from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:data_0006 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + EDAM_data:0582: + text: EDAM_data:0582 + description: Ontology + title: Ontology + EDAM_data:0842: + text: EDAM_data:0842 + description: Identifier + title: Identifier + EDAM_data:0844: + text: EDAM_data:0844 + description: Molecular mass + title: Molecular mass + EDAM_data:0845: + text: EDAM_data:0845 + description: Molecular charge + title: Molecular charge + EDAM_data:0846: + text: EDAM_data:0846 + description: Chemical formula + title: Chemical formula + EDAM_data:0847: + text: EDAM_data:0847 + description: QSAR descriptor + title: QSAR descriptor + EDAM_data:0849: + text: EDAM_data:0849 + description: Sequence record + title: Sequence record + EDAM_data:0850: + text: EDAM_data:0850 + description: Sequence set + title: Sequence set + EDAM_data:0856: + text: EDAM_data:0856 + description: Sequence feature source + title: Sequence feature source + EDAM_data:0857: + text: EDAM_data:0857 + description: Sequence search results + title: Sequence search results + EDAM_data:0858: + text: EDAM_data:0858 + description: Sequence signature matches + title: Sequence signature matches + EDAM_data:0860: + text: EDAM_data:0860 + description: Sequence signature data + title: Sequence signature data + EDAM_data:0862: + text: EDAM_data:0862 + description: Dotplot + title: Dotplot + EDAM_data:0863: + text: EDAM_data:0863 + description: Sequence alignment + title: Sequence alignment + EDAM_data:0865: + text: EDAM_data:0865 + description: Sequence similarity score + title: Sequence similarity score + EDAM_data:0867: + text: EDAM_data:0867 + description: Sequence alignment report + title: Sequence alignment report + EDAM_data:0870: + text: EDAM_data:0870 + description: Sequence distance matrix + title: Sequence distance matrix + EDAM_data:0871: + text: EDAM_data:0871 + description: Phylogenetic character data + title: Phylogenetic character data + EDAM_data:0872: + text: EDAM_data:0872 + description: Phylogenetic tree + title: Phylogenetic tree + EDAM_data:0874: + text: EDAM_data:0874 + description: Comparison matrix + title: Comparison matrix + EDAM_data:0878: + text: EDAM_data:0878 + description: Protein secondary structure alignment + title: Protein secondary structure alignment + EDAM_data:0880: + text: EDAM_data:0880 + description: RNA secondary structure + title: RNA secondary structure + EDAM_data:0881: + text: EDAM_data:0881 + description: RNA secondary structure alignment + title: RNA secondary structure alignment + EDAM_data:0883: + text: EDAM_data:0883 + description: Structure + title: Structure + EDAM_data:0886: + text: EDAM_data:0886 + description: Structure alignment + title: Structure alignment + EDAM_data:0887: + text: EDAM_data:0887 + description: Structure alignment report + title: Structure alignment report + EDAM_data:0888: + text: EDAM_data:0888 + description: Structure similarity score + title: Structure similarity score + EDAM_data:0889: + text: EDAM_data:0889 + description: Structural profile + title: Structural profile + EDAM_data:0890: + text: EDAM_data:0890 + description: Structural (3D) profile alignment + title: Structural (3D) profile alignment + EDAM_data:0892: + text: EDAM_data:0892 + description: Protein sequence-structure scoring matrix + title: Protein sequence-structure scoring matrix + EDAM_data:0893: + text: EDAM_data:0893 + description: Sequence-structure alignment + title: Sequence-structure alignment + EDAM_data:0896: + text: EDAM_data:0896 + description: Protein report + title: Protein report + EDAM_data:0897: + text: EDAM_data:0897 + description: Protein property + title: Protein property + EDAM_data:0905: + text: EDAM_data:0905 + description: Protein interaction raw data + title: Protein interaction raw data + EDAM_data:0906: + text: EDAM_data:0906 + description: Protein interaction data + title: Protein interaction data + EDAM_data:0907: + text: EDAM_data:0907 + description: Protein family report + title: Protein family report + EDAM_data:0909: + text: EDAM_data:0909 + description: Vmax + title: Vmax + EDAM_data:0910: + text: EDAM_data:0910 + description: Km + title: Km + EDAM_data:0912: + text: EDAM_data:0912 + description: Nucleic acid property + title: Nucleic acid property + EDAM_data:0914: + text: EDAM_data:0914 + description: Codon usage data + title: Codon usage data + EDAM_data:0916: + text: EDAM_data:0916 + description: Gene report + title: Gene report + EDAM_data:0919: + text: EDAM_data:0919 + description: Chromosome report + title: Chromosome report + EDAM_data:0920: + text: EDAM_data:0920 + description: Genotype/phenotype report + title: Genotype/phenotype report + EDAM_data:0924: + text: EDAM_data:0924 + description: Sequence trace + title: Sequence trace + EDAM_data:0925: + text: EDAM_data:0925 + description: Sequence assembly + title: Sequence assembly + EDAM_data:0926: + text: EDAM_data:0926 + description: RH scores + title: RH scores + EDAM_data:0927: + text: EDAM_data:0927 + description: Genetic linkage report + title: Genetic linkage report + EDAM_data:0928: + text: EDAM_data:0928 + description: Gene expression profile + title: Gene expression profile + EDAM_data:0937: + text: EDAM_data:0937 + description: Electron density map + title: Electron density map + EDAM_data:0938: + text: EDAM_data:0938 + description: Raw NMR data + title: Raw NMR data + EDAM_data:0939: + text: EDAM_data:0939 + description: CD spectra + title: CD spectra + EDAM_data:0940: + text: EDAM_data:0940 + description: Volume map + title: Volume map + EDAM_data:0942: + text: EDAM_data:0942 + description: 2D PAGE image + title: 2D PAGE image + EDAM_data:0943: + text: EDAM_data:0943 + description: Mass spectrum + title: Mass spectrum + EDAM_data:0944: + text: EDAM_data:0944 + description: Peptide mass fingerprint + title: Peptide mass fingerprint + EDAM_data:0945: + text: EDAM_data:0945 + description: Peptide identification + title: Peptide identification + EDAM_data:0949: + text: EDAM_data:0949 + description: Workflow metadata + title: Workflow metadata + EDAM_data:0950: + text: EDAM_data:0950 + description: Mathematical model + title: Mathematical model + EDAM_data:0951: + text: EDAM_data:0951 + description: Statistical estimate score + title: Statistical estimate score + EDAM_data:0954: + text: EDAM_data:0954 + description: Database cross-mapping + title: Database cross-mapping + EDAM_data:0955: + text: EDAM_data:0955 + description: Data index + title: Data index + EDAM_data:0956: + text: EDAM_data:0956 + description: Data index report + title: Data index report + EDAM_data:0957: + text: EDAM_data:0957 + description: Database metadata + title: Database metadata + EDAM_data:0958: + text: EDAM_data:0958 + description: Tool metadata + title: Tool metadata + EDAM_data:0960: + text: EDAM_data:0960 + description: User metadata + title: User metadata + EDAM_data:0962: + text: EDAM_data:0962 + description: Small molecule report + title: Small molecule report + EDAM_data:0963: + text: EDAM_data:0963 + description: Cell line report + title: Cell line report + EDAM_data:0966: + text: EDAM_data:0966 + description: Ontology term + title: Ontology term + EDAM_data:0967: + text: EDAM_data:0967 + description: Ontology concept data + title: Ontology concept data + EDAM_data:0968: + text: EDAM_data:0968 + description: Keyword + title: Keyword + EDAM_data:0970: + text: EDAM_data:0970 + description: Citation + title: Citation + EDAM_data:0971: + text: EDAM_data:0971 + description: Article + title: Article + EDAM_data:0972: + text: EDAM_data:0972 + description: Text mining report + title: Text mining report + EDAM_data:0976: + text: EDAM_data:0976 + description: Identifier (by type of entity) + title: Identifier (by type of entity) + EDAM_data:0977: + text: EDAM_data:0977 + description: Tool identifier + title: Tool identifier + EDAM_data:0982: + text: EDAM_data:0982 + description: Molecule identifier + title: Molecule identifier + EDAM_data:0983: + text: EDAM_data:0983 + description: Atom ID + title: Atom ID + EDAM_data:0984: + text: EDAM_data:0984 + description: Molecule name + title: Molecule name + EDAM_data:0987: + text: EDAM_data:0987 + description: Chromosome name + title: Chromosome name + EDAM_data:0988: + text: EDAM_data:0988 + description: Peptide identifier + title: Peptide identifier + EDAM_data:0989: + text: EDAM_data:0989 + description: Protein identifier + title: Protein identifier + EDAM_data:0990: + text: EDAM_data:0990 + description: Compound name + title: Compound name + EDAM_data:0991: + text: EDAM_data:0991 + description: Chemical registry number + title: Chemical registry number + EDAM_data:0993: + text: EDAM_data:0993 + description: Drug identifier + title: Drug identifier + EDAM_data:0994: + text: EDAM_data:0994 + description: Amino acid identifier + title: Amino acid identifier + EDAM_data:0995: + text: EDAM_data:0995 + description: Nucleotide identifier + title: Nucleotide identifier + EDAM_data:0996: + text: EDAM_data:0996 + description: Monosaccharide identifier + title: Monosaccharide identifier + EDAM_data:0997: + text: EDAM_data:0997 + description: Chemical name (ChEBI) + title: Chemical name (ChEBI) + EDAM_data:0998: + text: EDAM_data:0998 + description: Chemical name (IUPAC) + title: Chemical name (IUPAC) + EDAM_data:0999: + text: EDAM_data:0999 + description: Chemical name (INN) + title: Chemical name (INN) + EDAM_data:1000: + text: EDAM_data:1000 + description: Chemical name (brand) + title: Chemical name (brand) + EDAM_data:1001: + text: EDAM_data:1001 + description: Chemical name (synonymous) + title: Chemical name (synonymous) + EDAM_data:1002: + text: EDAM_data:1002 + description: CAS number + title: CAS number + EDAM_data:1003: + text: EDAM_data:1003 + description: Chemical registry number (Beilstein) + title: Chemical registry number (Beilstein) + EDAM_data:1004: + text: EDAM_data:1004 + description: Chemical registry number (Gmelin) + title: Chemical registry number (Gmelin) + EDAM_data:1005: + text: EDAM_data:1005 + description: HET group name + title: HET group name + EDAM_data:1006: + text: EDAM_data:1006 + description: Amino acid name + title: Amino acid name + EDAM_data:1007: + text: EDAM_data:1007 + description: Nucleotide code + title: Nucleotide code + EDAM_data:1008: + text: EDAM_data:1008 + description: Polypeptide chain ID + title: Polypeptide chain ID + EDAM_data:1009: + text: EDAM_data:1009 + description: Protein name + title: Protein name + EDAM_data:1010: + text: EDAM_data:1010 + description: Enzyme identifier + title: Enzyme identifier + EDAM_data:1011: + text: EDAM_data:1011 + description: EC number + title: EC number + EDAM_data:1012: + text: EDAM_data:1012 + description: Enzyme name + title: Enzyme name + EDAM_data:1013: + text: EDAM_data:1013 + description: Restriction enzyme name + title: Restriction enzyme name + EDAM_data:1015: + text: EDAM_data:1015 + description: Sequence feature ID + title: Sequence feature ID + EDAM_data:1016: + text: EDAM_data:1016 + description: Sequence position + title: Sequence position + EDAM_data:1017: + text: EDAM_data:1017 + description: Sequence range + title: Sequence range + EDAM_data:1020: + text: EDAM_data:1020 + description: Sequence feature key + title: Sequence feature key + EDAM_data:1021: + text: EDAM_data:1021 + description: Sequence feature qualifier + title: Sequence feature qualifier + EDAM_data:1022: + text: EDAM_data:1022 + description: Sequence feature label + title: Sequence feature label + EDAM_data:1023: + text: EDAM_data:1023 + description: EMBOSS Uniform Feature Object + title: EMBOSS Uniform Feature Object + EDAM_data:1025: + text: EDAM_data:1025 + description: Gene identifier + title: Gene identifier + EDAM_data:1026: + text: EDAM_data:1026 + description: Gene symbol + title: Gene symbol + EDAM_data:1027: + text: EDAM_data:1027 + description: Gene ID (NCBI) + title: Gene ID (NCBI) + EDAM_data:1031: + text: EDAM_data:1031 + description: Gene ID (CGD) + title: Gene ID (CGD) + EDAM_data:1032: + text: EDAM_data:1032 + description: Gene ID (DictyBase) + title: Gene ID (DictyBase) + EDAM_data:1033: + text: EDAM_data:1033 + description: Ensembl gene ID + title: Ensembl gene ID + EDAM_data:1034: + text: EDAM_data:1034 + description: Gene ID (SGD) + title: Gene ID (SGD) + EDAM_data:1035: + text: EDAM_data:1035 + description: Gene ID (GeneDB) + title: Gene ID (GeneDB) + EDAM_data:1036: + text: EDAM_data:1036 + description: TIGR identifier + title: TIGR identifier + EDAM_data:1037: + text: EDAM_data:1037 + description: TAIR accession (gene) + title: TAIR accession (gene) + EDAM_data:1038: + text: EDAM_data:1038 + description: Protein domain ID + title: Protein domain ID + EDAM_data:1039: + text: EDAM_data:1039 + description: SCOP domain identifier + title: SCOP domain identifier + EDAM_data:1040: + text: EDAM_data:1040 + description: CATH domain ID + title: CATH domain ID + EDAM_data:1041: + text: EDAM_data:1041 + description: SCOP concise classification string (sccs) + title: SCOP concise classification string (sccs) + EDAM_data:1042: + text: EDAM_data:1042 + description: SCOP sunid + title: SCOP sunid + EDAM_data:1043: + text: EDAM_data:1043 + description: CATH node ID + title: CATH node ID + EDAM_data:1044: + text: EDAM_data:1044 + description: Kingdom name + title: Kingdom name + EDAM_data:1045: + text: EDAM_data:1045 + description: Species name + title: Species name + EDAM_data:1046: + text: EDAM_data:1046 + description: Strain name + title: Strain name + EDAM_data:1047: + text: EDAM_data:1047 + description: URI + title: URI + EDAM_data:1048: + text: EDAM_data:1048 + description: Database ID + title: Database ID + EDAM_data:1049: + text: EDAM_data:1049 + description: Directory name + title: Directory name + EDAM_data:1050: + text: EDAM_data:1050 + description: File name + title: File name + EDAM_data:1051: + text: EDAM_data:1051 + description: Ontology name + title: Ontology name + EDAM_data:1052: + text: EDAM_data:1052 + description: URL + title: URL + EDAM_data:1053: + text: EDAM_data:1053 + description: URN + title: URN + EDAM_data:1055: + text: EDAM_data:1055 + description: LSID + title: LSID + EDAM_data:1056: + text: EDAM_data:1056 + description: Database name + title: Database name + EDAM_data:1058: + text: EDAM_data:1058 + description: Enumerated file name + title: Enumerated file name + EDAM_data:1059: + text: EDAM_data:1059 + description: File name extension + title: File name extension + EDAM_data:1060: + text: EDAM_data:1060 + description: File base name + title: File base name + EDAM_data:1061: + text: EDAM_data:1061 + description: QSAR descriptor name + title: QSAR descriptor name + EDAM_data:1063: + text: EDAM_data:1063 + description: Sequence identifier + title: Sequence identifier + EDAM_data:1064: + text: EDAM_data:1064 + description: Sequence set ID + title: Sequence set ID + EDAM_data:1066: + text: EDAM_data:1066 + description: Sequence alignment ID + title: Sequence alignment ID + EDAM_data:1068: + text: EDAM_data:1068 + description: Phylogenetic tree ID + title: Phylogenetic tree ID + EDAM_data:1069: + text: EDAM_data:1069 + description: Comparison matrix identifier + title: Comparison matrix identifier + EDAM_data:1070: + text: EDAM_data:1070 + description: Structure ID + title: Structure ID + EDAM_data:1071: + text: EDAM_data:1071 + description: Structural (3D) profile ID + title: Structural (3D) profile ID + EDAM_data:1072: + text: EDAM_data:1072 + description: Structure alignment ID + title: Structure alignment ID + EDAM_data:1073: + text: EDAM_data:1073 + description: Amino acid index ID + title: Amino acid index ID + EDAM_data:1074: + text: EDAM_data:1074 + description: Protein interaction ID + title: Protein interaction ID + EDAM_data:1075: + text: EDAM_data:1075 + description: Protein family identifier + title: Protein family identifier + EDAM_data:1076: + text: EDAM_data:1076 + description: Codon usage table name + title: Codon usage table name + EDAM_data:1077: + text: EDAM_data:1077 + description: Transcription factor identifier + title: Transcription factor identifier + EDAM_data:1078: + text: EDAM_data:1078 + description: Experiment annotation ID + title: Experiment annotation ID + EDAM_data:1079: + text: EDAM_data:1079 + description: Electron microscopy model ID + title: Electron microscopy model ID + EDAM_data:1080: + text: EDAM_data:1080 + description: Gene expression report ID + title: Gene expression report ID + EDAM_data:1081: + text: EDAM_data:1081 + description: Genotype and phenotype annotation ID + title: Genotype and phenotype annotation ID + EDAM_data:1082: + text: EDAM_data:1082 + description: Pathway or network identifier + title: Pathway or network identifier + EDAM_data:1083: + text: EDAM_data:1083 + description: Workflow ID + title: Workflow ID + EDAM_data:1084: + text: EDAM_data:1084 + description: Data resource definition ID + title: Data resource definition ID + EDAM_data:1085: + text: EDAM_data:1085 + description: Biological model ID + title: Biological model ID + EDAM_data:1086: + text: EDAM_data:1086 + description: Compound identifier + title: Compound identifier + EDAM_data:1087: + text: EDAM_data:1087 + description: Ontology concept ID + title: Ontology concept ID + EDAM_data:1088: + text: EDAM_data:1088 + description: Article ID + title: Article ID + EDAM_data:1089: + text: EDAM_data:1089 + description: FlyBase ID + title: FlyBase ID + EDAM_data:1091: + text: EDAM_data:1091 + description: WormBase name + title: WormBase name + EDAM_data:1092: + text: EDAM_data:1092 + description: WormBase class + title: WormBase class + EDAM_data:1093: + text: EDAM_data:1093 + description: Sequence accession + title: Sequence accession + EDAM_data:1095: + text: EDAM_data:1095 + description: EMBOSS Uniform Sequence Address + title: EMBOSS Uniform Sequence Address + EDAM_data:1096: + text: EDAM_data:1096 + description: Sequence accession (protein) + title: Sequence accession (protein) + EDAM_data:1097: + text: EDAM_data:1097 + description: Sequence accession (nucleic acid) + title: Sequence accession (nucleic acid) + EDAM_data:1098: + text: EDAM_data:1098 + description: RefSeq accession + title: RefSeq accession + EDAM_data:1100: + text: EDAM_data:1100 + description: PIR identifier + title: PIR identifier + EDAM_data:1102: + text: EDAM_data:1102 + description: Gramene primary identifier + title: Gramene primary identifier + EDAM_data:1103: + text: EDAM_data:1103 + description: EMBL/GenBank/DDBJ ID + title: EMBL/GenBank/DDBJ ID + EDAM_data:1104: + text: EDAM_data:1104 + description: Sequence cluster ID (UniGene) + title: Sequence cluster ID (UniGene) + EDAM_data:1105: + text: EDAM_data:1105 + description: dbEST accession + title: dbEST accession + EDAM_data:1106: + text: EDAM_data:1106 + description: dbSNP ID + title: dbSNP ID + EDAM_data:1112: + text: EDAM_data:1112 + description: Sequence cluster ID + title: Sequence cluster ID + EDAM_data:1113: + text: EDAM_data:1113 + description: Sequence cluster ID (COG) + title: Sequence cluster ID (COG) + EDAM_data:1114: + text: EDAM_data:1114 + description: Sequence motif identifier + title: Sequence motif identifier + EDAM_data:1115: + text: EDAM_data:1115 + description: Sequence profile ID + title: Sequence profile ID + EDAM_data:1116: + text: EDAM_data:1116 + description: ELM ID + title: ELM ID + EDAM_data:1117: + text: EDAM_data:1117 + description: Prosite accession number + title: Prosite accession number + EDAM_data:1118: + text: EDAM_data:1118 + description: HMMER hidden Markov model ID + title: HMMER hidden Markov model ID + EDAM_data:1119: + text: EDAM_data:1119 + description: JASPAR profile ID + title: JASPAR profile ID + EDAM_data:1123: + text: EDAM_data:1123 + description: TreeBASE study accession number + title: TreeBASE study accession number + EDAM_data:1124: + text: EDAM_data:1124 + description: TreeFam accession number + title: TreeFam accession number + EDAM_data:1126: + text: EDAM_data:1126 + description: Comparison matrix name + title: Comparison matrix name + EDAM_data:1127: + text: EDAM_data:1127 + description: PDB ID + title: PDB ID + EDAM_data:1128: + text: EDAM_data:1128 + description: AAindex ID + title: AAindex ID + EDAM_data:1129: + text: EDAM_data:1129 + description: BIND accession number + title: BIND accession number + EDAM_data:1130: + text: EDAM_data:1130 + description: IntAct accession number + title: IntAct accession number + EDAM_data:1131: + text: EDAM_data:1131 + description: Protein family name + title: Protein family name + EDAM_data:1132: + text: EDAM_data:1132 + description: InterPro entry name + title: InterPro entry name + EDAM_data:1133: + text: EDAM_data:1133 + description: InterPro accession + title: InterPro accession + EDAM_data:1134: + text: EDAM_data:1134 + description: InterPro secondary accession + title: InterPro secondary accession + EDAM_data:1135: + text: EDAM_data:1135 + description: Gene3D ID + title: Gene3D ID + EDAM_data:1136: + text: EDAM_data:1136 + description: PIRSF ID + title: PIRSF ID + EDAM_data:1137: + text: EDAM_data:1137 + description: PRINTS code + title: PRINTS code + EDAM_data:1138: + text: EDAM_data:1138 + description: Pfam accession number + title: Pfam accession number + EDAM_data:1139: + text: EDAM_data:1139 + description: SMART accession number + title: SMART accession number + EDAM_data:1140: + text: EDAM_data:1140 + description: Superfamily hidden Markov model number + title: Superfamily hidden Markov model number + EDAM_data:1141: + text: EDAM_data:1141 + description: TIGRFam ID + title: TIGRFam ID + EDAM_data:1142: + text: EDAM_data:1142 + description: ProDom accession number + title: ProDom accession number + EDAM_data:1143: + text: EDAM_data:1143 + description: TRANSFAC accession number + title: TRANSFAC accession number + EDAM_data:1144: + text: EDAM_data:1144 + description: ArrayExpress accession number + title: ArrayExpress accession number + EDAM_data:1145: + text: EDAM_data:1145 + description: PRIDE experiment accession number + title: PRIDE experiment accession number + EDAM_data:1146: + text: EDAM_data:1146 + description: EMDB ID + title: EMDB ID + EDAM_data:1147: + text: EDAM_data:1147 + description: GEO accession number + title: GEO accession number + EDAM_data:1148: + text: EDAM_data:1148 + description: GermOnline ID + title: GermOnline ID + EDAM_data:1149: + text: EDAM_data:1149 + description: EMAGE ID + title: EMAGE ID + EDAM_data:1150: + text: EDAM_data:1150 + description: Disease ID + title: Disease ID + EDAM_data:1151: + text: EDAM_data:1151 + description: HGVbase ID + title: HGVbase ID + EDAM_data:1153: + text: EDAM_data:1153 + description: OMIM ID + title: OMIM ID + EDAM_data:1154: + text: EDAM_data:1154 + description: KEGG object identifier + title: KEGG object identifier + EDAM_data:1155: + text: EDAM_data:1155 + description: Pathway ID (reactome) + title: Pathway ID (reactome) + EDAM_data:1157: + text: EDAM_data:1157 + description: Pathway ID (BioCyc) + title: Pathway ID (BioCyc) + EDAM_data:1158: + text: EDAM_data:1158 + description: Pathway ID (INOH) + title: Pathway ID (INOH) + EDAM_data:1159: + text: EDAM_data:1159 + description: Pathway ID (PATIKA) + title: Pathway ID (PATIKA) + EDAM_data:1160: + text: EDAM_data:1160 + description: Pathway ID (CPDB) + title: Pathway ID (CPDB) + EDAM_data:1161: + text: EDAM_data:1161 + description: Pathway ID (Panther) + title: Pathway ID (Panther) + EDAM_data:1162: + text: EDAM_data:1162 + description: MIRIAM identifier + title: MIRIAM identifier + EDAM_data:1163: + text: EDAM_data:1163 + description: MIRIAM data type name + title: MIRIAM data type name + EDAM_data:1164: + text: EDAM_data:1164 + description: MIRIAM URI + title: MIRIAM URI + EDAM_data:1165: + text: EDAM_data:1165 + description: MIRIAM data type primary name + title: MIRIAM data type primary name + EDAM_data:1166: + text: EDAM_data:1166 + description: MIRIAM data type synonymous name + title: MIRIAM data type synonymous name + EDAM_data:1167: + text: EDAM_data:1167 + description: Taverna workflow ID + title: Taverna workflow ID + EDAM_data:1170: + text: EDAM_data:1170 + description: Biological model name + title: Biological model name + EDAM_data:1171: + text: EDAM_data:1171 + description: BioModel ID + title: BioModel ID + EDAM_data:1172: + text: EDAM_data:1172 + description: PubChem CID + title: PubChem CID + EDAM_data:1173: + text: EDAM_data:1173 + description: ChemSpider ID + title: ChemSpider ID + EDAM_data:1174: + text: EDAM_data:1174 + description: ChEBI ID + title: ChEBI ID + EDAM_data:1175: + text: EDAM_data:1175 + description: BioPax concept ID + title: BioPax concept ID + EDAM_data:1176: + text: EDAM_data:1176 + description: GO concept ID + title: GO concept ID + EDAM_data:1177: + text: EDAM_data:1177 + description: MeSH concept ID + title: MeSH concept ID + EDAM_data:1178: + text: EDAM_data:1178 + description: HGNC concept ID + title: HGNC concept ID + EDAM_data:1179: + text: EDAM_data:1179 + description: NCBI taxonomy ID + title: NCBI taxonomy ID + EDAM_data:1180: + text: EDAM_data:1180 + description: Plant Ontology concept ID + title: Plant Ontology concept ID + EDAM_data:1181: + text: EDAM_data:1181 + description: UMLS concept ID + title: UMLS concept ID + EDAM_data:1182: + text: EDAM_data:1182 + description: FMA concept ID + title: FMA concept ID + EDAM_data:1183: + text: EDAM_data:1183 + description: EMAP concept ID + title: EMAP concept ID + EDAM_data:1184: + text: EDAM_data:1184 + description: ChEBI concept ID + title: ChEBI concept ID + EDAM_data:1185: + text: EDAM_data:1185 + description: MGED concept ID + title: MGED concept ID + EDAM_data:1186: + text: EDAM_data:1186 + description: myGrid concept ID + title: myGrid concept ID + EDAM_data:1187: + text: EDAM_data:1187 + description: PubMed ID + title: PubMed ID + EDAM_data:1188: + text: EDAM_data:1188 + description: DOI + title: DOI + EDAM_data:1189: + text: EDAM_data:1189 + description: Medline UI + title: Medline UI + EDAM_data:1190: + text: EDAM_data:1190 + description: Tool name + title: Tool name + EDAM_data:1191: + text: EDAM_data:1191 + description: Tool name (signature) + title: Tool name (signature) + EDAM_data:1192: + text: EDAM_data:1192 + description: Tool name (BLAST) + title: Tool name (BLAST) + EDAM_data:1193: + text: EDAM_data:1193 + description: Tool name (FASTA) + title: Tool name (FASTA) + EDAM_data:1194: + text: EDAM_data:1194 + description: Tool name (EMBOSS) + title: Tool name (EMBOSS) + EDAM_data:1195: + text: EDAM_data:1195 + description: Tool name (EMBASSY package) + title: Tool name (EMBASSY package) + EDAM_data:1201: + text: EDAM_data:1201 + description: QSAR descriptor (constitutional) + title: QSAR descriptor (constitutional) + EDAM_data:1202: + text: EDAM_data:1202 + description: QSAR descriptor (electronic) + title: QSAR descriptor (electronic) + EDAM_data:1203: + text: EDAM_data:1203 + description: QSAR descriptor (geometrical) + title: QSAR descriptor (geometrical) + EDAM_data:1204: + text: EDAM_data:1204 + description: QSAR descriptor (topological) + title: QSAR descriptor (topological) + EDAM_data:1205: + text: EDAM_data:1205 + description: QSAR descriptor (molecular) + title: QSAR descriptor (molecular) + EDAM_data:1233: + text: EDAM_data:1233 + description: Sequence set (protein) + title: Sequence set (protein) + EDAM_data:1234: + text: EDAM_data:1234 + description: Sequence set (nucleic acid) + title: Sequence set (nucleic acid) + EDAM_data:1235: + text: EDAM_data:1235 + description: Sequence cluster + title: Sequence cluster + EDAM_data:1238: + text: EDAM_data:1238 + description: Proteolytic digest + title: Proteolytic digest + EDAM_data:1239: + text: EDAM_data:1239 + description: Restriction digest + title: Restriction digest + EDAM_data:1240: + text: EDAM_data:1240 + description: PCR primers + title: PCR primers + EDAM_data:1245: + text: EDAM_data:1245 + description: Sequence cluster (protein) + title: Sequence cluster (protein) + EDAM_data:1246: + text: EDAM_data:1246 + description: Sequence cluster (nucleic acid) + title: Sequence cluster (nucleic acid) + EDAM_data:1249: + text: EDAM_data:1249 + description: Sequence length + title: Sequence length + EDAM_data:1254: + text: EDAM_data:1254 + description: Sequence property + title: Sequence property + EDAM_data:1255: + text: EDAM_data:1255 + description: Sequence features + title: Sequence features + EDAM_data:1259: + text: EDAM_data:1259 + description: Sequence complexity report + title: Sequence complexity report + EDAM_data:1260: + text: EDAM_data:1260 + description: Sequence ambiguity report + title: Sequence ambiguity report + EDAM_data:1261: + text: EDAM_data:1261 + description: Sequence composition report + title: Sequence composition report + EDAM_data:1262: + text: EDAM_data:1262 + description: Peptide molecular weight hits + title: Peptide molecular weight hits + EDAM_data:1263: + text: EDAM_data:1263 + description: Base position variability plot + title: Base position variability plot + EDAM_data:1265: + text: EDAM_data:1265 + description: Base frequencies table + title: Base frequencies table + EDAM_data:1266: + text: EDAM_data:1266 + description: Base word frequencies table + title: Base word frequencies table + EDAM_data:1267: + text: EDAM_data:1267 + description: Amino acid frequencies table + title: Amino acid frequencies table + EDAM_data:1268: + text: EDAM_data:1268 + description: Amino acid word frequencies table + title: Amino acid word frequencies table + EDAM_data:1270: + text: EDAM_data:1270 + description: Feature table + title: Feature table + EDAM_data:1274: + text: EDAM_data:1274 + description: Map + title: Map + EDAM_data:1276: + text: EDAM_data:1276 + description: Nucleic acid features + title: Nucleic acid features + EDAM_data:1277: + text: EDAM_data:1277 + description: Protein features + title: Protein features + EDAM_data:1278: + text: EDAM_data:1278 + description: Genetic map + title: Genetic map + EDAM_data:1279: + text: EDAM_data:1279 + description: Sequence map + title: Sequence map + EDAM_data:1280: + text: EDAM_data:1280 + description: Physical map + title: Physical map + EDAM_data:1283: + text: EDAM_data:1283 + description: Cytogenetic map + title: Cytogenetic map + EDAM_data:1284: + text: EDAM_data:1284 + description: DNA transduction map + title: DNA transduction map + EDAM_data:1285: + text: EDAM_data:1285 + description: Gene map + title: Gene map + EDAM_data:1286: + text: EDAM_data:1286 + description: Plasmid map + title: Plasmid map + EDAM_data:1288: + text: EDAM_data:1288 + description: Genome map + title: Genome map + EDAM_data:1289: + text: EDAM_data:1289 + description: Restriction map + title: Restriction map + EDAM_data:1347: + text: EDAM_data:1347 + description: Dirichlet distribution + title: Dirichlet distribution + EDAM_data:1352: + text: EDAM_data:1352 + description: Regular expression + title: Regular expression + EDAM_data:1353: + text: EDAM_data:1353 + description: Sequence motif + title: Sequence motif + EDAM_data:1354: + text: EDAM_data:1354 + description: Sequence profile + title: Sequence profile + EDAM_data:1355: + text: EDAM_data:1355 + description: Protein signature + title: Protein signature + EDAM_data:1361: + text: EDAM_data:1361 + description: Position frequency matrix + title: Position frequency matrix + EDAM_data:1362: + text: EDAM_data:1362 + description: Position weight matrix + title: Position weight matrix + EDAM_data:1363: + text: EDAM_data:1363 + description: Information content matrix + title: Information content matrix + EDAM_data:1364: + text: EDAM_data:1364 + description: Hidden Markov model + title: Hidden Markov model + EDAM_data:1365: + text: EDAM_data:1365 + description: Fingerprint + title: Fingerprint + EDAM_data:1381: + text: EDAM_data:1381 + description: Pair sequence alignment + title: Pair sequence alignment + EDAM_data:1383: + text: EDAM_data:1383 + description: Nucleic acid sequence alignment + title: Nucleic acid sequence alignment + EDAM_data:1384: + text: EDAM_data:1384 + description: Protein sequence alignment + title: Protein sequence alignment + EDAM_data:1385: + text: EDAM_data:1385 + description: Hybrid sequence alignment + title: Hybrid sequence alignment + EDAM_data:1394: + text: EDAM_data:1394 + description: Alignment score or penalty + title: Alignment score or penalty + EDAM_data:1397: + text: EDAM_data:1397 + description: Gap opening penalty + title: Gap opening penalty + EDAM_data:1398: + text: EDAM_data:1398 + description: Gap extension penalty + title: Gap extension penalty + EDAM_data:1399: + text: EDAM_data:1399 + description: Gap separation penalty + title: Gap separation penalty + EDAM_data:1401: + text: EDAM_data:1401 + description: Match reward score + title: Match reward score + EDAM_data:1402: + text: EDAM_data:1402 + description: Mismatch penalty score + title: Mismatch penalty score + EDAM_data:1403: + text: EDAM_data:1403 + description: Drop off score + title: Drop off score + EDAM_data:1410: + text: EDAM_data:1410 + description: Terminal gap opening penalty + title: Terminal gap opening penalty + EDAM_data:1411: + text: EDAM_data:1411 + description: Terminal gap extension penalty + title: Terminal gap extension penalty + EDAM_data:1412: + text: EDAM_data:1412 + description: Sequence identity + title: Sequence identity + EDAM_data:1413: + text: EDAM_data:1413 + description: Sequence similarity + title: Sequence similarity + EDAM_data:1426: + text: EDAM_data:1426 + description: Phylogenetic continuous quantitative data + title: Phylogenetic continuous quantitative data + EDAM_data:1427: + text: EDAM_data:1427 + description: Phylogenetic discrete data + title: Phylogenetic discrete data + EDAM_data:1428: + text: EDAM_data:1428 + description: Phylogenetic character cliques + title: Phylogenetic character cliques + EDAM_data:1429: + text: EDAM_data:1429 + description: Phylogenetic invariants + title: Phylogenetic invariants + EDAM_data:1439: + text: EDAM_data:1439 + description: DNA substitution model + title: DNA substitution model + EDAM_data:1442: + text: EDAM_data:1442 + description: Phylogenetic tree distances + title: Phylogenetic tree distances + EDAM_data:1444: + text: EDAM_data:1444 + description: Phylogenetic character contrasts + title: Phylogenetic character contrasts + EDAM_data:1448: + text: EDAM_data:1448 + description: Comparison matrix (nucleotide) + title: Comparison matrix (nucleotide) + EDAM_data:1449: + text: EDAM_data:1449 + description: Comparison matrix (amino acid) + title: Comparison matrix (amino acid) + EDAM_data:1459: + text: EDAM_data:1459 + description: Nucleic acid structure + title: Nucleic acid structure + EDAM_data:1460: + text: EDAM_data:1460 + description: Protein structure + title: Protein structure + EDAM_data:1461: + text: EDAM_data:1461 + description: Protein-ligand complex + title: Protein-ligand complex + EDAM_data:1462: + text: EDAM_data:1462 + description: Carbohydrate structure + title: Carbohydrate structure + EDAM_data:1463: + text: EDAM_data:1463 + description: Small molecule structure + title: Small molecule structure + EDAM_data:1464: + text: EDAM_data:1464 + description: DNA structure + title: DNA structure + EDAM_data:1465: + text: EDAM_data:1465 + description: RNA structure + title: RNA structure + EDAM_data:1466: + text: EDAM_data:1466 + description: tRNA structure + title: tRNA structure + EDAM_data:1467: + text: EDAM_data:1467 + description: Protein chain + title: Protein chain + EDAM_data:1468: + text: EDAM_data:1468 + description: Protein domain + title: Protein domain + EDAM_data:1470: + text: EDAM_data:1470 + description: C-alpha trace + title: C-alpha trace + EDAM_data:1479: + text: EDAM_data:1479 + description: Structure alignment (pair) + title: Structure alignment (pair) + EDAM_data:1481: + text: EDAM_data:1481 + description: Protein structure alignment + title: Protein structure alignment + EDAM_data:1482: + text: EDAM_data:1482 + description: Nucleic acid structure alignment + title: Nucleic acid structure alignment + EDAM_data:1493: + text: EDAM_data:1493 + description: RNA structure alignment + title: RNA structure alignment + EDAM_data:1494: + text: EDAM_data:1494 + description: Structural transformation matrix + title: Structural transformation matrix + EDAM_data:1497: + text: EDAM_data:1497 + description: Root-mean-square deviation + title: Root-mean-square deviation + EDAM_data:1498: + text: EDAM_data:1498 + description: Tanimoto similarity score + title: Tanimoto similarity score + EDAM_data:1499: + text: EDAM_data:1499 + description: 3D-1D scoring matrix + title: 3D-1D scoring matrix + EDAM_data:1501: + text: EDAM_data:1501 + description: Amino acid index + title: Amino acid index + EDAM_data:1502: + text: EDAM_data:1502 + description: Amino acid index (chemical classes) + title: Amino acid index (chemical classes) + EDAM_data:1503: + text: EDAM_data:1503 + description: Amino acid pair-wise contact potentials + title: Amino acid pair-wise contact potentials + EDAM_data:1505: + text: EDAM_data:1505 + description: Amino acid index (molecular weight) + title: Amino acid index (molecular weight) + EDAM_data:1506: + text: EDAM_data:1506 + description: Amino acid index (hydropathy) + title: Amino acid index (hydropathy) + EDAM_data:1507: + text: EDAM_data:1507 + description: Amino acid index (White-Wimley data) + title: Amino acid index (White-Wimley data) + EDAM_data:1508: + text: EDAM_data:1508 + description: Amino acid index (van der Waals radii) + title: Amino acid index (van der Waals radii) + EDAM_data:1519: + text: EDAM_data:1519 + description: Peptide molecular weights + title: Peptide molecular weights + EDAM_data:1520: + text: EDAM_data:1520 + description: Peptide hydrophobic moment + title: Peptide hydrophobic moment + EDAM_data:1521: + text: EDAM_data:1521 + description: Protein aliphatic index + title: Protein aliphatic index + EDAM_data:1522: + text: EDAM_data:1522 + description: Protein sequence hydropathy plot + title: Protein sequence hydropathy plot + EDAM_data:1523: + text: EDAM_data:1523 + description: Protein charge plot + title: Protein charge plot + EDAM_data:1524: + text: EDAM_data:1524 + description: Protein solubility + title: Protein solubility + EDAM_data:1525: + text: EDAM_data:1525 + description: Protein crystallizability + title: Protein crystallizability + EDAM_data:1526: + text: EDAM_data:1526 + description: Protein globularity + title: Protein globularity + EDAM_data:1527: + text: EDAM_data:1527 + description: Protein titration curve + title: Protein titration curve + EDAM_data:1528: + text: EDAM_data:1528 + description: Protein isoelectric point + title: Protein isoelectric point + EDAM_data:1529: + text: EDAM_data:1529 + description: Protein pKa value + title: Protein pKa value + EDAM_data:1530: + text: EDAM_data:1530 + description: Protein hydrogen exchange rate + title: Protein hydrogen exchange rate + EDAM_data:1531: + text: EDAM_data:1531 + description: Protein extinction coefficient + title: Protein extinction coefficient + EDAM_data:1532: + text: EDAM_data:1532 + description: Protein optical density + title: Protein optical density + EDAM_data:1534: + text: EDAM_data:1534 + description: Peptide immunogenicity data + title: Peptide immunogenicity data + EDAM_data:1537: + text: EDAM_data:1537 + description: Protein structure report + title: Protein structure report + EDAM_data:1539: + text: EDAM_data:1539 + description: Protein structural quality report + title: Protein structural quality report + EDAM_data:1542: + text: EDAM_data:1542 + description: Protein solvent accessibility + title: Protein solvent accessibility + EDAM_data:1544: + text: EDAM_data:1544 + description: Ramachandran plot + title: Ramachandran plot + EDAM_data:1545: + text: EDAM_data:1545 + description: Protein dipole moment + title: Protein dipole moment + EDAM_data:1546: + text: EDAM_data:1546 + description: Protein distance matrix + title: Protein distance matrix + EDAM_data:1547: + text: EDAM_data:1547 + description: Protein contact map + title: Protein contact map + EDAM_data:1548: + text: EDAM_data:1548 + description: Protein residue 3D cluster + title: Protein residue 3D cluster + EDAM_data:1549: + text: EDAM_data:1549 + description: Protein hydrogen bonds + title: Protein hydrogen bonds + EDAM_data:1566: + text: EDAM_data:1566 + description: Protein-ligand interaction report + title: Protein-ligand interaction report + EDAM_data:1583: + text: EDAM_data:1583 + description: Nucleic acid melting profile + title: Nucleic acid melting profile + EDAM_data:1584: + text: EDAM_data:1584 + description: Nucleic acid enthalpy + title: Nucleic acid enthalpy + EDAM_data:1585: + text: EDAM_data:1585 + description: Nucleic acid entropy + title: Nucleic acid entropy + EDAM_data:1588: + text: EDAM_data:1588 + description: DNA base pair stacking energies data + title: DNA base pair stacking energies data + EDAM_data:1589: + text: EDAM_data:1589 + description: DNA base pair twist angle data + title: DNA base pair twist angle data + EDAM_data:1590: + text: EDAM_data:1590 + description: DNA base trimer roll angles data + title: DNA base trimer roll angles data + EDAM_data:1595: + text: EDAM_data:1595 + description: Base pairing probability matrix dotplot + title: Base pairing probability matrix dotplot + EDAM_data:1596: + text: EDAM_data:1596 + description: Nucleic acid folding report + title: Nucleic acid folding report + EDAM_data:1597: + text: EDAM_data:1597 + description: Codon usage table + title: Codon usage table + EDAM_data:1598: + text: EDAM_data:1598 + description: Genetic code + title: Genetic code + EDAM_data:1600: + text: EDAM_data:1600 + description: Codon usage bias plot + title: Codon usage bias plot + EDAM_data:1602: + text: EDAM_data:1602 + description: Codon usage fraction difference + title: Codon usage fraction difference + EDAM_data:1621: + text: EDAM_data:1621 + description: Pharmacogenomic test report + title: Pharmacogenomic test report + EDAM_data:1622: + text: EDAM_data:1622 + description: Disease report + title: Disease report + EDAM_data:1636: + text: EDAM_data:1636 + description: Heat map + title: Heat map + EDAM_data:1667: + text: EDAM_data:1667 + description: E-value + title: E-value + EDAM_data:1668: + text: EDAM_data:1668 + description: Z-value + title: Z-value + EDAM_data:1669: + text: EDAM_data:1669 + description: P-value + title: P-value + EDAM_data:1689: + text: EDAM_data:1689 + description: Username + title: Username + EDAM_data:1690: + text: EDAM_data:1690 + description: Password + title: Password + EDAM_data:1691: + text: EDAM_data:1691 + description: Email address + title: Email address + EDAM_data:1692: + text: EDAM_data:1692 + description: Person name + title: Person name + EDAM_data:1696: + text: EDAM_data:1696 + description: Drug report + title: Drug report + EDAM_data:1707: + text: EDAM_data:1707 + description: Phylogenetic tree image + title: Phylogenetic tree image + EDAM_data:1708: + text: EDAM_data:1708 + description: RNA secondary structure image + title: RNA secondary structure image + EDAM_data:1709: + text: EDAM_data:1709 + description: Protein secondary structure image + title: Protein secondary structure image + EDAM_data:1710: + text: EDAM_data:1710 + description: Structure image + title: Structure image + EDAM_data:1711: + text: EDAM_data:1711 + description: Sequence alignment image + title: Sequence alignment image + EDAM_data:1712: + text: EDAM_data:1712 + description: Chemical structure image + title: Chemical structure image + EDAM_data:1713: + text: EDAM_data:1713 + description: Fate map + title: Fate map + EDAM_data:1714: + text: EDAM_data:1714 + description: Microarray spots image + title: Microarray spots image + EDAM_data:1731: + text: EDAM_data:1731 + description: Ontology concept definition + title: Ontology concept definition + EDAM_data:1742: + text: EDAM_data:1742 + description: PDB residue number + title: PDB residue number + EDAM_data:1743: + text: EDAM_data:1743 + description: Atomic coordinate + title: Atomic coordinate + EDAM_data:1748: + text: EDAM_data:1748 + description: PDB atom name + title: PDB atom name + EDAM_data:1755: + text: EDAM_data:1755 + description: Protein atom + title: Protein atom + EDAM_data:1756: + text: EDAM_data:1756 + description: Protein residue + title: Protein residue + EDAM_data:1757: + text: EDAM_data:1757 + description: Atom name + title: Atom name + EDAM_data:1758: + text: EDAM_data:1758 + description: PDB residue name + title: PDB residue name + EDAM_data:1759: + text: EDAM_data:1759 + description: PDB model number + title: PDB model number + EDAM_data:1771: + text: EDAM_data:1771 + description: Sequence version + title: Sequence version + EDAM_data:1772: + text: EDAM_data:1772 + description: Score + title: Score + EDAM_data:1794: + text: EDAM_data:1794 + description: Gene ID (PlasmoDB) + title: Gene ID (PlasmoDB) + EDAM_data:1795: + text: EDAM_data:1795 + description: Gene ID (EcoGene) + title: Gene ID (EcoGene) + EDAM_data:1796: + text: EDAM_data:1796 + description: Gene ID (FlyBase) + title: Gene ID (FlyBase) + EDAM_data:1802: + text: EDAM_data:1802 + description: Gene ID (Gramene) + title: Gene ID (Gramene) + EDAM_data:1803: + text: EDAM_data:1803 + description: Gene ID (Virginia microbial) + title: Gene ID (Virginia microbial) + EDAM_data:1804: + text: EDAM_data:1804 + description: Gene ID (SGN) + title: Gene ID (SGN) + EDAM_data:1805: + text: EDAM_data:1805 + description: Gene ID (WormBase) + title: Gene ID (WormBase) + EDAM_data:1807: + text: EDAM_data:1807 + description: ORF name + title: ORF name + EDAM_data:1855: + text: EDAM_data:1855 + description: Clone ID + title: Clone ID + EDAM_data:1856: + text: EDAM_data:1856 + description: PDB insertion code + title: PDB insertion code + EDAM_data:1857: + text: EDAM_data:1857 + description: Atomic occupancy + title: Atomic occupancy + EDAM_data:1858: + text: EDAM_data:1858 + description: Isotropic B factor + title: Isotropic B factor + EDAM_data:1859: + text: EDAM_data:1859 + description: Deletion map + title: Deletion map + EDAM_data:1860: + text: EDAM_data:1860 + description: QTL map + title: QTL map + EDAM_data:1863: + text: EDAM_data:1863 + description: Haplotype map + title: Haplotype map + EDAM_data:1867: + text: EDAM_data:1867 + description: Protein fold name + title: Protein fold name + EDAM_data:1868: + text: EDAM_data:1868 + description: Taxon + title: Taxon + EDAM_data:1869: + text: EDAM_data:1869 + description: Organism identifier + title: Organism identifier + EDAM_data:1870: + text: EDAM_data:1870 + description: Genus name + title: Genus name + EDAM_data:1872: + text: EDAM_data:1872 + description: Taxonomic classification + title: Taxonomic classification + EDAM_data:1873: + text: EDAM_data:1873 + description: iHOP organism ID + title: iHOP organism ID + EDAM_data:1874: + text: EDAM_data:1874 + description: Genbank common name + title: Genbank common name + EDAM_data:1875: + text: EDAM_data:1875 + description: NCBI taxon + title: NCBI taxon + EDAM_data:1881: + text: EDAM_data:1881 + description: Author ID + title: Author ID + EDAM_data:1882: + text: EDAM_data:1882 + description: DragonDB author identifier + title: DragonDB author identifier + EDAM_data:1883: + text: EDAM_data:1883 + description: Annotated URI + title: Annotated URI + EDAM_data:1885: + text: EDAM_data:1885 + description: Gene ID (GeneFarm) + title: Gene ID (GeneFarm) + EDAM_data:1886: + text: EDAM_data:1886 + description: Blattner number + title: Blattner number + EDAM_data:1891: + text: EDAM_data:1891 + description: iHOP symbol + title: iHOP symbol + EDAM_data:1893: + text: EDAM_data:1893 + description: Locus ID + title: Locus ID + EDAM_data:1895: + text: EDAM_data:1895 + description: Locus ID (AGI) + title: Locus ID (AGI) + EDAM_data:1896: + text: EDAM_data:1896 + description: Locus ID (ASPGD) + title: Locus ID (ASPGD) + EDAM_data:1897: + text: EDAM_data:1897 + description: Locus ID (MGG) + title: Locus ID (MGG) + EDAM_data:1898: + text: EDAM_data:1898 + description: Locus ID (CGD) + title: Locus ID (CGD) + EDAM_data:1899: + text: EDAM_data:1899 + description: Locus ID (CMR) + title: Locus ID (CMR) + EDAM_data:1900: + text: EDAM_data:1900 + description: NCBI locus tag + title: NCBI locus tag + EDAM_data:1901: + text: EDAM_data:1901 + description: Locus ID (SGD) + title: Locus ID (SGD) + EDAM_data:1902: + text: EDAM_data:1902 + description: Locus ID (MMP) + title: Locus ID (MMP) + EDAM_data:1903: + text: EDAM_data:1903 + description: Locus ID (DictyBase) + title: Locus ID (DictyBase) + EDAM_data:1904: + text: EDAM_data:1904 + description: Locus ID (EntrezGene) + title: Locus ID (EntrezGene) + EDAM_data:1905: + text: EDAM_data:1905 + description: Locus ID (MaizeGDB) + title: Locus ID (MaizeGDB) + EDAM_data:1907: + text: EDAM_data:1907 + description: Gene ID (KOME) + title: Gene ID (KOME) + EDAM_data:1908: + text: EDAM_data:1908 + description: Locus ID (Tropgene) + title: Locus ID (Tropgene) + EDAM_data:1916: + text: EDAM_data:1916 + description: Alignment + title: Alignment + EDAM_data:1917: + text: EDAM_data:1917 + description: Atomic property + title: Atomic property + EDAM_data:2007: + text: EDAM_data:2007 + description: UniProt keyword + title: UniProt keyword + EDAM_data:2012: + text: EDAM_data:2012 + description: Sequence coordinates + title: Sequence coordinates + EDAM_data:2016: + text: EDAM_data:2016 + description: Amino acid property + title: Amino acid property + EDAM_data:2019: + text: EDAM_data:2019 + description: Map data + title: Map data + EDAM_data:2024: + text: EDAM_data:2024 + description: Enzyme kinetics data + title: Enzyme kinetics data + EDAM_data:2025: + text: EDAM_data:2025 + description: Michaelis Menten plot + title: Michaelis Menten plot + EDAM_data:2026: + text: EDAM_data:2026 + description: Hanes Woolf plot + title: Hanes Woolf plot + EDAM_data:2042: + text: EDAM_data:2042 + description: Evidence + title: Evidence + EDAM_data:2044: + text: EDAM_data:2044 + description: Sequence + title: Sequence + EDAM_data:2048: + text: EDAM_data:2048 + description: Report + title: Report + EDAM_data:2050: + text: EDAM_data:2050 + description: Molecular property (general) + title: Molecular property (general) + EDAM_data:2070: + text: EDAM_data:2070 + description: Sequence motif (nucleic acid) + title: Sequence motif (nucleic acid) + EDAM_data:2071: + text: EDAM_data:2071 + description: Sequence motif (protein) + title: Sequence motif (protein) + EDAM_data:2080: + text: EDAM_data:2080 + description: Database search results + title: Database search results + EDAM_data:2082: + text: EDAM_data:2082 + description: Matrix + title: Matrix + EDAM_data:2084: + text: EDAM_data:2084 + description: Nucleic acid report + title: Nucleic acid report + EDAM_data:2085: + text: EDAM_data:2085 + description: Structure report + title: Structure report + EDAM_data:2087: + text: EDAM_data:2087 + description: Molecular property + title: Molecular property + EDAM_data:2088: + text: EDAM_data:2088 + description: DNA base structural data + title: DNA base structural data + EDAM_data:2091: + text: EDAM_data:2091 + description: Accession + title: Accession + EDAM_data:2093: + text: EDAM_data:2093 + description: Data reference + title: Data reference + EDAM_data:2098: + text: EDAM_data:2098 + description: Job identifier + title: Job identifier + EDAM_data:2099: + text: EDAM_data:2099 + description: Name + title: Name + EDAM_data:2101: + text: EDAM_data:2101 + description: Account authentication + title: Account authentication + EDAM_data:2102: + text: EDAM_data:2102 + description: KEGG organism code + title: KEGG organism code + EDAM_data:2104: + text: EDAM_data:2104 + description: BioCyc ID + title: BioCyc ID + EDAM_data:2105: + text: EDAM_data:2105 + description: Compound ID (BioCyc) + title: Compound ID (BioCyc) + EDAM_data:2106: + text: EDAM_data:2106 + description: Reaction ID (BioCyc) + title: Reaction ID (BioCyc) + EDAM_data:2107: + text: EDAM_data:2107 + description: Enzyme ID (BioCyc) + title: Enzyme ID (BioCyc) + EDAM_data:2108: + text: EDAM_data:2108 + description: Reaction ID + title: Reaction ID + EDAM_data:2109: + text: EDAM_data:2109 + description: Identifier (hybrid) + title: Identifier (hybrid) + EDAM_data:2110: + text: EDAM_data:2110 + description: Molecular property identifier + title: Molecular property identifier + EDAM_data:2111: + text: EDAM_data:2111 + description: Codon usage table ID + title: Codon usage table ID + EDAM_data:2112: + text: EDAM_data:2112 + description: FlyBase primary identifier + title: FlyBase primary identifier + EDAM_data:2113: + text: EDAM_data:2113 + description: WormBase identifier + title: WormBase identifier + EDAM_data:2114: + text: EDAM_data:2114 + description: WormBase wormpep ID + title: WormBase wormpep ID + EDAM_data:2117: + text: EDAM_data:2117 + description: Map identifier + title: Map identifier + EDAM_data:2118: + text: EDAM_data:2118 + description: Person identifier + title: Person identifier + EDAM_data:2119: + text: EDAM_data:2119 + description: Nucleic acid identifier + title: Nucleic acid identifier + EDAM_data:2127: + text: EDAM_data:2127 + description: Genetic code identifier + title: Genetic code identifier + EDAM_data:2128: + text: EDAM_data:2128 + description: Genetic code name + title: Genetic code name + EDAM_data:2129: + text: EDAM_data:2129 + description: File format name + title: File format name + EDAM_data:2131: + text: EDAM_data:2131 + description: Operating system name + title: Operating system name + EDAM_data:2133: + text: EDAM_data:2133 + description: Logical operator + title: Logical operator + EDAM_data:2137: + text: EDAM_data:2137 + description: Gap penalty + title: Gap penalty + EDAM_data:2139: + text: EDAM_data:2139 + description: Nucleic acid melting temperature + title: Nucleic acid melting temperature + EDAM_data:2140: + text: EDAM_data:2140 + description: Concentration + title: Concentration + EDAM_data:2154: + text: EDAM_data:2154 + description: Sequence name + title: Sequence name + EDAM_data:2160: + text: EDAM_data:2160 + description: Fickett testcode plot + title: Fickett testcode plot + EDAM_data:2161: + text: EDAM_data:2161 + description: Sequence similarity plot + title: Sequence similarity plot + EDAM_data:2162: + text: EDAM_data:2162 + description: Helical wheel + title: Helical wheel + EDAM_data:2163: + text: EDAM_data:2163 + description: Helical net + title: Helical net + EDAM_data:2165: + text: EDAM_data:2165 + description: Protein ionisation curve + title: Protein ionisation curve + EDAM_data:2166: + text: EDAM_data:2166 + description: Sequence composition plot + title: Sequence composition plot + EDAM_data:2167: + text: EDAM_data:2167 + description: Nucleic acid density plot + title: Nucleic acid density plot + EDAM_data:2168: + text: EDAM_data:2168 + description: Sequence trace image + title: Sequence trace image + EDAM_data:2174: + text: EDAM_data:2174 + description: FlyBase secondary identifier + title: FlyBase secondary identifier + EDAM_data:2190: + text: EDAM_data:2190 + description: Sequence checksum + title: Sequence checksum + EDAM_data:2193: + text: EDAM_data:2193 + description: Database entry metadata + title: Database entry metadata + EDAM_data:2208: + text: EDAM_data:2208 + description: Plasmid identifier + title: Plasmid identifier + EDAM_data:2209: + text: EDAM_data:2209 + description: Mutation ID + title: Mutation ID + EDAM_data:2216: + text: EDAM_data:2216 + description: Codon number + title: Codon number + EDAM_data:2219: + text: EDAM_data:2219 + description: Database field name + title: Database field name + EDAM_data:2220: + text: EDAM_data:2220 + description: Sequence cluster ID (SYSTERS) + title: Sequence cluster ID (SYSTERS) + EDAM_data:2223: + text: EDAM_data:2223 + description: Ontology metadata + title: Ontology metadata + EDAM_data:2253: + text: EDAM_data:2253 + description: Data resource definition name + title: Data resource definition name + EDAM_data:2254: + text: EDAM_data:2254 + description: OBO file format name + title: OBO file format name + EDAM_data:2285: + text: EDAM_data:2285 + description: Gene ID (MIPS) + title: Gene ID (MIPS) + EDAM_data:2290: + text: EDAM_data:2290 + description: EMBL accession + title: EMBL accession + EDAM_data:2291: + text: EDAM_data:2291 + description: UniProt ID + title: UniProt ID + EDAM_data:2292: + text: EDAM_data:2292 + description: GenBank accession + title: GenBank accession + EDAM_data:2293: + text: EDAM_data:2293 + description: Gramene secondary identifier + title: Gramene secondary identifier + EDAM_data:2294: + text: EDAM_data:2294 + description: Sequence variation ID + title: Sequence variation ID + EDAM_data:2295: + text: EDAM_data:2295 + description: Gene ID + title: Gene ID + EDAM_data:2297: + text: EDAM_data:2297 + description: Gene ID (ECK) + title: Gene ID (ECK) + EDAM_data:2298: + text: EDAM_data:2298 + description: Gene ID (HGNC) + title: Gene ID (HGNC) + EDAM_data:2299: + text: EDAM_data:2299 + description: Gene name + title: Gene name + EDAM_data:2301: + text: EDAM_data:2301 + description: SMILES string + title: SMILES string + EDAM_data:2302: + text: EDAM_data:2302 + description: STRING ID + title: STRING ID + EDAM_data:2309: + text: EDAM_data:2309 + description: Reaction ID (SABIO-RK) + title: Reaction ID (SABIO-RK) + EDAM_data:2313: + text: EDAM_data:2313 + description: Carbohydrate report + title: Carbohydrate report + EDAM_data:2314: + text: EDAM_data:2314 + description: GI number + title: GI number + EDAM_data:2315: + text: EDAM_data:2315 + description: NCBI version + title: NCBI version + EDAM_data:2316: + text: EDAM_data:2316 + description: Cell line name + title: Cell line name + EDAM_data:2317: + text: EDAM_data:2317 + description: Cell line name (exact) + title: Cell line name (exact) + EDAM_data:2318: + text: EDAM_data:2318 + description: Cell line name (truncated) + title: Cell line name (truncated) + EDAM_data:2319: + text: EDAM_data:2319 + description: Cell line name (no punctuation) + title: Cell line name (no punctuation) + EDAM_data:2320: + text: EDAM_data:2320 + description: Cell line name (assonant) + title: Cell line name (assonant) + EDAM_data:2321: + text: EDAM_data:2321 + description: Enzyme ID + title: Enzyme ID + EDAM_data:2325: + text: EDAM_data:2325 + description: REBASE enzyme number + title: REBASE enzyme number + EDAM_data:2326: + text: EDAM_data:2326 + description: DrugBank ID + title: DrugBank ID + EDAM_data:2327: + text: EDAM_data:2327 + description: GI number (protein) + title: GI number (protein) + EDAM_data:2335: + text: EDAM_data:2335 + description: Bit score + title: Bit score + EDAM_data:2337: + text: EDAM_data:2337 + description: Resource metadata + title: Resource metadata + EDAM_data:2338: + text: EDAM_data:2338 + description: Ontology identifier + title: Ontology identifier + EDAM_data:2339: + text: EDAM_data:2339 + description: Ontology concept name + title: Ontology concept name + EDAM_data:2340: + text: EDAM_data:2340 + description: Genome build identifier + title: Genome build identifier + EDAM_data:2342: + text: EDAM_data:2342 + description: Pathway or network name + title: Pathway or network name + EDAM_data:2343: + text: EDAM_data:2343 + description: Pathway ID (KEGG) + title: Pathway ID (KEGG) + EDAM_data:2344: + text: EDAM_data:2344 + description: Pathway ID (NCI-Nature) + title: Pathway ID (NCI-Nature) + EDAM_data:2345: + text: EDAM_data:2345 + description: Pathway ID (ConsensusPathDB) + title: Pathway ID (ConsensusPathDB) + EDAM_data:2346: + text: EDAM_data:2346 + description: Sequence cluster ID (UniRef) + title: Sequence cluster ID (UniRef) + EDAM_data:2347: + text: EDAM_data:2347 + description: Sequence cluster ID (UniRef100) + title: Sequence cluster ID (UniRef100) + EDAM_data:2348: + text: EDAM_data:2348 + description: Sequence cluster ID (UniRef90) + title: Sequence cluster ID (UniRef90) + EDAM_data:2349: + text: EDAM_data:2349 + description: Sequence cluster ID (UniRef50) + title: Sequence cluster ID (UniRef50) + EDAM_data:2353: + text: EDAM_data:2353 + description: Ontology data + title: Ontology data + EDAM_data:2354: + text: EDAM_data:2354 + description: RNA family report + title: RNA family report + EDAM_data:2355: + text: EDAM_data:2355 + description: RNA family identifier + title: RNA family identifier + EDAM_data:2356: + text: EDAM_data:2356 + description: RFAM accession + title: RFAM accession + EDAM_data:2362: + text: EDAM_data:2362 + description: Sequence accession (hybrid) + title: Sequence accession (hybrid) + EDAM_data:2365: + text: EDAM_data:2365 + description: Pathway or network accession + title: Pathway or network accession + EDAM_data:2366: + text: EDAM_data:2366 + description: Secondary structure alignment + title: Secondary structure alignment + EDAM_data:2367: + text: EDAM_data:2367 + description: ASTD ID + title: ASTD ID + EDAM_data:2368: + text: EDAM_data:2368 + description: ASTD ID (exon) + title: ASTD ID (exon) + EDAM_data:2369: + text: EDAM_data:2369 + description: ASTD ID (intron) + title: ASTD ID (intron) + EDAM_data:2370: + text: EDAM_data:2370 + description: ASTD ID (polya) + title: ASTD ID (polya) + EDAM_data:2371: + text: EDAM_data:2371 + description: ASTD ID (tss) + title: ASTD ID (tss) + EDAM_data:2373: + text: EDAM_data:2373 + description: Spot ID + title: Spot ID + EDAM_data:2374: + text: EDAM_data:2374 + description: Spot serial number + title: Spot serial number + EDAM_data:2375: + text: EDAM_data:2375 + description: Spot ID (HSC-2DPAGE) + title: Spot ID (HSC-2DPAGE) + EDAM_data:2379: + text: EDAM_data:2379 + description: Strain identifier + title: Strain identifier + EDAM_data:2380: + text: EDAM_data:2380 + description: CABRI accession + title: CABRI accession + EDAM_data:2382: + text: EDAM_data:2382 + description: Genotype experiment ID + title: Genotype experiment ID + EDAM_data:2383: + text: EDAM_data:2383 + description: EGA accession + title: EGA accession + EDAM_data:2384: + text: EDAM_data:2384 + description: IPI protein ID + title: IPI protein ID + EDAM_data:2385: + text: EDAM_data:2385 + description: RefSeq accession (protein) + title: RefSeq accession (protein) + EDAM_data:2386: + text: EDAM_data:2386 + description: EPD ID + title: EPD ID + EDAM_data:2387: + text: EDAM_data:2387 + description: TAIR accession + title: TAIR accession + EDAM_data:2388: + text: EDAM_data:2388 + description: TAIR accession (At gene) + title: TAIR accession (At gene) + EDAM_data:2389: + text: EDAM_data:2389 + description: UniSTS accession + title: UniSTS accession + EDAM_data:2390: + text: EDAM_data:2390 + description: UNITE accession + title: UNITE accession + EDAM_data:2391: + text: EDAM_data:2391 + description: UTR accession + title: UTR accession + EDAM_data:2392: + text: EDAM_data:2392 + description: UniParc accession + title: UniParc accession + EDAM_data:2393: + text: EDAM_data:2393 + description: mFLJ/mKIAA number + title: mFLJ/mKIAA number + EDAM_data:2398: + text: EDAM_data:2398 + description: Ensembl protein ID + title: Ensembl protein ID + EDAM_data:2523: + text: EDAM_data:2523 + description: Phylogenetic data + title: Phylogenetic data + EDAM_data:2526: + text: EDAM_data:2526 + description: Text data + title: Text data + EDAM_data:2530: + text: EDAM_data:2530 + description: Organism report + title: Organism report + EDAM_data:2531: + text: EDAM_data:2531 + description: Protocol + title: Protocol + EDAM_data:2534: + text: EDAM_data:2534 + description: Sequence attribute + title: Sequence attribute + EDAM_data:2535: + text: EDAM_data:2535 + description: Sequence tag profile + title: Sequence tag profile + EDAM_data:2536: + text: EDAM_data:2536 + description: Mass spectrometry data + title: Mass spectrometry data + EDAM_data:2537: + text: EDAM_data:2537 + description: Protein structure raw data + title: Protein structure raw data + EDAM_data:2538: + text: EDAM_data:2538 + description: Mutation identifier + title: Mutation identifier + EDAM_data:2563: + text: EDAM_data:2563 + description: Amino acid name (single letter) + title: Amino acid name (single letter) + EDAM_data:2564: + text: EDAM_data:2564 + description: Amino acid name (three letter) + title: Amino acid name (three letter) + EDAM_data:2565: + text: EDAM_data:2565 + description: Amino acid name (full name) + title: Amino acid name (full name) + EDAM_data:2576: + text: EDAM_data:2576 + description: Toxin identifier + title: Toxin identifier + EDAM_data:2578: + text: EDAM_data:2578 + description: ArachnoServer ID + title: ArachnoServer ID + EDAM_data:2580: + text: EDAM_data:2580 + description: BindingDB Monomer ID + title: BindingDB Monomer ID + EDAM_data:2582: + text: EDAM_data:2582 + description: GO concept ID (biological process) + title: GO concept ID (biological process) + EDAM_data:2583: + text: EDAM_data:2583 + description: GO concept ID (molecular function) + title: GO concept ID (molecular function) + EDAM_data:2586: + text: EDAM_data:2586 + description: Northern blot image + title: Northern blot image + EDAM_data:2587: + text: EDAM_data:2587 + description: Blot ID + title: Blot ID + EDAM_data:2588: + text: EDAM_data:2588 + description: BlotBase blot ID + title: BlotBase blot ID + EDAM_data:2589: + text: EDAM_data:2589 + description: Hierarchy + title: Hierarchy + EDAM_data:2591: + text: EDAM_data:2591 + description: Brite hierarchy ID + title: Brite hierarchy ID + EDAM_data:2593: + text: EDAM_data:2593 + description: BRENDA organism ID + title: BRENDA organism ID + EDAM_data:2594: + text: EDAM_data:2594 + description: UniGene taxon + title: UniGene taxon + EDAM_data:2595: + text: EDAM_data:2595 + description: UTRdb taxon + title: UTRdb taxon + EDAM_data:2596: + text: EDAM_data:2596 + description: Catalogue ID + title: Catalogue ID + EDAM_data:2597: + text: EDAM_data:2597 + description: CABRI catalogue name + title: CABRI catalogue name + EDAM_data:2600: + text: EDAM_data:2600 + description: Pathway or network + title: Pathway or network + EDAM_data:2603: + text: EDAM_data:2603 + description: Expression data + title: Expression data + EDAM_data:2605: + text: EDAM_data:2605 + description: Compound ID (KEGG) + title: Compound ID (KEGG) + EDAM_data:2606: + text: EDAM_data:2606 + description: RFAM name + title: RFAM name + EDAM_data:2608: + text: EDAM_data:2608 + description: Reaction ID (KEGG) + title: Reaction ID (KEGG) + EDAM_data:2609: + text: EDAM_data:2609 + description: Drug ID (KEGG) + title: Drug ID (KEGG) + EDAM_data:2610: + text: EDAM_data:2610 + description: Ensembl ID + title: Ensembl ID + EDAM_data:2611: + text: EDAM_data:2611 + description: ICD identifier + title: ICD identifier + EDAM_data:2612: + text: EDAM_data:2612 + description: Sequence cluster ID (CluSTr) + title: Sequence cluster ID (CluSTr) + EDAM_data:2613: + text: EDAM_data:2613 + description: KEGG Glycan ID + title: KEGG Glycan ID + EDAM_data:2614: + text: EDAM_data:2614 + description: TCDB ID + title: TCDB ID + EDAM_data:2615: + text: EDAM_data:2615 + description: MINT ID + title: MINT ID + EDAM_data:2616: + text: EDAM_data:2616 + description: DIP ID + title: DIP ID + EDAM_data:2617: + text: EDAM_data:2617 + description: Signaling Gateway protein ID + title: Signaling Gateway protein ID + EDAM_data:2618: + text: EDAM_data:2618 + description: Protein modification ID + title: Protein modification ID + EDAM_data:2619: + text: EDAM_data:2619 + description: RESID ID + title: RESID ID + EDAM_data:2620: + text: EDAM_data:2620 + description: RGD ID + title: RGD ID + EDAM_data:2621: + text: EDAM_data:2621 + description: TAIR accession (protein) + title: TAIR accession (protein) + EDAM_data:2622: + text: EDAM_data:2622 + description: Compound ID (HMDB) + title: Compound ID (HMDB) + EDAM_data:2625: + text: EDAM_data:2625 + description: LIPID MAPS ID + title: LIPID MAPS ID + EDAM_data:2626: + text: EDAM_data:2626 + description: PeptideAtlas ID + title: PeptideAtlas ID + EDAM_data:2628: + text: EDAM_data:2628 + description: BioGRID interaction ID + title: BioGRID interaction ID + EDAM_data:2629: + text: EDAM_data:2629 + description: Enzyme ID (MEROPS) + title: Enzyme ID (MEROPS) + EDAM_data:2630: + text: EDAM_data:2630 + description: Mobile genetic element ID + title: Mobile genetic element ID + EDAM_data:2631: + text: EDAM_data:2631 + description: ACLAME ID + title: ACLAME ID + EDAM_data:2632: + text: EDAM_data:2632 + description: SGD ID + title: SGD ID + EDAM_data:2633: + text: EDAM_data:2633 + description: Book ID + title: Book ID + EDAM_data:2634: + text: EDAM_data:2634 + description: ISBN + title: ISBN + EDAM_data:2635: + text: EDAM_data:2635 + description: Compound ID (3DMET) + title: Compound ID (3DMET) + EDAM_data:2636: + text: EDAM_data:2636 + description: MatrixDB interaction ID + title: MatrixDB interaction ID + EDAM_data:2637: + text: EDAM_data:2637 + description: cPath ID + title: cPath ID + EDAM_data:2638: + text: EDAM_data:2638 + description: PubChem bioassay ID + title: PubChem bioassay ID + EDAM_data:2639: + text: EDAM_data:2639 + description: PubChem ID + title: PubChem ID + EDAM_data:2641: + text: EDAM_data:2641 + description: Reaction ID (MACie) + title: Reaction ID (MACie) + EDAM_data:2642: + text: EDAM_data:2642 + description: Gene ID (miRBase) + title: Gene ID (miRBase) + EDAM_data:2643: + text: EDAM_data:2643 + description: Gene ID (ZFIN) + title: Gene ID (ZFIN) + EDAM_data:2644: + text: EDAM_data:2644 + description: Reaction ID (Rhea) + title: Reaction ID (Rhea) + EDAM_data:2645: + text: EDAM_data:2645 + description: Pathway ID (Unipathway) + title: Pathway ID (Unipathway) + EDAM_data:2646: + text: EDAM_data:2646 + description: Compound ID (ChEMBL) + title: Compound ID (ChEMBL) + EDAM_data:2647: + text: EDAM_data:2647 + description: LGICdb identifier + title: LGICdb identifier + EDAM_data:2648: + text: EDAM_data:2648 + description: Reaction kinetics ID (SABIO-RK) + title: Reaction kinetics ID (SABIO-RK) + EDAM_data:2649: + text: EDAM_data:2649 + description: PharmGKB ID + title: PharmGKB ID + EDAM_data:2650: + text: EDAM_data:2650 + description: Pathway ID (PharmGKB) + title: Pathway ID (PharmGKB) + EDAM_data:2651: + text: EDAM_data:2651 + description: Disease ID (PharmGKB) + title: Disease ID (PharmGKB) + EDAM_data:2652: + text: EDAM_data:2652 + description: Drug ID (PharmGKB) + title: Drug ID (PharmGKB) + EDAM_data:2653: + text: EDAM_data:2653 + description: Drug ID (TTD) + title: Drug ID (TTD) + EDAM_data:2654: + text: EDAM_data:2654 + description: Target ID (TTD) + title: Target ID (TTD) + EDAM_data:2655: + text: EDAM_data:2655 + description: Cell type identifier + title: Cell type identifier + EDAM_data:2656: + text: EDAM_data:2656 + description: NeuronDB ID + title: NeuronDB ID + EDAM_data:2657: + text: EDAM_data:2657 + description: NeuroMorpho ID + title: NeuroMorpho ID + EDAM_data:2658: + text: EDAM_data:2658 + description: Compound ID (ChemIDplus) + title: Compound ID (ChemIDplus) + EDAM_data:2659: + text: EDAM_data:2659 + description: Pathway ID (SMPDB) + title: Pathway ID (SMPDB) + EDAM_data:2660: + text: EDAM_data:2660 + description: BioNumbers ID + title: BioNumbers ID + EDAM_data:2662: + text: EDAM_data:2662 + description: T3DB ID + title: T3DB ID + EDAM_data:2663: + text: EDAM_data:2663 + description: Carbohydrate identifier + title: Carbohydrate identifier + EDAM_data:2664: + text: EDAM_data:2664 + description: GlycomeDB ID + title: GlycomeDB ID + EDAM_data:2665: + text: EDAM_data:2665 + description: LipidBank ID + title: LipidBank ID + EDAM_data:2666: + text: EDAM_data:2666 + description: CDD ID + title: CDD ID + EDAM_data:2667: + text: EDAM_data:2667 + description: MMDB ID + title: MMDB ID + EDAM_data:2668: + text: EDAM_data:2668 + description: iRefIndex ID + title: iRefIndex ID + EDAM_data:2669: + text: EDAM_data:2669 + description: ModelDB ID + title: ModelDB ID + EDAM_data:2670: + text: EDAM_data:2670 + description: Pathway ID (DQCS) + title: Pathway ID (DQCS) + EDAM_data:2700: + text: EDAM_data:2700 + description: CATH identifier + title: CATH identifier + EDAM_data:2701: + text: EDAM_data:2701 + description: CATH node ID (family) + title: CATH node ID (family) + EDAM_data:2702: + text: EDAM_data:2702 + description: Enzyme ID (CAZy) + title: Enzyme ID (CAZy) + EDAM_data:2704: + text: EDAM_data:2704 + description: Clone ID (IMAGE) + title: Clone ID (IMAGE) + EDAM_data:2705: + text: EDAM_data:2705 + description: GO concept ID (cellular component) + title: GO concept ID (cellular component) + EDAM_data:2706: + text: EDAM_data:2706 + description: Chromosome name (BioCyc) + title: Chromosome name (BioCyc) + EDAM_data:2709: + text: EDAM_data:2709 + description: CleanEx entry name + title: CleanEx entry name + EDAM_data:2710: + text: EDAM_data:2710 + description: CleanEx dataset code + title: CleanEx dataset code + EDAM_data:2711: + text: EDAM_data:2711 + description: Genome report + title: Genome report + EDAM_data:2713: + text: EDAM_data:2713 + description: Protein ID (CORUM) + title: Protein ID (CORUM) + EDAM_data:2714: + text: EDAM_data:2714 + description: CDD PSSM-ID + title: CDD PSSM-ID + EDAM_data:2715: + text: EDAM_data:2715 + description: Protein ID (CuticleDB) + title: Protein ID (CuticleDB) + EDAM_data:2716: + text: EDAM_data:2716 + description: DBD ID + title: DBD ID + EDAM_data:2717: + text: EDAM_data:2717 + description: Oligonucleotide probe annotation + title: Oligonucleotide probe annotation + EDAM_data:2718: + text: EDAM_data:2718 + description: Oligonucleotide ID + title: Oligonucleotide ID + EDAM_data:2719: + text: EDAM_data:2719 + description: dbProbe ID + title: dbProbe ID + EDAM_data:2720: + text: EDAM_data:2720 + description: Dinucleotide property + title: Dinucleotide property + EDAM_data:2721: + text: EDAM_data:2721 + description: DiProDB ID + title: DiProDB ID + EDAM_data:2723: + text: EDAM_data:2723 + description: Protein ID (DisProt) + title: Protein ID (DisProt) + EDAM_data:2725: + text: EDAM_data:2725 + description: Ensembl transcript ID + title: Ensembl transcript ID + EDAM_data:2727: + text: EDAM_data:2727 + description: Promoter ID + title: Promoter ID + EDAM_data:2728: + text: EDAM_data:2728 + description: EST accession + title: EST accession + EDAM_data:2729: + text: EDAM_data:2729 + description: COGEME EST ID + title: COGEME EST ID + EDAM_data:2730: + text: EDAM_data:2730 + description: COGEME unisequence ID + title: COGEME unisequence ID + EDAM_data:2731: + text: EDAM_data:2731 + description: Protein family ID (GeneFarm) + title: Protein family ID (GeneFarm) + EDAM_data:2732: + text: EDAM_data:2732 + description: Family name + title: Family name + EDAM_data:2736: + text: EDAM_data:2736 + description: Sequence feature ID (SwissRegulon) + title: Sequence feature ID (SwissRegulon) + EDAM_data:2737: + text: EDAM_data:2737 + description: FIG ID + title: FIG ID + EDAM_data:2738: + text: EDAM_data:2738 + description: Gene ID (Xenbase) + title: Gene ID (Xenbase) + EDAM_data:2739: + text: EDAM_data:2739 + description: Gene ID (Genolist) + title: Gene ID (Genolist) + EDAM_data:2741: + text: EDAM_data:2741 + description: ABS ID + title: ABS ID + EDAM_data:2742: + text: EDAM_data:2742 + description: AraC-XylS ID + title: AraC-XylS ID + EDAM_data:2744: + text: EDAM_data:2744 + description: Locus ID (PseudoCAP) + title: Locus ID (PseudoCAP) + EDAM_data:2745: + text: EDAM_data:2745 + description: Locus ID (UTR) + title: Locus ID (UTR) + EDAM_data:2746: + text: EDAM_data:2746 + description: MonosaccharideDB ID + title: MonosaccharideDB ID + EDAM_data:2749: + text: EDAM_data:2749 + description: Genome identifier + title: Genome identifier + EDAM_data:2752: + text: EDAM_data:2752 + description: GlycoMap ID + title: GlycoMap ID + EDAM_data:2753: + text: EDAM_data:2753 + description: Carbohydrate conformational map + title: Carbohydrate conformational map + EDAM_data:2755: + text: EDAM_data:2755 + description: Transcription factor name + title: Transcription factor name + EDAM_data:2756: + text: EDAM_data:2756 + description: TCID + title: TCID + EDAM_data:2757: + text: EDAM_data:2757 + description: Pfam domain name + title: Pfam domain name + EDAM_data:2758: + text: EDAM_data:2758 + description: Pfam clan ID + title: Pfam clan ID + EDAM_data:2759: + text: EDAM_data:2759 + description: Gene ID (VectorBase) + title: Gene ID (VectorBase) + EDAM_data:2761: + text: EDAM_data:2761 + description: UTRSite ID + title: UTRSite ID + EDAM_data:2762: + text: EDAM_data:2762 + description: Sequence signature report + title: Sequence signature report + EDAM_data:2764: + text: EDAM_data:2764 + description: Protein name (UniProt) + title: Protein name (UniProt) + EDAM_data:2766: + text: EDAM_data:2766 + description: HAMAP ID + title: HAMAP ID + EDAM_data:2769: + text: EDAM_data:2769 + description: Transcript ID + title: Transcript ID + EDAM_data:2770: + text: EDAM_data:2770 + description: HIT ID + title: HIT ID + EDAM_data:2771: + text: EDAM_data:2771 + description: HIX ID + title: HIX ID + EDAM_data:2772: + text: EDAM_data:2772 + description: HPA antibody id + title: HPA antibody id + EDAM_data:2773: + text: EDAM_data:2773 + description: IMGT/HLA ID + title: IMGT/HLA ID + EDAM_data:2774: + text: EDAM_data:2774 + description: Gene ID (JCVI) + title: Gene ID (JCVI) + EDAM_data:2775: + text: EDAM_data:2775 + description: Kinase name + title: Kinase name + EDAM_data:2776: + text: EDAM_data:2776 + description: ConsensusPathDB entity ID + title: ConsensusPathDB entity ID + EDAM_data:2777: + text: EDAM_data:2777 + description: ConsensusPathDB entity name + title: ConsensusPathDB entity name + EDAM_data:2778: + text: EDAM_data:2778 + description: CCAP strain number + title: CCAP strain number + EDAM_data:2779: + text: EDAM_data:2779 + description: Stock number + title: Stock number + EDAM_data:2780: + text: EDAM_data:2780 + description: Stock number (TAIR) + title: Stock number (TAIR) + EDAM_data:2781: + text: EDAM_data:2781 + description: REDIdb ID + title: REDIdb ID + EDAM_data:2782: + text: EDAM_data:2782 + description: SMART domain name + title: SMART domain name + EDAM_data:2783: + text: EDAM_data:2783 + description: Protein family ID (PANTHER) + title: Protein family ID (PANTHER) + EDAM_data:2784: + text: EDAM_data:2784 + description: RNAVirusDB ID + title: RNAVirusDB ID + EDAM_data:2785: + text: EDAM_data:2785 + description: Virus identifier + title: Virus identifier + EDAM_data:2786: + text: EDAM_data:2786 + description: NCBI Genome Project ID + title: NCBI Genome Project ID + EDAM_data:2787: + text: EDAM_data:2787 + description: NCBI genome accession + title: NCBI genome accession + EDAM_data:2789: + text: EDAM_data:2789 + description: Protein ID (TopDB) + title: Protein ID (TopDB) + EDAM_data:2790: + text: EDAM_data:2790 + description: Gel ID + title: Gel ID + EDAM_data:2791: + text: EDAM_data:2791 + description: Reference map name (SWISS-2DPAGE) + title: Reference map name (SWISS-2DPAGE) + EDAM_data:2792: + text: EDAM_data:2792 + description: Protein ID (PeroxiBase) + title: Protein ID (PeroxiBase) + EDAM_data:2793: + text: EDAM_data:2793 + description: SISYPHUS ID + title: SISYPHUS ID + EDAM_data:2794: + text: EDAM_data:2794 + description: ORF ID + title: ORF ID + EDAM_data:2795: + text: EDAM_data:2795 + description: ORF identifier + title: ORF identifier + EDAM_data:2796: + text: EDAM_data:2796 + description: LINUCS ID + title: LINUCS ID + EDAM_data:2797: + text: EDAM_data:2797 + description: Protein ID (LGICdb) + title: Protein ID (LGICdb) + EDAM_data:2798: + text: EDAM_data:2798 + description: MaizeDB ID + title: MaizeDB ID + EDAM_data:2799: + text: EDAM_data:2799 + description: Gene ID (MfunGD) + title: Gene ID (MfunGD) + EDAM_data:2800: + text: EDAM_data:2800 + description: Orpha number + title: Orpha number + EDAM_data:2802: + text: EDAM_data:2802 + description: Protein ID (EcID) + title: Protein ID (EcID) + EDAM_data:2803: + text: EDAM_data:2803 + description: Clone ID (RefSeq) + title: Clone ID (RefSeq) + EDAM_data:2804: + text: EDAM_data:2804 + description: Protein ID (ConoServer) + title: Protein ID (ConoServer) + EDAM_data:2805: + text: EDAM_data:2805 + description: GeneSNP ID + title: GeneSNP ID + EDAM_data:2812: + text: EDAM_data:2812 + description: Lipid identifier + title: Lipid identifier + EDAM_data:2835: + text: EDAM_data:2835 + description: Gene ID (VBASE2) + title: Gene ID (VBASE2) + EDAM_data:2836: + text: EDAM_data:2836 + description: DPVweb ID + title: DPVweb ID + EDAM_data:2837: + text: EDAM_data:2837 + description: Pathway ID (BioSystems) + title: Pathway ID (BioSystems) + EDAM_data:2849: + text: EDAM_data:2849 + description: Abstract + title: Abstract + EDAM_data:2850: + text: EDAM_data:2850 + description: Lipid structure + title: Lipid structure + EDAM_data:2851: + text: EDAM_data:2851 + description: Drug structure + title: Drug structure + EDAM_data:2852: + text: EDAM_data:2852 + description: Toxin structure + title: Toxin structure + EDAM_data:2854: + text: EDAM_data:2854 + description: Position-specific scoring matrix + title: Position-specific scoring matrix + EDAM_data:2855: + text: EDAM_data:2855 + description: Distance matrix + title: Distance matrix + EDAM_data:2856: + text: EDAM_data:2856 + description: Structural distance matrix + title: Structural distance matrix + EDAM_data:2858: + text: EDAM_data:2858 + description: Ontology concept + title: Ontology concept + EDAM_data:2865: + text: EDAM_data:2865 + description: Codon usage bias + title: Codon usage bias + EDAM_data:2870: + text: EDAM_data:2870 + description: Radiation hybrid map + title: Radiation hybrid map + EDAM_data:2872: + text: EDAM_data:2872 + description: ID list + title: ID list + EDAM_data:2873: + text: EDAM_data:2873 + description: Phylogenetic gene frequencies data + title: Phylogenetic gene frequencies data + EDAM_data:2877: + text: EDAM_data:2877 + description: Protein complex + title: Protein complex + EDAM_data:2878: + text: EDAM_data:2878 + description: Protein structural motif + title: Protein structural motif + EDAM_data:2879: + text: EDAM_data:2879 + description: Lipid report + title: Lipid report + EDAM_data:2884: + text: EDAM_data:2884 + description: Plot + title: Plot + EDAM_data:2886: + text: EDAM_data:2886 + description: Protein sequence record + title: Protein sequence record + EDAM_data:2887: + text: EDAM_data:2887 + description: Nucleic acid sequence record + title: Nucleic acid sequence record + EDAM_data:2891: + text: EDAM_data:2891 + description: Biological model accession + title: Biological model accession + EDAM_data:2892: + text: EDAM_data:2892 + description: Cell type name + title: Cell type name + EDAM_data:2893: + text: EDAM_data:2893 + description: Cell type accession + title: Cell type accession + EDAM_data:2894: + text: EDAM_data:2894 + description: Compound accession + title: Compound accession + EDAM_data:2895: + text: EDAM_data:2895 + description: Drug accession + title: Drug accession + EDAM_data:2896: + text: EDAM_data:2896 + description: Toxin name + title: Toxin name + EDAM_data:2897: + text: EDAM_data:2897 + description: Toxin accession + title: Toxin accession + EDAM_data:2898: + text: EDAM_data:2898 + description: Monosaccharide accession + title: Monosaccharide accession + EDAM_data:2899: + text: EDAM_data:2899 + description: Drug name + title: Drug name + EDAM_data:2900: + text: EDAM_data:2900 + description: Carbohydrate accession + title: Carbohydrate accession + EDAM_data:2901: + text: EDAM_data:2901 + description: Molecule accession + title: Molecule accession + EDAM_data:2902: + text: EDAM_data:2902 + description: Data resource definition accession + title: Data resource definition accession + EDAM_data:2903: + text: EDAM_data:2903 + description: Genome accession + title: Genome accession + EDAM_data:2904: + text: EDAM_data:2904 + description: Map accession + title: Map accession + EDAM_data:2905: + text: EDAM_data:2905 + description: Lipid accession + title: Lipid accession + EDAM_data:2906: + text: EDAM_data:2906 + description: Peptide ID + title: Peptide ID + EDAM_data:2907: + text: EDAM_data:2907 + description: Protein accession + title: Protein accession + EDAM_data:2908: + text: EDAM_data:2908 + description: Organism accession + title: Organism accession + EDAM_data:2909: + text: EDAM_data:2909 + description: Organism name + title: Organism name + EDAM_data:2910: + text: EDAM_data:2910 + description: Protein family accession + title: Protein family accession + EDAM_data:2911: + text: EDAM_data:2911 + description: Transcription factor accession + title: Transcription factor accession + EDAM_data:2912: + text: EDAM_data:2912 + description: Strain accession + title: Strain accession + EDAM_data:2914: + text: EDAM_data:2914 + description: Sequence features metadata + title: Sequence features metadata + EDAM_data:2915: + text: EDAM_data:2915 + description: Gramene identifier + title: Gramene identifier + EDAM_data:2916: + text: EDAM_data:2916 + description: DDBJ accession + title: DDBJ accession + EDAM_data:2917: + text: EDAM_data:2917 + description: ConsensusPathDB identifier + title: ConsensusPathDB identifier + EDAM_data:2955: + text: EDAM_data:2955 + description: Sequence report + title: Sequence report + EDAM_data:2956: + text: EDAM_data:2956 + description: Protein secondary structure + title: Protein secondary structure + EDAM_data:2957: + text: EDAM_data:2957 + description: Hopp and Woods plot + title: Hopp and Woods plot + EDAM_data:2968: + text: EDAM_data:2968 + description: Image + title: Image + EDAM_data:2969: + text: EDAM_data:2969 + description: Sequence image + title: Sequence image + EDAM_data:2970: + text: EDAM_data:2970 + description: Protein hydropathy data + title: Protein hydropathy data + EDAM_data:2976: + text: EDAM_data:2976 + description: Protein sequence + title: Protein sequence + EDAM_data:2977: + text: EDAM_data:2977 + description: Nucleic acid sequence + title: Nucleic acid sequence + EDAM_data:2978: + text: EDAM_data:2978 + description: Reaction data + title: Reaction data + EDAM_data:2979: + text: EDAM_data:2979 + description: Peptide property + title: Peptide property + EDAM_data:2984: + text: EDAM_data:2984 + description: Pathway or network report + title: Pathway or network report + EDAM_data:2985: + text: EDAM_data:2985 + description: Nucleic acid thermodynamic data + title: Nucleic acid thermodynamic data + EDAM_data:2991: + text: EDAM_data:2991 + description: Protein geometry data + title: Protein geometry data + EDAM_data:2992: + text: EDAM_data:2992 + description: Protein structure image + title: Protein structure image + EDAM_data:2994: + text: EDAM_data:2994 + description: Phylogenetic character weights + title: Phylogenetic character weights + EDAM_data:3002: + text: EDAM_data:3002 + description: Annotation track + title: Annotation track + EDAM_data:3021: + text: EDAM_data:3021 + description: UniProt accession + title: UniProt accession + EDAM_data:3022: + text: EDAM_data:3022 + description: NCBI genetic code ID + title: NCBI genetic code ID + EDAM_data:3025: + text: EDAM_data:3025 + description: Ontology concept identifier + title: Ontology concept identifier + EDAM_data:3028: + text: EDAM_data:3028 + description: Taxonomy + title: Taxonomy + EDAM_data:3029: + text: EDAM_data:3029 + description: Protein ID (EMBL/GenBank/DDBJ) + title: Protein ID (EMBL/GenBank/DDBJ) + EDAM_data:3034: + text: EDAM_data:3034 + description: Sequence feature identifier + title: Sequence feature identifier + EDAM_data:3035: + text: EDAM_data:3035 + description: Structure identifier + title: Structure identifier + EDAM_data:3036: + text: EDAM_data:3036 + description: Matrix identifier + title: Matrix identifier + EDAM_data:3103: + text: EDAM_data:3103 + description: ATC code + title: ATC code + EDAM_data:3104: + text: EDAM_data:3104 + description: UNII + title: UNII + EDAM_data:3106: + text: EDAM_data:3106 + description: System metadata + title: System metadata + EDAM_data:3108: + text: EDAM_data:3108 + description: Experimental measurement + title: Experimental measurement + EDAM_data:3110: + text: EDAM_data:3110 + description: Raw microarray data + title: Raw microarray data + EDAM_data:3111: + text: EDAM_data:3111 + description: Processed microarray data + title: Processed microarray data + EDAM_data:3112: + text: EDAM_data:3112 + description: Gene expression matrix + title: Gene expression matrix + EDAM_data:3113: + text: EDAM_data:3113 + description: Sample annotation + title: Sample annotation + EDAM_data:3115: + text: EDAM_data:3115 + description: Microarray metadata + title: Microarray metadata + EDAM_data:3117: + text: EDAM_data:3117 + description: Microarray hybridisation data + title: Microarray hybridisation data + EDAM_data:3128: + text: EDAM_data:3128 + description: Nucleic acid structure report + title: Nucleic acid structure report + EDAM_data:3134: + text: EDAM_data:3134 + description: Gene transcript report + title: Gene transcript report + EDAM_data:3148: + text: EDAM_data:3148 + description: Gene family report + title: Gene family report + EDAM_data:3153: + text: EDAM_data:3153 + description: Protein image + title: Protein image + EDAM_data:3181: + text: EDAM_data:3181 + description: Sequence assembly report + title: Sequence assembly report + EDAM_data:3210: + text: EDAM_data:3210 + description: Genome index + title: Genome index + EDAM_data:3236: + text: EDAM_data:3236 + description: Cytoband position + title: Cytoband position + EDAM_data:3238: + text: EDAM_data:3238 + description: Cell type ontology ID + title: Cell type ontology ID + EDAM_data:3241: + text: EDAM_data:3241 + description: Kinetic model + title: Kinetic model + EDAM_data:3264: + text: EDAM_data:3264 + description: COSMIC ID + title: COSMIC ID + EDAM_data:3265: + text: EDAM_data:3265 + description: HGMD ID + title: HGMD ID + EDAM_data:3266: + text: EDAM_data:3266 + description: Sequence assembly ID + title: Sequence assembly ID + EDAM_data:3270: + text: EDAM_data:3270 + description: Ensembl gene tree ID + title: Ensembl gene tree ID + EDAM_data:3271: + text: EDAM_data:3271 + description: Gene tree + title: Gene tree + EDAM_data:3272: + text: EDAM_data:3272 + description: Species tree + title: Species tree + EDAM_data:3273: + text: EDAM_data:3273 + description: Sample ID + title: Sample ID + EDAM_data:3274: + text: EDAM_data:3274 + description: MGI accession + title: MGI accession + EDAM_data:3275: + text: EDAM_data:3275 + description: Phenotype name + title: Phenotype name + EDAM_data:3354: + text: EDAM_data:3354 + description: Transition matrix + title: Transition matrix + EDAM_data:3355: + text: EDAM_data:3355 + description: Emission matrix + title: Emission matrix + EDAM_data:3358: + text: EDAM_data:3358 + description: Format identifier + title: Format identifier + EDAM_data:3424: + text: EDAM_data:3424 + description: Raw image + title: Raw image + EDAM_data:3425: + text: EDAM_data:3425 + description: Carbohydrate property + title: Carbohydrate property + EDAM_data:3442: + text: EDAM_data:3442 + description: MRI image + title: MRI image + EDAM_data:3449: + text: EDAM_data:3449 + description: Cell migration track image + title: Cell migration track image + EDAM_data:3451: + text: EDAM_data:3451 + description: Rate of association + title: Rate of association + EDAM_data:3479: + text: EDAM_data:3479 + description: Gene order + title: Gene order + EDAM_data:3483: + text: EDAM_data:3483 + description: Spectrum + title: Spectrum + EDAM_data:3488: + text: EDAM_data:3488 + description: NMR spectrum + title: NMR spectrum + EDAM_data:3492: + text: EDAM_data:3492 + description: Nucleic acid signature + title: Nucleic acid signature + EDAM_data:3494: + text: EDAM_data:3494 + description: DNA sequence + title: DNA sequence + EDAM_data:3495: + text: EDAM_data:3495 + description: RNA sequence + title: RNA sequence + EDAM_data:3498: + text: EDAM_data:3498 + description: Sequence variations + title: Sequence variations + EDAM_data:3505: + text: EDAM_data:3505 + description: Bibliography + title: Bibliography + EDAM_data:3509: + text: EDAM_data:3509 + description: Ontology mapping + title: Ontology mapping + EDAM_data:3546: + text: EDAM_data:3546 + description: Image metadata + title: Image metadata + EDAM_data:3558: + text: EDAM_data:3558 + description: Clinical trial report + title: Clinical trial report + EDAM_data:3567: + text: EDAM_data:3567 + description: Reference sample report + title: Reference sample report + EDAM_data:3568: + text: EDAM_data:3568 + description: Gene Expression Atlas Experiment ID + title: Gene Expression Atlas Experiment ID + EDAM_data:3667: + text: EDAM_data:3667 + description: Disease identifier + title: Disease identifier + EDAM_data:3668: + text: EDAM_data:3668 + description: Disease name + title: Disease name + EDAM_data:3669: + text: EDAM_data:3669 + description: Learning material + title: Learning material + EDAM_data:3670: + text: EDAM_data:3670 + description: Online course + title: Online course + EDAM_data:3671: + text: EDAM_data:3671 + description: Text + title: Text + EDAM_data:3707: + text: EDAM_data:3707 + description: Biodiversity data + title: Biodiversity data + EDAM_data:3716: + text: EDAM_data:3716 + description: Biosafety report + title: Biosafety report + EDAM_data:3717: + text: EDAM_data:3717 + description: Isolation report + title: Isolation report + EDAM_data:3718: + text: EDAM_data:3718 + description: Pathogenicity report + title: Pathogenicity report + EDAM_data:3719: + text: EDAM_data:3719 + description: Biosafety classification + title: Biosafety classification + EDAM_data:3720: + text: EDAM_data:3720 + description: Geographic location + title: Geographic location + EDAM_data:3721: + text: EDAM_data:3721 + description: Isolation source + title: Isolation source + EDAM_data:3722: + text: EDAM_data:3722 + description: Physiology parameter + title: Physiology parameter + EDAM_data:3723: + text: EDAM_data:3723 + description: Morphology parameter + title: Morphology parameter + EDAM_data:3724: + text: EDAM_data:3724 + description: Cultivation parameter + title: Cultivation parameter + EDAM_data:3732: + text: EDAM_data:3732 + description: Sequencing metadata name + title: Sequencing metadata name + EDAM_data:3733: + text: EDAM_data:3733 + description: Flow cell identifier + title: Flow cell identifier + EDAM_data:3734: + text: EDAM_data:3734 + description: Lane identifier + title: Lane identifier + EDAM_data:3735: + text: EDAM_data:3735 + description: Run number + title: Run number + EDAM_data:3736: + text: EDAM_data:3736 + description: Ecological data + title: Ecological data + EDAM_data:3737: + text: EDAM_data:3737 + description: Alpha diversity data + title: Alpha diversity data + EDAM_data:3738: + text: EDAM_data:3738 + description: Beta diversity data + title: Beta diversity data + EDAM_data:3739: + text: EDAM_data:3739 + description: Gamma diversity data + title: Gamma diversity data + EDAM_data:3743: + text: EDAM_data:3743 + description: Ordination plot + title: Ordination plot + EDAM_data:3753: + text: EDAM_data:3753 + description: Over-representation data + title: Over-representation data + EDAM_data:3754: + text: EDAM_data:3754 + description: GO-term enrichment data + title: GO-term enrichment data + EDAM_data:3756: + text: EDAM_data:3756 + description: Localisation score + title: Localisation score + EDAM_data:3757: + text: EDAM_data:3757 + description: Unimod ID + title: Unimod ID + EDAM_data:3759: + text: EDAM_data:3759 + description: ProteomeXchange ID + title: ProteomeXchange ID + EDAM_data:3768: + text: EDAM_data:3768 + description: Clustered expression profiles + title: Clustered expression profiles + EDAM_data:3769: + text: EDAM_data:3769 + description: BRENDA ontology concept ID + title: BRENDA ontology concept ID + EDAM_data:3779: + text: EDAM_data:3779 + description: Annotated text + title: Annotated text + EDAM_data:3786: + text: EDAM_data:3786 + description: Query script + title: Query script + EDAM_data:3805: + text: EDAM_data:3805 + description: 3D EM Map + title: 3D EM Map + EDAM_data:3806: + text: EDAM_data:3806 + description: 3D EM Mask + title: 3D EM Mask + EDAM_data:3807: + text: EDAM_data:3807 + description: EM Movie + title: EM Movie + EDAM_data:3808: + text: EDAM_data:3808 + description: EM Micrograph + title: EM Micrograph + EDAM_data:3842: + text: EDAM_data:3842 + description: Molecular simulation data + title: Molecular simulation data + EDAM_data:3856: + text: EDAM_data:3856 + description: RNA central ID + title: RNA central ID + EDAM_data:3861: + text: EDAM_data:3861 + description: Electronic health record + title: Electronic health record + EDAM_data:3869: + text: EDAM_data:3869 + description: Simulation + title: Simulation + EDAM_data:3870: + text: EDAM_data:3870 + description: Trajectory data + title: Trajectory data + EDAM_data:3871: + text: EDAM_data:3871 + description: Forcefield parameters + title: Forcefield parameters + EDAM_data:3872: + text: EDAM_data:3872 + description: Topology data + title: Topology data + EDAM_data:3905: + text: EDAM_data:3905 + description: Histogram + title: Histogram + EDAM_data:3914: + text: EDAM_data:3914 + description: Quality control report + title: Quality control report + EDAM_data:3917: + text: EDAM_data:3917 + description: Count matrix + title: Count matrix + EDAM_data:3924: + text: EDAM_data:3924 + description: DNA structure alignment + title: DNA structure alignment + EDAM_data:3932: + text: EDAM_data:3932 + description: Q-value + title: Q-value + EDAM_data:3949: + text: EDAM_data:3949 + description: Profile HMM + title: Profile HMM + EDAM_data:3952: + text: EDAM_data:3952 + description: Pathway ID (WikiPathways) + title: Pathway ID (WikiPathways) + EDAM_data:3953: + text: EDAM_data:3953 + description: Pathway overrepresentation data + title: Pathway overrepresentation data + EDAM_data:4022: + text: EDAM_data:4022 + description: ORCID Identifier + title: ORCID Identifier + EDAM_data:4040: + text: EDAM_data:4040 + description: Data management plan + title: Data management plan diff --git a/src/cam_expanded_enums/schema/EnumEDAMFormats.yaml b/src/cam_expanded_enums/schema/EnumEDAMFormats.yaml new file mode 100644 index 0000000..8f4436c --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumEDAMFormats.yaml @@ -0,0 +1,2513 @@ +id: https://includedcc.org/common-access-model/EnumEDAMFormats +name: EnumEDAMFormats +enums: + EnumEDAMFormats: + description: Data formats from the EDAM ontology. + reachable_from: + source_ontology: bioregistry:edam + source_nodes: + - edam:format_1915 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + EDAM_format:1196: + text: EDAM_format:1196 + description: SMILES + title: SMILES + EDAM_format:1197: + text: EDAM_format:1197 + description: InChI + title: InChI + EDAM_format:1198: + text: EDAM_format:1198 + description: mf + title: mf + EDAM_format:1199: + text: EDAM_format:1199 + description: InChIKey + title: InChIKey + EDAM_format:1200: + text: EDAM_format:1200 + description: smarts + title: smarts + EDAM_format:1206: + text: EDAM_format:1206 + description: unambiguous pure + title: unambiguous pure + EDAM_format:1207: + text: EDAM_format:1207 + description: nucleotide + title: nucleotide + EDAM_format:1208: + text: EDAM_format:1208 + description: protein + title: protein + EDAM_format:1209: + text: EDAM_format:1209 + description: consensus + title: consensus + EDAM_format:1210: + text: EDAM_format:1210 + description: pure nucleotide + title: pure nucleotide + EDAM_format:1211: + text: EDAM_format:1211 + description: unambiguous pure nucleotide + title: unambiguous pure nucleotide + EDAM_format:1212: + text: EDAM_format:1212 + description: dna + title: dna + EDAM_format:1213: + text: EDAM_format:1213 + description: rna + title: rna + EDAM_format:1214: + text: EDAM_format:1214 + description: unambiguous pure dna + title: unambiguous pure dna + EDAM_format:1215: + text: EDAM_format:1215 + description: pure dna + title: pure dna + EDAM_format:1216: + text: EDAM_format:1216 + description: unambiguous pure rna sequence + title: unambiguous pure rna sequence + EDAM_format:1217: + text: EDAM_format:1217 + description: pure rna + title: pure rna + EDAM_format:1218: + text: EDAM_format:1218 + description: unambiguous pure protein + title: unambiguous pure protein + EDAM_format:1219: + text: EDAM_format:1219 + description: pure protein + title: pure protein + EDAM_format:1248: + text: EDAM_format:1248 + description: EMBL feature location + title: EMBL feature location + EDAM_format:1295: + text: EDAM_format:1295 + description: quicktandem + title: quicktandem + EDAM_format:1296: + text: EDAM_format:1296 + description: Sanger inverted repeats + title: Sanger inverted repeats + EDAM_format:1297: + text: EDAM_format:1297 + description: EMBOSS repeat + title: EMBOSS repeat + EDAM_format:1316: + text: EDAM_format:1316 + description: est2genome format + title: est2genome format + EDAM_format:1318: + text: EDAM_format:1318 + description: restrict format + title: restrict format + EDAM_format:1319: + text: EDAM_format:1319 + description: restover format + title: restover format + EDAM_format:1320: + text: EDAM_format:1320 + description: REBASE restriction sites + title: REBASE restriction sites + EDAM_format:1332: + text: EDAM_format:1332 + description: FASTA search results format + title: FASTA search results format + EDAM_format:1333: + text: EDAM_format:1333 + description: BLAST results + title: BLAST results + EDAM_format:1334: + text: EDAM_format:1334 + description: mspcrunch + title: mspcrunch + EDAM_format:1335: + text: EDAM_format:1335 + description: Smith-Waterman format + title: Smith-Waterman format + EDAM_format:1336: + text: EDAM_format:1336 + description: dhf + title: dhf + EDAM_format:1337: + text: EDAM_format:1337 + description: lhf + title: lhf + EDAM_format:1341: + text: EDAM_format:1341 + description: InterPro hits format + title: InterPro hits format + EDAM_format:1342: + text: EDAM_format:1342 + description: InterPro protein view report format + title: InterPro protein view report format + EDAM_format:1343: + text: EDAM_format:1343 + description: InterPro match table format + title: InterPro match table format + EDAM_format:1349: + text: EDAM_format:1349 + description: HMMER Dirichlet prior + title: HMMER Dirichlet prior + EDAM_format:1350: + text: EDAM_format:1350 + description: MEME Dirichlet prior + title: MEME Dirichlet prior + EDAM_format:1351: + text: EDAM_format:1351 + description: HMMER emission and transition + title: HMMER emission and transition + EDAM_format:1356: + text: EDAM_format:1356 + description: prosite-pattern + title: prosite-pattern + EDAM_format:1357: + text: EDAM_format:1357 + description: EMBOSS sequence pattern + title: EMBOSS sequence pattern + EDAM_format:1360: + text: EDAM_format:1360 + description: meme-motif + title: meme-motif + EDAM_format:1366: + text: EDAM_format:1366 + description: prosite-profile + title: prosite-profile + EDAM_format:1367: + text: EDAM_format:1367 + description: JASPAR format + title: JASPAR format + EDAM_format:1369: + text: EDAM_format:1369 + description: MEME background Markov model + title: MEME background Markov model + EDAM_format:1370: + text: EDAM_format:1370 + description: HMMER format + title: HMMER format + EDAM_format:1391: + text: EDAM_format:1391 + description: HMMER-aln + title: HMMER-aln + EDAM_format:1392: + text: EDAM_format:1392 + description: DIALIGN format + title: DIALIGN format + EDAM_format:1393: + text: EDAM_format:1393 + description: daf + title: daf + EDAM_format:1419: + text: EDAM_format:1419 + description: Sequence-MEME profile alignment + title: Sequence-MEME profile alignment + EDAM_format:1421: + text: EDAM_format:1421 + description: HMMER profile alignment (sequences versus HMMs) + title: HMMER profile alignment (sequences versus HMMs) + EDAM_format:1422: + text: EDAM_format:1422 + description: HMMER profile alignment (HMM versus sequences) + title: HMMER profile alignment (HMM versus sequences) + EDAM_format:1423: + text: EDAM_format:1423 + description: Phylip distance matrix + title: Phylip distance matrix + EDAM_format:1424: + text: EDAM_format:1424 + description: ClustalW dendrogram + title: ClustalW dendrogram + EDAM_format:1425: + text: EDAM_format:1425 + description: Phylip tree raw + title: Phylip tree raw + EDAM_format:1430: + text: EDAM_format:1430 + description: Phylip continuous quantitative characters + title: Phylip continuous quantitative characters + EDAM_format:1432: + text: EDAM_format:1432 + description: Phylip character frequencies format + title: Phylip character frequencies format + EDAM_format:1433: + text: EDAM_format:1433 + description: Phylip discrete states format + title: Phylip discrete states format + EDAM_format:1434: + text: EDAM_format:1434 + description: Phylip cliques format + title: Phylip cliques format + EDAM_format:1435: + text: EDAM_format:1435 + description: Phylip tree format + title: Phylip tree format + EDAM_format:1436: + text: EDAM_format:1436 + description: TreeBASE format + title: TreeBASE format + EDAM_format:1437: + text: EDAM_format:1437 + description: TreeFam format + title: TreeFam format + EDAM_format:1445: + text: EDAM_format:1445 + description: Phylip tree distance format + title: Phylip tree distance format + EDAM_format:1454: + text: EDAM_format:1454 + description: dssp + title: dssp + EDAM_format:1455: + text: EDAM_format:1455 + description: hssp + title: hssp + EDAM_format:1457: + text: EDAM_format:1457 + description: Dot-bracket format + title: Dot-bracket format + EDAM_format:1458: + text: EDAM_format:1458 + description: Vienna local RNA secondary structure format + title: Vienna local RNA secondary structure format + EDAM_format:1475: + text: EDAM_format:1475 + description: PDB database entry format + title: PDB database entry format + EDAM_format:1476: + text: EDAM_format:1476 + description: PDB + title: PDB + EDAM_format:1477: + text: EDAM_format:1477 + description: mmCIF + title: mmCIF + EDAM_format:1478: + text: EDAM_format:1478 + description: PDBML + title: PDBML + EDAM_format:1504: + text: EDAM_format:1504 + description: aaindex + title: aaindex + EDAM_format:1551: + text: EDAM_format:1551 + description: Pcons report format + title: Pcons report format + EDAM_format:1552: + text: EDAM_format:1552 + description: ProQ report format + title: ProQ report format + EDAM_format:1582: + text: EDAM_format:1582 + description: findkm + title: findkm + EDAM_format:1627: + text: EDAM_format:1627 + description: Primer3 primer + title: Primer3 primer + EDAM_format:1628: + text: EDAM_format:1628 + description: ABI + title: ABI + EDAM_format:1629: + text: EDAM_format:1629 + description: mira + title: mira + EDAM_format:1630: + text: EDAM_format:1630 + description: CAF + title: CAF + EDAM_format:1631: + text: EDAM_format:1631 + description: EXP + title: EXP + EDAM_format:1632: + text: EDAM_format:1632 + description: SCF + title: SCF + EDAM_format:1633: + text: EDAM_format:1633 + description: PHD + title: PHD + EDAM_format:1637: + text: EDAM_format:1637 + description: dat + title: dat + EDAM_format:1638: + text: EDAM_format:1638 + description: cel + title: cel + EDAM_format:1639: + text: EDAM_format:1639 + description: affymetrix + title: affymetrix + EDAM_format:1641: + text: EDAM_format:1641 + description: affymetrix-exp + title: affymetrix-exp + EDAM_format:1644: + text: EDAM_format:1644 + description: CHP + title: CHP + EDAM_format:1665: + text: EDAM_format:1665 + description: Taverna workflow format + title: Taverna workflow format + EDAM_format:1705: + text: EDAM_format:1705 + description: HET group dictionary entry format + title: HET group dictionary entry format + EDAM_format:1734: + text: EDAM_format:1734 + description: PubMed citation + title: PubMed citation + EDAM_format:1735: + text: EDAM_format:1735 + description: Medline Display Format + title: Medline Display Format + EDAM_format:1736: + text: EDAM_format:1736 + description: CiteXplore-core + title: CiteXplore-core + EDAM_format:1737: + text: EDAM_format:1737 + description: CiteXplore-all + title: CiteXplore-all + EDAM_format:1739: + text: EDAM_format:1739 + description: pmc + title: pmc + EDAM_format:1740: + text: EDAM_format:1740 + description: iHOP format + title: iHOP format + EDAM_format:1741: + text: EDAM_format:1741 + description: OSCAR format + title: OSCAR format + EDAM_format:1861: + text: EDAM_format:1861 + description: PlasMapper TextMap + title: PlasMapper TextMap + EDAM_format:1910: + text: EDAM_format:1910 + description: newick + title: newick + EDAM_format:1911: + text: EDAM_format:1911 + description: TreeCon format + title: TreeCon format + EDAM_format:1912: + text: EDAM_format:1912 + description: Nexus format + title: Nexus format + EDAM_format:1919: + text: EDAM_format:1919 + description: Sequence record format + title: Sequence record format + EDAM_format:1920: + text: EDAM_format:1920 + description: Sequence feature annotation format + title: Sequence feature annotation format + EDAM_format:1921: + text: EDAM_format:1921 + description: Alignment format + title: Alignment format + EDAM_format:1923: + text: EDAM_format:1923 + description: acedb + title: acedb + EDAM_format:1925: + text: EDAM_format:1925 + description: codata + title: codata + EDAM_format:1926: + text: EDAM_format:1926 + description: dbid + title: dbid + EDAM_format:1927: + text: EDAM_format:1927 + description: EMBL format + title: EMBL format + EDAM_format:1928: + text: EDAM_format:1928 + description: Staden experiment format + title: Staden experiment format + EDAM_format:1929: + text: EDAM_format:1929 + description: FASTA + title: FASTA + EDAM_format:1930: + text: EDAM_format:1930 + description: FASTQ + title: FASTQ + EDAM_format:1931: + text: EDAM_format:1931 + description: FASTQ-illumina + title: FASTQ-illumina + EDAM_format:1932: + text: EDAM_format:1932 + description: FASTQ-sanger + title: FASTQ-sanger + EDAM_format:1933: + text: EDAM_format:1933 + description: FASTQ-solexa + title: FASTQ-solexa + EDAM_format:1934: + text: EDAM_format:1934 + description: fitch program + title: fitch program + EDAM_format:1935: + text: EDAM_format:1935 + description: GCG + title: GCG + EDAM_format:1936: + text: EDAM_format:1936 + description: GenBank format + title: GenBank format + EDAM_format:1937: + text: EDAM_format:1937 + description: genpept + title: genpept + EDAM_format:1938: + text: EDAM_format:1938 + description: GFF2-seq + title: GFF2-seq + EDAM_format:1939: + text: EDAM_format:1939 + description: GFF3-seq + title: GFF3-seq + EDAM_format:1940: + text: EDAM_format:1940 + description: giFASTA format + title: giFASTA format + EDAM_format:1941: + text: EDAM_format:1941 + description: hennig86 + title: hennig86 + EDAM_format:1942: + text: EDAM_format:1942 + description: ig + title: ig + EDAM_format:1943: + text: EDAM_format:1943 + description: igstrict + title: igstrict + EDAM_format:1944: + text: EDAM_format:1944 + description: jackknifer + title: jackknifer + EDAM_format:1945: + text: EDAM_format:1945 + description: mase format + title: mase format + EDAM_format:1946: + text: EDAM_format:1946 + description: mega-seq + title: mega-seq + EDAM_format:1947: + text: EDAM_format:1947 + description: GCG MSF + title: GCG MSF + EDAM_format:1948: + text: EDAM_format:1948 + description: nbrf/pir + title: nbrf/pir + EDAM_format:1949: + text: EDAM_format:1949 + description: nexus-seq + title: nexus-seq + EDAM_format:1950: + text: EDAM_format:1950 + description: pdbatom + title: pdbatom + EDAM_format:1951: + text: EDAM_format:1951 + description: pdbatomnuc + title: pdbatomnuc + EDAM_format:1952: + text: EDAM_format:1952 + description: pdbseqresnuc + title: pdbseqresnuc + EDAM_format:1953: + text: EDAM_format:1953 + description: pdbseqres + title: pdbseqres + EDAM_format:1954: + text: EDAM_format:1954 + description: Pearson format + title: Pearson format + EDAM_format:1957: + text: EDAM_format:1957 + description: raw + title: raw + EDAM_format:1958: + text: EDAM_format:1958 + description: refseqp + title: refseqp + EDAM_format:1960: + text: EDAM_format:1960 + description: Staden format + title: Staden format + EDAM_format:1961: + text: EDAM_format:1961 + description: Stockholm format + title: Stockholm format + EDAM_format:1962: + text: EDAM_format:1962 + description: strider format + title: strider format + EDAM_format:1963: + text: EDAM_format:1963 + description: UniProtKB format + title: UniProtKB format + EDAM_format:1964: + text: EDAM_format:1964 + description: plain text format (unformatted) + title: plain text format (unformatted) + EDAM_format:1966: + text: EDAM_format:1966 + description: ASN.1 sequence format + title: ASN.1 sequence format + EDAM_format:1967: + text: EDAM_format:1967 + description: DAS format + title: DAS format + EDAM_format:1968: + text: EDAM_format:1968 + description: dasdna + title: dasdna + EDAM_format:1969: + text: EDAM_format:1969 + description: debug-seq + title: debug-seq + EDAM_format:1970: + text: EDAM_format:1970 + description: jackknifernon + title: jackknifernon + EDAM_format:1972: + text: EDAM_format:1972 + description: NCBI format + title: NCBI format + EDAM_format:1973: + text: EDAM_format:1973 + description: nexusnon + title: nexusnon + EDAM_format:1974: + text: EDAM_format:1974 + description: GFF2 + title: GFF2 + EDAM_format:1975: + text: EDAM_format:1975 + description: GFF3 + title: GFF3 + EDAM_format:1978: + text: EDAM_format:1978 + description: DASGFF + title: DASGFF + EDAM_format:1979: + text: EDAM_format:1979 + description: debug-feat + title: debug-feat + EDAM_format:1982: + text: EDAM_format:1982 + description: ClustalW format + title: ClustalW format + EDAM_format:1983: + text: EDAM_format:1983 + description: debug + title: debug + EDAM_format:1984: + text: EDAM_format:1984 + description: FASTA-aln + title: FASTA-aln + EDAM_format:1985: + text: EDAM_format:1985 + description: markx0 + title: markx0 + EDAM_format:1986: + text: EDAM_format:1986 + description: markx1 + title: markx1 + EDAM_format:1987: + text: EDAM_format:1987 + description: markx10 + title: markx10 + EDAM_format:1988: + text: EDAM_format:1988 + description: markx2 + title: markx2 + EDAM_format:1989: + text: EDAM_format:1989 + description: markx3 + title: markx3 + EDAM_format:1990: + text: EDAM_format:1990 + description: match + title: match + EDAM_format:1991: + text: EDAM_format:1991 + description: mega + title: mega + EDAM_format:1992: + text: EDAM_format:1992 + description: meganon + title: meganon + EDAM_format:1996: + text: EDAM_format:1996 + description: pair + title: pair + EDAM_format:1997: + text: EDAM_format:1997 + description: PHYLIP format + title: PHYLIP format + EDAM_format:1998: + text: EDAM_format:1998 + description: PHYLIP sequential + title: PHYLIP sequential + EDAM_format:1999: + text: EDAM_format:1999 + description: scores format + title: scores format + EDAM_format:2000: + text: EDAM_format:2000 + description: selex + title: selex + EDAM_format:2001: + text: EDAM_format:2001 + description: EMBOSS simple format + title: EMBOSS simple format + EDAM_format:2002: + text: EDAM_format:2002 + description: srs format + title: srs format + EDAM_format:2003: + text: EDAM_format:2003 + description: srspair + title: srspair + EDAM_format:2004: + text: EDAM_format:2004 + description: T-Coffee format + title: T-Coffee format + EDAM_format:2005: + text: EDAM_format:2005 + description: TreeCon-seq + title: TreeCon-seq + EDAM_format:2006: + text: EDAM_format:2006 + description: Phylogenetic tree format + title: Phylogenetic tree format + EDAM_format:2013: + text: EDAM_format:2013 + description: Biological pathway or network format + title: Biological pathway or network format + EDAM_format:2014: + text: EDAM_format:2014 + description: Sequence-profile alignment format + title: Sequence-profile alignment format + EDAM_format:2017: + text: EDAM_format:2017 + description: Amino acid index format + title: Amino acid index format + EDAM_format:2020: + text: EDAM_format:2020 + description: Article format + title: Article format + EDAM_format:2021: + text: EDAM_format:2021 + description: Text mining report format + title: Text mining report format + EDAM_format:2027: + text: EDAM_format:2027 + description: Enzyme kinetics report format + title: Enzyme kinetics report format + EDAM_format:2030: + text: EDAM_format:2030 + description: Chemical data format + title: Chemical data format + EDAM_format:2031: + text: EDAM_format:2031 + description: Gene annotation format + title: Gene annotation format + EDAM_format:2032: + text: EDAM_format:2032 + description: Workflow format + title: Workflow format + EDAM_format:2033: + text: EDAM_format:2033 + description: Tertiary structure format + title: Tertiary structure format + EDAM_format:2035: + text: EDAM_format:2035 + description: Chemical formula format + title: Chemical formula format + EDAM_format:2036: + text: EDAM_format:2036 + description: Phylogenetic character data format + title: Phylogenetic character data format + EDAM_format:2037: + text: EDAM_format:2037 + description: Phylogenetic continuous quantitative character format + title: Phylogenetic continuous quantitative character format + EDAM_format:2038: + text: EDAM_format:2038 + description: Phylogenetic discrete states format + title: Phylogenetic discrete states format + EDAM_format:2039: + text: EDAM_format:2039 + description: Phylogenetic tree report (cliques) format + title: Phylogenetic tree report (cliques) format + EDAM_format:2040: + text: EDAM_format:2040 + description: Phylogenetic tree report (invariants) format + title: Phylogenetic tree report (invariants) format + EDAM_format:2049: + text: EDAM_format:2049 + description: Phylogenetic tree report (tree distances) format + title: Phylogenetic tree report (tree distances) format + EDAM_format:2052: + text: EDAM_format:2052 + description: Protein family report format + title: Protein family report format + EDAM_format:2054: + text: EDAM_format:2054 + description: Protein interaction format + title: Protein interaction format + EDAM_format:2055: + text: EDAM_format:2055 + description: Sequence assembly format + title: Sequence assembly format + EDAM_format:2056: + text: EDAM_format:2056 + description: Microarray experiment data format + title: Microarray experiment data format + EDAM_format:2057: + text: EDAM_format:2057 + description: Sequence trace format + title: Sequence trace format + EDAM_format:2058: + text: EDAM_format:2058 + description: Gene expression report format + title: Gene expression report format + EDAM_format:2060: + text: EDAM_format:2060 + description: Map format + title: Map format + EDAM_format:2061: + text: EDAM_format:2061 + description: Nucleic acid features (primers) format + title: Nucleic acid features (primers) format + EDAM_format:2062: + text: EDAM_format:2062 + description: Protein report format + title: Protein report format + EDAM_format:2064: + text: EDAM_format:2064 + description: 3D-1D scoring matrix format + title: 3D-1D scoring matrix format + EDAM_format:2065: + text: EDAM_format:2065 + description: Protein structure report (quality evaluation) format + title: Protein structure report (quality evaluation) format + EDAM_format:2066: + text: EDAM_format:2066 + description: Database hits (sequence) format + title: Database hits (sequence) format + EDAM_format:2067: + text: EDAM_format:2067 + description: Sequence distance matrix format + title: Sequence distance matrix format + EDAM_format:2068: + text: EDAM_format:2068 + description: Sequence motif format + title: Sequence motif format + EDAM_format:2069: + text: EDAM_format:2069 + description: Sequence profile format + title: Sequence profile format + EDAM_format:2072: + text: EDAM_format:2072 + description: Hidden Markov model format + title: Hidden Markov model format + EDAM_format:2074: + text: EDAM_format:2074 + description: Dirichlet distribution format + title: Dirichlet distribution format + EDAM_format:2075: + text: EDAM_format:2075 + description: HMM emission and transition counts format + title: HMM emission and transition counts format + EDAM_format:2076: + text: EDAM_format:2076 + description: RNA secondary structure format + title: RNA secondary structure format + EDAM_format:2077: + text: EDAM_format:2077 + description: Protein secondary structure format + title: Protein secondary structure format + EDAM_format:2078: + text: EDAM_format:2078 + description: Sequence range format + title: Sequence range format + EDAM_format:2094: + text: EDAM_format:2094 + description: pure + title: pure + EDAM_format:2095: + text: EDAM_format:2095 + description: unpure + title: unpure + EDAM_format:2096: + text: EDAM_format:2096 + description: unambiguous sequence + title: unambiguous sequence + EDAM_format:2097: + text: EDAM_format:2097 + description: ambiguous + title: ambiguous + EDAM_format:2155: + text: EDAM_format:2155 + description: Sequence features (repeats) format + title: Sequence features (repeats) format + EDAM_format:2158: + text: EDAM_format:2158 + description: Nucleic acid features (restriction sites) format + title: Nucleic acid features (restriction sites) format + EDAM_format:2170: + text: EDAM_format:2170 + description: Sequence cluster format + title: Sequence cluster format + EDAM_format:2171: + text: EDAM_format:2171 + description: Sequence cluster format (protein) + title: Sequence cluster format (protein) + EDAM_format:2172: + text: EDAM_format:2172 + description: Sequence cluster format (nucleic acid) + title: Sequence cluster format (nucleic acid) + EDAM_format:2181: + text: EDAM_format:2181 + description: EMBL-like (text) + title: EMBL-like (text) + EDAM_format:2182: + text: EDAM_format:2182 + description: FASTQ-like format (text) + title: FASTQ-like format (text) + EDAM_format:2183: + text: EDAM_format:2183 + description: EMBLXML + title: EMBLXML + EDAM_format:2184: + text: EDAM_format:2184 + description: cdsxml + title: cdsxml + EDAM_format:2185: + text: EDAM_format:2185 + description: INSDSeq + title: INSDSeq + EDAM_format:2186: + text: EDAM_format:2186 + description: geneseq + title: geneseq + EDAM_format:2187: + text: EDAM_format:2187 + description: UniProt-like (text) + title: UniProt-like (text) + EDAM_format:2194: + text: EDAM_format:2194 + description: medline + title: medline + EDAM_format:2195: + text: EDAM_format:2195 + description: Ontology format + title: Ontology format + EDAM_format:2196: + text: EDAM_format:2196 + description: OBO format + title: OBO format + EDAM_format:2197: + text: EDAM_format:2197 + description: OWL format + title: OWL format + EDAM_format:2200: + text: EDAM_format:2200 + description: FASTA-like (text) + title: FASTA-like (text) + EDAM_format:2204: + text: EDAM_format:2204 + description: EMBL format (XML) + title: EMBL format (XML) + EDAM_format:2205: + text: EDAM_format:2205 + description: GenBank-like format (text) + title: GenBank-like format (text) + EDAM_format:2206: + text: EDAM_format:2206 + description: Sequence feature table format (text) + title: Sequence feature table format (text) + EDAM_format:2304: + text: EDAM_format:2304 + description: STRING entry format (XML) + title: STRING entry format (XML) + EDAM_format:2305: + text: EDAM_format:2305 + description: GFF + title: GFF + EDAM_format:2306: + text: EDAM_format:2306 + description: GTF + title: GTF + EDAM_format:2310: + text: EDAM_format:2310 + description: FASTA-HTML + title: FASTA-HTML + EDAM_format:2311: + text: EDAM_format:2311 + description: EMBL-HTML + title: EMBL-HTML + EDAM_format:2330: + text: EDAM_format:2330 + description: Textual format + title: Textual format + EDAM_format:2331: + text: EDAM_format:2331 + description: HTML + title: HTML + EDAM_format:2332: + text: EDAM_format:2332 + description: XML + title: XML + EDAM_format:2333: + text: EDAM_format:2333 + description: Binary format + title: Binary format + EDAM_format:2350: + text: EDAM_format:2350 + description: Format (by type of data) + title: Format (by type of data) + EDAM_format:2352: + text: EDAM_format:2352 + description: BioXSD (XML) + title: BioXSD (XML) + EDAM_format:2376: + text: EDAM_format:2376 + description: RDF format + title: RDF format + EDAM_format:2532: + text: EDAM_format:2532 + description: GenBank-HTML + title: GenBank-HTML + EDAM_format:2543: + text: EDAM_format:2543 + description: EMBL-like format + title: EMBL-like format + EDAM_format:2545: + text: EDAM_format:2545 + description: FASTQ-like format + title: FASTQ-like format + EDAM_format:2546: + text: EDAM_format:2546 + description: FASTA-like + title: FASTA-like + EDAM_format:2547: + text: EDAM_format:2547 + description: uniprotkb-like format + title: uniprotkb-like format + EDAM_format:2548: + text: EDAM_format:2548 + description: Sequence feature table format + title: Sequence feature table format + EDAM_format:2549: + text: EDAM_format:2549 + description: OBO + title: OBO + EDAM_format:2550: + text: EDAM_format:2550 + description: OBO-XML + title: OBO-XML + EDAM_format:2551: + text: EDAM_format:2551 + description: Sequence record format (text) + title: Sequence record format (text) + EDAM_format:2552: + text: EDAM_format:2552 + description: Sequence record format (XML) + title: Sequence record format (XML) + EDAM_format:2553: + text: EDAM_format:2553 + description: Sequence feature table format (XML) + title: Sequence feature table format (XML) + EDAM_format:2554: + text: EDAM_format:2554 + description: Alignment format (text) + title: Alignment format (text) + EDAM_format:2555: + text: EDAM_format:2555 + description: Alignment format (XML) + title: Alignment format (XML) + EDAM_format:2556: + text: EDAM_format:2556 + description: Phylogenetic tree format (text) + title: Phylogenetic tree format (text) + EDAM_format:2557: + text: EDAM_format:2557 + description: Phylogenetic tree format (XML) + title: Phylogenetic tree format (XML) + EDAM_format:2558: + text: EDAM_format:2558 + description: EMBL-like (XML) + title: EMBL-like (XML) + EDAM_format:2559: + text: EDAM_format:2559 + description: GenBank-like format + title: GenBank-like format + EDAM_format:2561: + text: EDAM_format:2561 + description: Sequence assembly format (text) + title: Sequence assembly format (text) + EDAM_format:2566: + text: EDAM_format:2566 + description: completely unambiguous + title: completely unambiguous + EDAM_format:2567: + text: EDAM_format:2567 + description: completely unambiguous pure + title: completely unambiguous pure + EDAM_format:2568: + text: EDAM_format:2568 + description: completely unambiguous pure nucleotide + title: completely unambiguous pure nucleotide + EDAM_format:2569: + text: EDAM_format:2569 + description: completely unambiguous pure dna + title: completely unambiguous pure dna + EDAM_format:2570: + text: EDAM_format:2570 + description: completely unambiguous pure rna sequence + title: completely unambiguous pure rna sequence + EDAM_format:2571: + text: EDAM_format:2571 + description: Raw sequence format + title: Raw sequence format + EDAM_format:2572: + text: EDAM_format:2572 + description: BAM + title: BAM + EDAM_format:2573: + text: EDAM_format:2573 + description: SAM + title: SAM + EDAM_format:2585: + text: EDAM_format:2585 + description: SBML + title: SBML + EDAM_format:2607: + text: EDAM_format:2607 + description: completely unambiguous pure protein + title: completely unambiguous pure protein + EDAM_format:2848: + text: EDAM_format:2848 + description: Bibliographic reference format + title: Bibliographic reference format + EDAM_format:2919: + text: EDAM_format:2919 + description: Sequence annotation track format + title: Sequence annotation track format + EDAM_format:2920: + text: EDAM_format:2920 + description: Alignment format (pair only) + title: Alignment format (pair only) + EDAM_format:2921: + text: EDAM_format:2921 + description: Sequence variation annotation format + title: Sequence variation annotation format + EDAM_format:2922: + text: EDAM_format:2922 + description: markx0 variant + title: markx0 variant + EDAM_format:2923: + text: EDAM_format:2923 + description: mega variant + title: mega variant + EDAM_format:2924: + text: EDAM_format:2924 + description: Phylip format variant + title: Phylip format variant + EDAM_format:3000: + text: EDAM_format:3000 + description: AB1 + title: AB1 + EDAM_format:3001: + text: EDAM_format:3001 + description: ACE + title: ACE + EDAM_format:3003: + text: EDAM_format:3003 + description: BED + title: BED + EDAM_format:3004: + text: EDAM_format:3004 + description: bigBed + title: bigBed + EDAM_format:3005: + text: EDAM_format:3005 + description: WIG + title: WIG + EDAM_format:3006: + text: EDAM_format:3006 + description: bigWig + title: bigWig + EDAM_format:3007: + text: EDAM_format:3007 + description: PSL + title: PSL + EDAM_format:3008: + text: EDAM_format:3008 + description: MAF + title: MAF + EDAM_format:3009: + text: EDAM_format:3009 + description: 2bit + title: 2bit + EDAM_format:3010: + text: EDAM_format:3010 + description: .nib + title: .nib + EDAM_format:3011: + text: EDAM_format:3011 + description: genePred + title: genePred + EDAM_format:3012: + text: EDAM_format:3012 + description: pgSnp + title: pgSnp + EDAM_format:3013: + text: EDAM_format:3013 + description: axt + title: axt + EDAM_format:3014: + text: EDAM_format:3014 + description: LAV + title: LAV + EDAM_format:3015: + text: EDAM_format:3015 + description: Pileup + title: Pileup + EDAM_format:3016: + text: EDAM_format:3016 + description: VCF + title: VCF + EDAM_format:3017: + text: EDAM_format:3017 + description: SRF + title: SRF + EDAM_format:3018: + text: EDAM_format:3018 + description: ZTR + title: ZTR + EDAM_format:3019: + text: EDAM_format:3019 + description: GVF + title: GVF + EDAM_format:3020: + text: EDAM_format:3020 + description: BCF + title: BCF + EDAM_format:3033: + text: EDAM_format:3033 + description: Matrix format + title: Matrix format + EDAM_format:3097: + text: EDAM_format:3097 + description: Protein domain classification format + title: Protein domain classification format + EDAM_format:3098: + text: EDAM_format:3098 + description: Raw SCOP domain classification format + title: Raw SCOP domain classification format + EDAM_format:3099: + text: EDAM_format:3099 + description: Raw CATH domain classification format + title: Raw CATH domain classification format + EDAM_format:3100: + text: EDAM_format:3100 + description: CATH domain report format + title: CATH domain report format + EDAM_format:3155: + text: EDAM_format:3155 + description: SBRML + title: SBRML + EDAM_format:3156: + text: EDAM_format:3156 + description: BioPAX + title: BioPAX + EDAM_format:3157: + text: EDAM_format:3157 + description: EBI Application Result XML + title: EBI Application Result XML + EDAM_format:3158: + text: EDAM_format:3158 + description: PSI MI XML (MIF) + title: PSI MI XML (MIF) + EDAM_format:3159: + text: EDAM_format:3159 + description: phyloXML + title: phyloXML + EDAM_format:3160: + text: EDAM_format:3160 + description: NeXML + title: NeXML + EDAM_format:3161: + text: EDAM_format:3161 + description: MAGE-ML + title: MAGE-ML + EDAM_format:3162: + text: EDAM_format:3162 + description: MAGE-TAB + title: MAGE-TAB + EDAM_format:3163: + text: EDAM_format:3163 + description: GCDML + title: GCDML + EDAM_format:3164: + text: EDAM_format:3164 + description: GTrack + title: GTrack + EDAM_format:3166: + text: EDAM_format:3166 + description: Biological pathway or network report format + title: Biological pathway or network report format + EDAM_format:3167: + text: EDAM_format:3167 + description: Experiment annotation format + title: Experiment annotation format + EDAM_format:3235: + text: EDAM_format:3235 + description: Cytoband format + title: Cytoband format + EDAM_format:3239: + text: EDAM_format:3239 + description: CopasiML + title: CopasiML + EDAM_format:3240: + text: EDAM_format:3240 + description: CellML + title: CellML + EDAM_format:3242: + text: EDAM_format:3242 + description: PSI MI TAB (MITAB) + title: PSI MI TAB (MITAB) + EDAM_format:3243: + text: EDAM_format:3243 + description: PSI-PAR + title: PSI-PAR + EDAM_format:3244: + text: EDAM_format:3244 + description: mzML + title: mzML + EDAM_format:3245: + text: EDAM_format:3245 + description: Mass spectrometry data format + title: Mass spectrometry data format + EDAM_format:3246: + text: EDAM_format:3246 + description: TraML + title: TraML + EDAM_format:3247: + text: EDAM_format:3247 + description: mzIdentML + title: mzIdentML + EDAM_format:3248: + text: EDAM_format:3248 + description: mzQuantML + title: mzQuantML + EDAM_format:3249: + text: EDAM_format:3249 + description: GelML + title: GelML + EDAM_format:3250: + text: EDAM_format:3250 + description: spML + title: spML + EDAM_format:3252: + text: EDAM_format:3252 + description: OWL Functional Syntax + title: OWL Functional Syntax + EDAM_format:3253: + text: EDAM_format:3253 + description: Manchester OWL Syntax + title: Manchester OWL Syntax + EDAM_format:3254: + text: EDAM_format:3254 + description: KRSS2 Syntax + title: KRSS2 Syntax + EDAM_format:3255: + text: EDAM_format:3255 + description: Turtle + title: Turtle + EDAM_format:3256: + text: EDAM_format:3256 + description: N-Triples + title: N-Triples + EDAM_format:3257: + text: EDAM_format:3257 + description: Notation3 + title: Notation3 + EDAM_format:3261: + text: EDAM_format:3261 + description: RDF/XML + title: RDF/XML + EDAM_format:3262: + text: EDAM_format:3262 + description: OWL/XML + title: OWL/XML + EDAM_format:3281: + text: EDAM_format:3281 + description: A2M + title: A2M + EDAM_format:3284: + text: EDAM_format:3284 + description: SFF + title: SFF + EDAM_format:3285: + text: EDAM_format:3285 + description: MAP + title: MAP + EDAM_format:3286: + text: EDAM_format:3286 + description: PED + title: PED + EDAM_format:3287: + text: EDAM_format:3287 + description: Individual genetic data format + title: Individual genetic data format + EDAM_format:3288: + text: EDAM_format:3288 + description: PED/MAP + title: PED/MAP + EDAM_format:3309: + text: EDAM_format:3309 + description: CT + title: CT + EDAM_format:3310: + text: EDAM_format:3310 + description: SS + title: SS + EDAM_format:3311: + text: EDAM_format:3311 + description: RNAML + title: RNAML + EDAM_format:3312: + text: EDAM_format:3312 + description: GDE + title: GDE + EDAM_format:3313: + text: EDAM_format:3313 + description: BLC + title: BLC + EDAM_format:3326: + text: EDAM_format:3326 + description: Data index format + title: Data index format + EDAM_format:3327: + text: EDAM_format:3327 + description: BAI + title: BAI + EDAM_format:3328: + text: EDAM_format:3328 + description: HMMER2 + title: HMMER2 + EDAM_format:3329: + text: EDAM_format:3329 + description: HMMER3 + title: HMMER3 + EDAM_format:3330: + text: EDAM_format:3330 + description: PO + title: PO + EDAM_format:3331: + text: EDAM_format:3331 + description: BLAST XML results format + title: BLAST XML results format + EDAM_format:3462: + text: EDAM_format:3462 + description: CRAM + title: CRAM + EDAM_format:3464: + text: EDAM_format:3464 + description: JSON + title: JSON + EDAM_format:3466: + text: EDAM_format:3466 + description: EPS + title: EPS + EDAM_format:3467: + text: EDAM_format:3467 + description: GIF + title: GIF + EDAM_format:3468: + text: EDAM_format:3468 + description: xls + title: xls + EDAM_format:3475: + text: EDAM_format:3475 + description: TSV + title: TSV + EDAM_format:3477: + text: EDAM_format:3477 + description: Cytoscape input file format + title: Cytoscape input file format + EDAM_format:3484: + text: EDAM_format:3484 + description: ebwt + title: ebwt + EDAM_format:3485: + text: EDAM_format:3485 + description: RSF + title: RSF + EDAM_format:3486: + text: EDAM_format:3486 + description: GCG format variant + title: GCG format variant + EDAM_format:3487: + text: EDAM_format:3487 + description: BSML + title: BSML + EDAM_format:3491: + text: EDAM_format:3491 + description: ebwtl + title: ebwtl + EDAM_format:3499: + text: EDAM_format:3499 + description: Ensembl variation file format + title: Ensembl variation file format + EDAM_format:3506: + text: EDAM_format:3506 + description: docx + title: docx + EDAM_format:3507: + text: EDAM_format:3507 + description: Document format + title: Document format + EDAM_format:3508: + text: EDAM_format:3508 + description: PDF + title: PDF + EDAM_format:3547: + text: EDAM_format:3547 + description: Image format + title: Image format + EDAM_format:3548: + text: EDAM_format:3548 + description: DICOM format + title: DICOM format + EDAM_format:3549: + text: EDAM_format:3549 + description: nii + title: nii + EDAM_format:3550: + text: EDAM_format:3550 + description: mhd + title: mhd + EDAM_format:3551: + text: EDAM_format:3551 + description: nrrd + title: nrrd + EDAM_format:3554: + text: EDAM_format:3554 + description: R file format + title: R file format + EDAM_format:3555: + text: EDAM_format:3555 + description: SPSS + title: SPSS + EDAM_format:3556: + text: EDAM_format:3556 + description: MHTML + title: MHTML + EDAM_format:3578: + text: EDAM_format:3578 + description: IDAT + title: IDAT + EDAM_format:3579: + text: EDAM_format:3579 + description: JPG + title: JPG + EDAM_format:3580: + text: EDAM_format:3580 + description: rcc + title: rcc + EDAM_format:3581: + text: EDAM_format:3581 + description: arff + title: arff + EDAM_format:3582: + text: EDAM_format:3582 + description: afg + title: afg + EDAM_format:3583: + text: EDAM_format:3583 + description: bedgraph + title: bedgraph + EDAM_format:3584: + text: EDAM_format:3584 + description: bedstrict + title: bedstrict + EDAM_format:3585: + text: EDAM_format:3585 + description: bed6 + title: bed6 + EDAM_format:3586: + text: EDAM_format:3586 + description: bed12 + title: bed12 + EDAM_format:3587: + text: EDAM_format:3587 + description: chrominfo + title: chrominfo + EDAM_format:3588: + text: EDAM_format:3588 + description: customtrack + title: customtrack + EDAM_format:3589: + text: EDAM_format:3589 + description: csfasta + title: csfasta + EDAM_format:3590: + text: EDAM_format:3590 + description: HDF5 + title: HDF5 + EDAM_format:3591: + text: EDAM_format:3591 + description: TIFF + title: TIFF + EDAM_format:3592: + text: EDAM_format:3592 + description: BMP + title: BMP + EDAM_format:3593: + text: EDAM_format:3593 + description: im + title: im + EDAM_format:3594: + text: EDAM_format:3594 + description: pcd + title: pcd + EDAM_format:3595: + text: EDAM_format:3595 + description: pcx + title: pcx + EDAM_format:3596: + text: EDAM_format:3596 + description: ppm + title: ppm + EDAM_format:3597: + text: EDAM_format:3597 + description: psd + title: psd + EDAM_format:3598: + text: EDAM_format:3598 + description: xbm + title: xbm + EDAM_format:3599: + text: EDAM_format:3599 + description: xpm + title: xpm + EDAM_format:3600: + text: EDAM_format:3600 + description: rgb + title: rgb + EDAM_format:3601: + text: EDAM_format:3601 + description: pbm + title: pbm + EDAM_format:3602: + text: EDAM_format:3602 + description: pgm + title: pgm + EDAM_format:3603: + text: EDAM_format:3603 + description: PNG + title: PNG + EDAM_format:3604: + text: EDAM_format:3604 + description: SVG + title: SVG + EDAM_format:3605: + text: EDAM_format:3605 + description: rast + title: rast + EDAM_format:3606: + text: EDAM_format:3606 + description: Sequence quality report format (text) + title: Sequence quality report format (text) + EDAM_format:3607: + text: EDAM_format:3607 + description: qual + title: qual + EDAM_format:3608: + text: EDAM_format:3608 + description: qualsolexa + title: qualsolexa + EDAM_format:3609: + text: EDAM_format:3609 + description: qualillumina + title: qualillumina + EDAM_format:3610: + text: EDAM_format:3610 + description: qualsolid + title: qualsolid + EDAM_format:3611: + text: EDAM_format:3611 + description: qual454 + title: qual454 + EDAM_format:3612: + text: EDAM_format:3612 + description: ENCODE peak format + title: ENCODE peak format + EDAM_format:3613: + text: EDAM_format:3613 + description: ENCODE narrow peak format + title: ENCODE narrow peak format + EDAM_format:3614: + text: EDAM_format:3614 + description: ENCODE broad peak format + title: ENCODE broad peak format + EDAM_format:3615: + text: EDAM_format:3615 + description: bgzip + title: bgzip + EDAM_format:3616: + text: EDAM_format:3616 + description: tabix + title: tabix + EDAM_format:3617: + text: EDAM_format:3617 + description: Graph format + title: Graph format + EDAM_format:3618: + text: EDAM_format:3618 + description: xgmml + title: xgmml + EDAM_format:3619: + text: EDAM_format:3619 + description: sif + title: sif + EDAM_format:3620: + text: EDAM_format:3620 + description: xlsx + title: xlsx + EDAM_format:3621: + text: EDAM_format:3621 + description: SQLite format + title: SQLite format + EDAM_format:3622: + text: EDAM_format:3622 + description: Gemini SQLite format + title: Gemini SQLite format + EDAM_format:3624: + text: EDAM_format:3624 + description: snpeffdb + title: snpeffdb + EDAM_format:3626: + text: EDAM_format:3626 + description: MAT + title: MAT + EDAM_format:3650: + text: EDAM_format:3650 + description: NetCDF + title: NetCDF + EDAM_format:3651: + text: EDAM_format:3651 + description: MGF + title: MGF + EDAM_format:3652: + text: EDAM_format:3652 + description: dta + title: dta + EDAM_format:3653: + text: EDAM_format:3653 + description: pkl + title: pkl + EDAM_format:3654: + text: EDAM_format:3654 + description: mzXML + title: mzXML + EDAM_format:3655: + text: EDAM_format:3655 + description: pepXML + title: pepXML + EDAM_format:3657: + text: EDAM_format:3657 + description: GPML + title: GPML + EDAM_format:3665: + text: EDAM_format:3665 + description: K-mer countgraph + title: K-mer countgraph + EDAM_format:3681: + text: EDAM_format:3681 + description: mzTab + title: mzTab + EDAM_format:3682: + text: EDAM_format:3682 + description: imzML metadata file + title: imzML metadata file + EDAM_format:3683: + text: EDAM_format:3683 + description: qcML + title: qcML + EDAM_format:3684: + text: EDAM_format:3684 + description: PRIDE XML + title: PRIDE XML + EDAM_format:3685: + text: EDAM_format:3685 + description: SED-ML + title: SED-ML + EDAM_format:3686: + text: EDAM_format:3686 + description: COMBINE OMEX + title: COMBINE OMEX + EDAM_format:3687: + text: EDAM_format:3687 + description: ISA-TAB + title: ISA-TAB + EDAM_format:3688: + text: EDAM_format:3688 + description: SBtab + title: SBtab + EDAM_format:3689: + text: EDAM_format:3689 + description: BCML + title: BCML + EDAM_format:3690: + text: EDAM_format:3690 + description: BDML + title: BDML + EDAM_format:3691: + text: EDAM_format:3691 + description: BEL + title: BEL + EDAM_format:3692: + text: EDAM_format:3692 + description: SBGN-ML + title: SBGN-ML + EDAM_format:3693: + text: EDAM_format:3693 + description: AGP + title: AGP + EDAM_format:3696: + text: EDAM_format:3696 + description: PS + title: PS + EDAM_format:3698: + text: EDAM_format:3698 + description: SRA format + title: SRA format + EDAM_format:3699: + text: EDAM_format:3699 + description: VDB + title: VDB + EDAM_format:3701: + text: EDAM_format:3701 + description: Sequin format + title: Sequin format + EDAM_format:3702: + text: EDAM_format:3702 + description: MSF + title: MSF + EDAM_format:3706: + text: EDAM_format:3706 + description: Biodiversity data format + title: Biodiversity data format + EDAM_format:3708: + text: EDAM_format:3708 + description: ABCD format + title: ABCD format + EDAM_format:3709: + text: EDAM_format:3709 + description: GCT/Res format + title: GCT/Res format + EDAM_format:3710: + text: EDAM_format:3710 + description: WIFF format + title: WIFF format + EDAM_format:3711: + text: EDAM_format:3711 + description: X!Tandem XML + title: X!Tandem XML + EDAM_format:3712: + text: EDAM_format:3712 + description: Thermo RAW + title: Thermo RAW + EDAM_format:3713: + text: EDAM_format:3713 + description: Mascot .dat file + title: Mascot .dat file + EDAM_format:3714: + text: EDAM_format:3714 + description: MaxQuant APL peaklist format + title: MaxQuant APL peaklist format + EDAM_format:3725: + text: EDAM_format:3725 + description: SBOL + title: SBOL + EDAM_format:3726: + text: EDAM_format:3726 + description: PMML + title: PMML + EDAM_format:3727: + text: EDAM_format:3727 + description: OME-TIFF + title: OME-TIFF + EDAM_format:3728: + text: EDAM_format:3728 + description: LocARNA PP + title: LocARNA PP + EDAM_format:3729: + text: EDAM_format:3729 + description: dbGaP format + title: dbGaP format + EDAM_format:3746: + text: EDAM_format:3746 + description: BIOM format + title: BIOM format + EDAM_format:3747: + text: EDAM_format:3747 + description: protXML + title: protXML + EDAM_format:3748: + text: EDAM_format:3748 + description: Linked data format + title: Linked data format + EDAM_format:3749: + text: EDAM_format:3749 + description: JSON-LD + title: JSON-LD + EDAM_format:3750: + text: EDAM_format:3750 + description: YAML + title: YAML + EDAM_format:3751: + text: EDAM_format:3751 + description: DSV + title: DSV + EDAM_format:3752: + text: EDAM_format:3752 + description: CSV + title: CSV + EDAM_format:3758: + text: EDAM_format:3758 + description: SEQUEST .out file + title: SEQUEST .out file + EDAM_format:3764: + text: EDAM_format:3764 + description: idXML + title: idXML + EDAM_format:3765: + text: EDAM_format:3765 + description: KNIME datatable format + title: KNIME datatable format + EDAM_format:3770: + text: EDAM_format:3770 + description: UniProtKB XML + title: UniProtKB XML + EDAM_format:3771: + text: EDAM_format:3771 + description: UniProtKB RDF + title: UniProtKB RDF + EDAM_format:3772: + text: EDAM_format:3772 + description: BioJSON (BioXSD) + title: BioJSON (BioXSD) + EDAM_format:3773: + text: EDAM_format:3773 + description: BioYAML + title: BioYAML + EDAM_format:3774: + text: EDAM_format:3774 + description: BioJSON (Jalview) + title: BioJSON (Jalview) + EDAM_format:3775: + text: EDAM_format:3775 + description: GSuite + title: GSuite + EDAM_format:3776: + text: EDAM_format:3776 + description: BTrack + title: BTrack + EDAM_format:3777: + text: EDAM_format:3777 + description: MCPD + title: MCPD + EDAM_format:3780: + text: EDAM_format:3780 + description: Annotated text format + title: Annotated text format + EDAM_format:3781: + text: EDAM_format:3781 + description: PubAnnotation format + title: PubAnnotation format + EDAM_format:3782: + text: EDAM_format:3782 + description: BioC + title: BioC + EDAM_format:3783: + text: EDAM_format:3783 + description: PubTator format + title: PubTator format + EDAM_format:3784: + text: EDAM_format:3784 + description: Open Annotation format + title: Open Annotation format + EDAM_format:3785: + text: EDAM_format:3785 + description: BioNLP Shared Task format + title: BioNLP Shared Task format + EDAM_format:3787: + text: EDAM_format:3787 + description: Query language + title: Query language + EDAM_format:3788: + text: EDAM_format:3788 + description: SQL + title: SQL + EDAM_format:3789: + text: EDAM_format:3789 + description: XQuery + title: XQuery + EDAM_format:3790: + text: EDAM_format:3790 + description: SPARQL + title: SPARQL + EDAM_format:3804: + text: EDAM_format:3804 + description: xsd + title: xsd + EDAM_format:3811: + text: EDAM_format:3811 + description: XMFA + title: XMFA + EDAM_format:3812: + text: EDAM_format:3812 + description: GEN + title: GEN + EDAM_format:3813: + text: EDAM_format:3813 + description: SAMPLE file format + title: SAMPLE file format + EDAM_format:3814: + text: EDAM_format:3814 + description: SDF + title: SDF + EDAM_format:3815: + text: EDAM_format:3815 + description: Molfile + title: Molfile + EDAM_format:3816: + text: EDAM_format:3816 + description: Mol2 + title: Mol2 + EDAM_format:3817: + text: EDAM_format:3817 + description: latex + title: latex + EDAM_format:3818: + text: EDAM_format:3818 + description: ELAND format + title: ELAND format + EDAM_format:3819: + text: EDAM_format:3819 + description: Relaxed PHYLIP Interleaved + title: Relaxed PHYLIP Interleaved + EDAM_format:3820: + text: EDAM_format:3820 + description: Relaxed PHYLIP Sequential + title: Relaxed PHYLIP Sequential + EDAM_format:3821: + text: EDAM_format:3821 + description: VisML + title: VisML + EDAM_format:3822: + text: EDAM_format:3822 + description: GML + title: GML + EDAM_format:3823: + text: EDAM_format:3823 + description: FASTG + title: FASTG + EDAM_format:3824: + text: EDAM_format:3824 + description: NMR data format + title: NMR data format + EDAM_format:3825: + text: EDAM_format:3825 + description: nmrML + title: nmrML + EDAM_format:3826: + text: EDAM_format:3826 + description: proBAM + title: proBAM + EDAM_format:3827: + text: EDAM_format:3827 + description: proBED + title: proBED + EDAM_format:3828: + text: EDAM_format:3828 + description: Raw microarray data format + title: Raw microarray data format + EDAM_format:3829: + text: EDAM_format:3829 + description: GPR + title: GPR + EDAM_format:3830: + text: EDAM_format:3830 + description: ARB + title: ARB + EDAM_format:3832: + text: EDAM_format:3832 + description: consensusXML + title: consensusXML + EDAM_format:3833: + text: EDAM_format:3833 + description: featureXML + title: featureXML + EDAM_format:3834: + text: EDAM_format:3834 + description: mzData + title: mzData + EDAM_format:3835: + text: EDAM_format:3835 + description: TIDE TXT + title: TIDE TXT + EDAM_format:3836: + text: EDAM_format:3836 + description: BLAST XML v2 results format + title: BLAST XML v2 results format + EDAM_format:3838: + text: EDAM_format:3838 + description: pptx + title: pptx + EDAM_format:3839: + text: EDAM_format:3839 + description: ibd + title: ibd + EDAM_format:3841: + text: EDAM_format:3841 + description: NLP format + title: NLP format + EDAM_format:3843: + text: EDAM_format:3843 + description: BEAST + title: BEAST + EDAM_format:3844: + text: EDAM_format:3844 + description: Chado-XML + title: Chado-XML + EDAM_format:3845: + text: EDAM_format:3845 + description: HSAML + title: HSAML + EDAM_format:3846: + text: EDAM_format:3846 + description: InterProScan XML + title: InterProScan XML + EDAM_format:3847: + text: EDAM_format:3847 + description: KGML + title: KGML + EDAM_format:3848: + text: EDAM_format:3848 + description: PubMed XML + title: PubMed XML + EDAM_format:3849: + text: EDAM_format:3849 + description: MSAML + title: MSAML + EDAM_format:3850: + text: EDAM_format:3850 + description: OrthoXML + title: OrthoXML + EDAM_format:3851: + text: EDAM_format:3851 + description: PSDML + title: PSDML + EDAM_format:3852: + text: EDAM_format:3852 + description: SeqXML + title: SeqXML + EDAM_format:3853: + text: EDAM_format:3853 + description: UniParc XML + title: UniParc XML + EDAM_format:3854: + text: EDAM_format:3854 + description: UniRef XML + title: UniRef XML + EDAM_format:3857: + text: EDAM_format:3857 + description: CWL + title: CWL + EDAM_format:3858: + text: EDAM_format:3858 + description: Waters RAW + title: Waters RAW + EDAM_format:3859: + text: EDAM_format:3859 + description: JCAMP-DX + title: JCAMP-DX + EDAM_format:3862: + text: EDAM_format:3862 + description: NLP annotation format + title: NLP annotation format + EDAM_format:3863: + text: EDAM_format:3863 + description: NLP corpus format + title: NLP corpus format + EDAM_format:3864: + text: EDAM_format:3864 + description: mirGFF3 + title: mirGFF3 + EDAM_format:3865: + text: EDAM_format:3865 + description: RNA annotation format + title: RNA annotation format + EDAM_format:3866: + text: EDAM_format:3866 + description: Trajectory format + title: Trajectory format + EDAM_format:3867: + text: EDAM_format:3867 + description: Trajectory format (binary) + title: Trajectory format (binary) + EDAM_format:3868: + text: EDAM_format:3868 + description: Trajectory format (text) + title: Trajectory format (text) + EDAM_format:3873: + text: EDAM_format:3873 + description: HDF + title: HDF + EDAM_format:3874: + text: EDAM_format:3874 + description: PCAzip + title: PCAzip + EDAM_format:3875: + text: EDAM_format:3875 + description: XTC + title: XTC + EDAM_format:3876: + text: EDAM_format:3876 + description: TNG + title: TNG + EDAM_format:3877: + text: EDAM_format:3877 + description: XYZ + title: XYZ + EDAM_format:3878: + text: EDAM_format:3878 + description: mdcrd + title: mdcrd + EDAM_format:3879: + text: EDAM_format:3879 + description: Topology format + title: Topology format + EDAM_format:3880: + text: EDAM_format:3880 + description: GROMACS top + title: GROMACS top + EDAM_format:3881: + text: EDAM_format:3881 + description: AMBER top + title: AMBER top + EDAM_format:3882: + text: EDAM_format:3882 + description: PSF + title: PSF + EDAM_format:3883: + text: EDAM_format:3883 + description: GROMACS itp + title: GROMACS itp + EDAM_format:3884: + text: EDAM_format:3884 + description: FF parameter format + title: FF parameter format + EDAM_format:3885: + text: EDAM_format:3885 + description: BinPos + title: BinPos + EDAM_format:3886: + text: EDAM_format:3886 + description: RST + title: RST + EDAM_format:3887: + text: EDAM_format:3887 + description: CHARMM rtf + title: CHARMM rtf + EDAM_format:3888: + text: EDAM_format:3888 + description: AMBER frcmod + title: AMBER frcmod + EDAM_format:3889: + text: EDAM_format:3889 + description: AMBER off + title: AMBER off + EDAM_format:3906: + text: EDAM_format:3906 + description: NMReDATA + title: NMReDATA + EDAM_format:3909: + text: EDAM_format:3909 + description: BpForms + title: BpForms + EDAM_format:3910: + text: EDAM_format:3910 + description: trr + title: trr + EDAM_format:3911: + text: EDAM_format:3911 + description: msh + title: msh + EDAM_format:3913: + text: EDAM_format:3913 + description: Loom + title: Loom + EDAM_format:3915: + text: EDAM_format:3915 + description: Zarr + title: Zarr + EDAM_format:3916: + text: EDAM_format:3916 + description: MTX + title: MTX + EDAM_format:3951: + text: EDAM_format:3951 + description: BcForms + title: BcForms + EDAM_format:3956: + text: EDAM_format:3956 + description: N-Quads + title: N-Quads + EDAM_format:3969: + text: EDAM_format:3969 + description: Vega + title: Vega + EDAM_format:3970: + text: EDAM_format:3970 + description: Vega-lite + title: Vega-lite + EDAM_format:3971: + text: EDAM_format:3971 + description: NeuroML + title: NeuroML + EDAM_format:3972: + text: EDAM_format:3972 + description: BNGL + title: BNGL + EDAM_format:3973: + text: EDAM_format:3973 + description: Docker image + title: Docker image + EDAM_format:3975: + text: EDAM_format:3975 + description: GFA 1 + title: GFA 1 + EDAM_format:3976: + text: EDAM_format:3976 + description: GFA 2 + title: GFA 2 + EDAM_format:3977: + text: EDAM_format:3977 + description: ObjTables + title: ObjTables + EDAM_format:3978: + text: EDAM_format:3978 + description: CONTIG + title: CONTIG + EDAM_format:3979: + text: EDAM_format:3979 + description: WEGO + title: WEGO + EDAM_format:3980: + text: EDAM_format:3980 + description: RPKM + title: RPKM + EDAM_format:3981: + text: EDAM_format:3981 + description: TAR format + title: TAR format + EDAM_format:3982: + text: EDAM_format:3982 + description: CHAIN + title: CHAIN + EDAM_format:3983: + text: EDAM_format:3983 + description: NET + title: NET + EDAM_format:3984: + text: EDAM_format:3984 + description: QMAP + title: QMAP + EDAM_format:3985: + text: EDAM_format:3985 + description: gxformat2 + title: gxformat2 + EDAM_format:3986: + text: EDAM_format:3986 + description: WMV + title: WMV + EDAM_format:3987: + text: EDAM_format:3987 + description: ZIP format + title: ZIP format + EDAM_format:3988: + text: EDAM_format:3988 + description: LSM + title: LSM + EDAM_format:3989: + text: EDAM_format:3989 + description: GZIP format + title: GZIP format + EDAM_format:3990: + text: EDAM_format:3990 + description: AVI + title: AVI + EDAM_format:3991: + text: EDAM_format:3991 + description: TrackDB + title: TrackDB + EDAM_format:3992: + text: EDAM_format:3992 + description: CIGAR format + title: CIGAR format + EDAM_format:3993: + text: EDAM_format:3993 + description: Stereolithography format + title: Stereolithography format + EDAM_format:3994: + text: EDAM_format:3994 + description: U3D + title: U3D + EDAM_format:3995: + text: EDAM_format:3995 + description: Texture file format + title: Texture file format + EDAM_format:3996: + text: EDAM_format:3996 + description: Python script + title: Python script + EDAM_format:3997: + text: EDAM_format:3997 + description: MPEG-4 + title: MPEG-4 + EDAM_format:3998: + text: EDAM_format:3998 + description: Perl script + title: Perl script + EDAM_format:3999: + text: EDAM_format:3999 + description: R script + title: R script + EDAM_format:4000: + text: EDAM_format:4000 + description: R markdown + title: R markdown + EDAM_format:4002: + text: EDAM_format:4002 + description: pickle + title: pickle + EDAM_format:4003: + text: EDAM_format:4003 + description: NumPy format + title: NumPy format + EDAM_format:4004: + text: EDAM_format:4004 + description: SimTools repertoire file format + title: SimTools repertoire file format + EDAM_format:4005: + text: EDAM_format:4005 + description: Configuration file format + title: Configuration file format + EDAM_format:4006: + text: EDAM_format:4006 + description: Zstandard format + title: Zstandard format + EDAM_format:4007: + text: EDAM_format:4007 + description: MATLAB script + title: MATLAB script + EDAM_format:4015: + text: EDAM_format:4015 + description: PEtab + title: PEtab + EDAM_format:4018: + text: EDAM_format:4018 + description: gVCF + title: gVCF + EDAM_format:4023: + text: EDAM_format:4023 + description: cml + title: cml + EDAM_format:4024: + text: EDAM_format:4024 + description: cif + title: cif + EDAM_format:4025: + text: EDAM_format:4025 + description: BioSimulators format for the specifications of biosimulation + tools + title: BioSimulators format for the specifications of biosimulation tools + EDAM_format:4026: + text: EDAM_format:4026 + description: BioSimulators standard for command-line interfaces for biosimulation + tools + title: BioSimulators standard for command-line interfaces for biosimulation + tools + EDAM_format:4035: + text: EDAM_format:4035 + description: PQR + title: PQR + EDAM_format:4036: + text: EDAM_format:4036 + description: PDBQT + title: PDBQT + EDAM_format:4039: + text: EDAM_format:4039 + description: MSP + title: MSP + EDAM_format:4041: + text: EDAM_format:4041 + description: maDMP + title: maDMP + EDAM_format:4048: + text: EDAM_format:4048 + description: Nextflow + title: Nextflow + EDAM_format:4049: + text: EDAM_format:4049 + description: Snakemake + title: Snakemake + EDAM_format:4050: + text: EDAM_format:4050 + description: SDRF + title: SDRF + EDAM_format:4058: + text: EDAM_format:4058 + description: mzTab-M + title: mzTab-M + EDAM_format:4059: + text: EDAM_format:4059 + description: mzTab-L + title: mzTab-L diff --git a/src/cam_expanded_enums/schema/EnumEthnicity.yaml b/src/cam_expanded_enums/schema/EnumEthnicity.yaml new file mode 100644 index 0000000..4dca250 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumEthnicity.yaml @@ -0,0 +1,19 @@ +--- +id: https://includedcc.org/common-access-model/EnumEthnicity +name: EnumEthnicity +enums: + EnumEthnicity: + description: Participant ethnicity, specific to Hispanic or Latino. + permissible_values: + hispanic_or_latino: + title: Hispanic or Latino + meaning: NCIT:C17459 + not_hispanic_or_latino: + title: Not Hispanic or Latino + meaning: NCIT:C41222 + prefer_not_to_answer: + title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + title: Unknown + meaning: NCIT:C17998 diff --git a/src/cam_expanded_enums/schema/EnumFamilyType.yaml b/src/cam_expanded_enums/schema/EnumFamilyType.yaml new file mode 100644 index 0000000..38575bf --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumFamilyType.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumFamilyType +name: EnumFamilyType +enums: + EnumFamilyType: + description: Enumerations describing research family type + is_a: EnumNull + permissible_values: + control_only: + title: Control-only + description: Control Only + duo: + title: Duo + description: Duo + proband_only: + title: Proband-only + description: Proband Only + trio: + title: Trio + description: Trio (2 parents and affected child) + trio_plus: + title: Trio+ + description: 2 Parents and 2 or more children diff --git a/src/cam_expanded_enums/schema/EnumFileHashType.yaml b/src/cam_expanded_enums/schema/EnumFileHashType.yaml new file mode 100644 index 0000000..d0950ed --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumFileHashType.yaml @@ -0,0 +1,13 @@ +--- +id: https://includedcc.org/common-access-model/EnumFileHashType +name: EnumFileHashType +enums: + EnumFileHashType: + description: Types of file hashes supported. + permissible_values: + md5: + title: MD5 + etag: + title: ETag + sha1: + title: SHA-1 diff --git a/src/cam_expanded_enums/schema/EnumNull.yaml b/src/cam_expanded_enums/schema/EnumNull.yaml new file mode 100644 index 0000000..c6582e6 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumNull.yaml @@ -0,0 +1,10 @@ +--- +id: https://includedcc.org/common-access-model/EnumNull +name: EnumNull +enums: + EnumNull: + description: Base enumeration providing null options. + permissible_values: + unknown: + title: Unknown + meaning: NCIT:C17998 diff --git a/src/cam_expanded_enums/schema/EnumParticipantLifespanStage.yaml b/src/cam_expanded_enums/schema/EnumParticipantLifespanStage.yaml new file mode 100644 index 0000000..b134d03 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumParticipantLifespanStage.yaml @@ -0,0 +1,20 @@ +--- +id: https://includedcc.org/common-access-model/EnumParticipantLifespanStage +name: EnumParticipantLifespanStage +enums: + EnumParticipantLifespanStage: + title: Participant Lifespan Stage + description: Stages of life during which participants may be recruited. + permissible_values: + fetal: + title: Fetal + description: Before birth + neonatal: + title: Neonatal + description: 0-28 days old + pediatric: + title: Pediatric + description: Birth-17 years old + adult: + title: Adult + description: 18+ years old diff --git a/src/cam_expanded_enums/schema/EnumProgram.yaml b/src/cam_expanded_enums/schema/EnumProgram.yaml new file mode 100644 index 0000000..de6b598 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumProgram.yaml @@ -0,0 +1,14 @@ +--- +id: https://includedcc.org/common-access-model/EnumProgram +name: EnumProgram +enums: + EnumProgram: + title: Funding Programs + description: Funding programs relevant to inform operations. + permissible_values: + include: + title: INCLUDE + kf: + title: KF + other: + title: Other diff --git a/src/cam_expanded_enums/schema/EnumRace.yaml b/src/cam_expanded_enums/schema/EnumRace.yaml new file mode 100644 index 0000000..3d89953 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumRace.yaml @@ -0,0 +1,50 @@ +--- +id: https://includedcc.org/common-access-model/EnumRace +name: EnumRace +enums: + EnumRace: + description: Participant Race + permissible_values: + american_indian_or_alaska_native: + title: American Indian or Alaska Native + meaning: NCIT:C41259 + asian: + title: Asian + meaning: NCIT:C41260 + black_or_african_american: + title: Black or African American + meaning: NCIT:C16352 + more_than_one_race: + title: More than one race + meaning: NCIT:C67109 + native_hawaiian_or_other_pacific_islander: + title: Native Hawaiian or Other Pacific Islander + meaning: NCIT:C41219 + other: + title: Other + meaning: NCIT:C17649 + white: + title: White + meaning: NCIT:C41261 + prefer_not_to_answer: + title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + title: Unknown + meaning: NCIT:C17998 + east_asian: + title: East Asian + description: UK only; do not use for US data + meaning: NCIT:C161419 + latin_american: + title: Latin American + description: UK only; do not use for US data + meaning: NCIT:C126531 + middle_eastern_or_north_african: + title: Middle Eastern or North African + description: UK only; do not use for US data + meaning: NCIT:C43866 + south_asian: + title: South Asian + description: UK only; do not use for US data + meaning: NCIT:C41263 diff --git a/src/cam_expanded_enums/schema/EnumResearchDomain.yaml b/src/cam_expanded_enums/schema/EnumResearchDomain.yaml new file mode 100644 index 0000000..b4aba2c --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumResearchDomain.yaml @@ -0,0 +1,34 @@ +--- +id: https://includedcc.org/common-access-model/EnumResearchDomain +name: EnumResearchDomain +enums: + EnumResearchDomain: + title: Research Domain + description: Domains of Research used to find studies. + permissible_values: + behavior_and_behavior_mechanisms: + title: Behavior and Behavior Mechanisms + meaning: mesh:D001520 + congenital_heart_defects: + title: Congenital Heart Defects + meaning: mesh:D006330 + immune_system_diseases: + title: Immune System Diseases + meaning: mesh:D007154 + hematologic_diseases: + title: Hematologic Diseases + meaning: mesh:D006402 + neurodevelopment: + title: Neurodevelopment + meaning: mesh:D065886 + sleep_wake_disorders: + title: Sleep Wake Disorders + meaning: mesh:D012893 + all_co_occurring_conditions: + title: All Co-occurring Conditions + meaning: mesh:D013568 + physical_fitness: + title: Physical Fitness + meaning: mesh:D010809 + other: + title: Other diff --git a/src/cam_expanded_enums/schema/EnumSex.yaml b/src/cam_expanded_enums/schema/EnumSex.yaml new file mode 100644 index 0000000..585b6aa --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumSex.yaml @@ -0,0 +1,19 @@ +--- +id: https://includedcc.org/common-access-model/EnumSex +name: EnumSex +enums: + EnumSex: + description: Subject Sex + permissible_values: + female: + title: Female + meaning: NCIT:C16576 + male: + title: Male + meaning: NCIT:C20197 + other: + title: Other + meaning: NCIT:C17649 + unknown: + title: Unknown + meaning: NCIT:C17998 diff --git a/src/cam_expanded_enums/schema/EnumSpatialQualifiers.yaml b/src/cam_expanded_enums/schema/EnumSpatialQualifiers.yaml new file mode 100644 index 0000000..7ae7d80 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumSpatialQualifiers.yaml @@ -0,0 +1,3123 @@ +id: https://includedcc.org/common-access-model/EnumSpatialQualifiers +name: EnumSpatialQualifiers +enums: + EnumSpatialQualifiers: + description: Any spatial/location qualifiers. + enum_uri: http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs + reachable_from: + source_ontology: bioregistry:snomedct + source_nodes: + - snomedct:106233006 + - snomedct:272424004 + - snomedct:51440002 + - snomedct:399488007 + - snomedct:24028007 + - snomedct:7771000 + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + SNOMED:103339001: + text: SNOMED:103339001 + description: Long axis + title: Long axis + SNOMED:103340004: + text: SNOMED:103340004 + description: Short axis + title: Short axis + SNOMED:103341000: + text: SNOMED:103341000 + description: Off axis + title: Off axis + SNOMED:103342007: + text: SNOMED:103342007 + description: Mid-longitudinal + title: Mid-longitudinal + SNOMED:103343002: + text: SNOMED:103343002 + description: Parasagittal + title: Parasagittal + SNOMED:103344008: + text: SNOMED:103344008 + description: Transvesical + title: Transvesical + SNOMED:103345009: + text: SNOMED:103345009 + description: Transthecal + title: Transthecal + SNOMED:103346005: + text: SNOMED:103346005 + description: Transsplenic + title: Transsplenic + SNOMED:103347001: + text: SNOMED:103347001 + description: Transrenal + title: Transrenal + SNOMED:103348006: + text: SNOMED:103348006 + description: Transpleural + title: Transpleural + SNOMED:103349003: + text: SNOMED:103349003 + description: Transpancreatic + title: Transpancreatic + SNOMED:103353001: + text: SNOMED:103353001 + description: Transgastric + title: Transgastric + SNOMED:103354007: + text: SNOMED:103354007 + description: Transmural + title: Transmural + SNOMED:11070000: + text: SNOMED:11070000 + description: Capsular + title: Capsular + SNOMED:1146002: + text: SNOMED:1146002 + description: Arcuate + title: Arcuate + SNOMED:11896004: + text: SNOMED:11896004 + description: Intermediate + title: Intermediate + SNOMED:1217011006: + text: SNOMED:1217011006 + description: Non-adjacent + title: Non-adjacent + SNOMED:131183008: + text: SNOMED:131183008 + description: Intra-articular + title: Intra-articular + SNOMED:131184002: + text: SNOMED:131184002 + description: Area of defined region + title: Area of defined region + SNOMED:131185001: + text: SNOMED:131185001 + description: Vertical long axis + title: Vertical long axis + SNOMED:131186000: + text: SNOMED:131186000 + description: Horizontal long axis + title: Horizontal long axis + SNOMED:131187009: + text: SNOMED:131187009 + description: Major Axis + title: Major Axis + SNOMED:131188004: + text: SNOMED:131188004 + description: Minor Axis + title: Minor Axis + SNOMED:131189007: + text: SNOMED:131189007 + description: Perpendicular axis + title: Perpendicular axis + SNOMED:131190003: + text: SNOMED:131190003 + description: Radius + title: Radius + SNOMED:131191004: + text: SNOMED:131191004 + description: Perimeter + title: Perimeter + SNOMED:14414005: + text: SNOMED:14414005 + description: Peripheral + title: Peripheral + SNOMED:1483009: + text: SNOMED:1483009 + description: Angular + title: Angular + SNOMED:18769003: + text: SNOMED:18769003 + description: Juxta-posed + title: Juxta-posed + SNOMED:21006006: + text: SNOMED:21006006 + description: Hemispheric + title: Hemispheric + SNOMED:21481007: + text: SNOMED:21481007 + description: Over + title: Over + SNOMED:24020000: + text: SNOMED:24020000 + description: Horizontal + title: Horizontal + SNOMED:24028007: + text: SNOMED:24028007 + description: Right + title: Right + SNOMED:24422004: + text: SNOMED:24422004 + description: Axial + title: Axial + SNOMED:255527003: + text: SNOMED:255527003 + description: Horizontal - 3 and 9 + title: Horizontal - 3 and 9 + SNOMED:255528008: + text: SNOMED:255528008 + description: Horizontal and vertical + title: Horizontal and vertical + SNOMED:261129000: + text: SNOMED:261129000 + description: Mediolateral + title: Mediolateral + SNOMED:26216008: + text: SNOMED:26216008 + description: Central + title: Central + SNOMED:26283006: + text: SNOMED:26283006 + description: Superficial + title: Superficial + SNOMED:263687007: + text: SNOMED:263687007 + description: Bony extra-articular + title: Bony extra-articular + SNOMED:263688002: + text: SNOMED:263688002 + description: Bony intra-articular + title: Bony intra-articular + SNOMED:264731004: + text: SNOMED:264731004 + description: Lateral to the left + title: Lateral to the left + SNOMED:264732006: + text: SNOMED:264732006 + description: Lateral to the right + title: Lateral to the right + SNOMED:264733001: + text: SNOMED:264733001 + description: Linear longitudinal + title: Linear longitudinal + SNOMED:264737000: + text: SNOMED:264737000 + description: Linear transverse + title: Linear transverse + SNOMED:264741001: + text: SNOMED:264741001 + description: Posterolateral to the left + title: Posterolateral to the left + SNOMED:264742008: + text: SNOMED:264742008 + description: Posterolateral to the right + title: Posterolateral to the right + SNOMED:264839005: + text: SNOMED:264839005 + description: Horizontal cleavage + title: Horizontal cleavage + SNOMED:27237009: + text: SNOMED:27237009 + description: Triangular + title: Triangular + SNOMED:28241006: + text: SNOMED:28241006 + description: Rhomboid + title: Rhomboid + SNOMED:28947002: + text: SNOMED:28947002 + description: Right curve + title: Right curve + SNOMED:30730003: + text: SNOMED:30730003 + description: Sagittal + title: Sagittal + SNOMED:30899007: + text: SNOMED:30899007 + description: Quadrangular + title: Quadrangular + SNOMED:32381004: + text: SNOMED:32381004 + description: Portal + title: Portal + SNOMED:32400000: + text: SNOMED:32400000 + description: Preaxial + title: Preaxial + SNOMED:33096000: + text: SNOMED:33096000 + description: Vertical + title: Vertical + SNOMED:33843005: + text: SNOMED:33843005 + description: Efferent + title: Efferent + SNOMED:350722008: + text: SNOMED:350722008 + description: Behind + title: Behind + SNOMED:351726001: + text: SNOMED:351726001 + description: Below + title: Below + SNOMED:352730000: + text: SNOMED:352730000 + description: Supra- + title: Supra- + SNOMED:353734004: + text: SNOMED:353734004 + description: Upward + title: Upward + SNOMED:354652004: + text: SNOMED:354652004 + description: Circular + title: Circular + SNOMED:355648006: + text: SNOMED:355648006 + description: Surrounding + title: Surrounding + SNOMED:37197008: + text: SNOMED:37197008 + description: Anterolateral + title: Anterolateral + SNOMED:38717003: + text: SNOMED:38717003 + description: Longitudinal + title: Longitudinal + SNOMED:39187007: + text: SNOMED:39187007 + description: Bent + title: Bent + SNOMED:40415009: + text: SNOMED:40415009 + description: Proximal + title: Proximal + SNOMED:410674003: + text: SNOMED:410674003 + description: Regional + title: Regional + SNOMED:410679008: + text: SNOMED:410679008 + description: Surface + title: Surface + SNOMED:42798000: + text: SNOMED:42798000 + description: Area + title: Area + SNOMED:43674008: + text: SNOMED:43674008 + description: Apical + title: Apical + SNOMED:45226003: + text: SNOMED:45226003 + description: Cylindrical + title: Cylindrical + SNOMED:46053002: + text: SNOMED:46053002 + description: Distal + title: Distal + SNOMED:47021000: + text: SNOMED:47021000 + description: Left curve + title: Left curve + SNOMED:49370004: + text: SNOMED:49370004 + description: Lateral + title: Lateral + SNOMED:49530007: + text: SNOMED:49530007 + description: Afferent + title: Afferent + SNOMED:50009006: + text: SNOMED:50009006 + description: Linear + title: Linear + SNOMED:50362007: + text: SNOMED:50362007 + description: Stellate + title: Stellate + SNOMED:50974003: + text: SNOMED:50974003 + description: Junctional + title: Junctional + SNOMED:51440002: + text: SNOMED:51440002 + description: Right and left + title: Right and left + SNOMED:5686001: + text: SNOMED:5686001 + description: Remote + title: Remote + SNOMED:56924007: + text: SNOMED:56924007 + description: Square + title: Square + SNOMED:57183005: + text: SNOMED:57183005 + description: Along edge + title: Along edge + SNOMED:57195005: + text: SNOMED:57195005 + description: Basal + title: Basal + SNOMED:59410002: + text: SNOMED:59410002 + description: Rectangular + title: Rectangular + SNOMED:60301000: + text: SNOMED:60301000 + description: Curved + title: Curved + SNOMED:60583000: + text: SNOMED:60583000 + description: Postaxial + title: Postaxial + SNOMED:61397002: + text: SNOMED:61397002 + description: Subcapsular + title: Subcapsular + SNOMED:62083003: + text: SNOMED:62083003 + description: Sectional + title: Sectional + SNOMED:62372003: + text: SNOMED:62372003 + description: Segmental + title: Segmental + SNOMED:62824007: + text: SNOMED:62824007 + description: Transverse + title: Transverse + SNOMED:66787007: + text: SNOMED:66787007 + description: Cephalic + title: Cephalic + SNOMED:68493006: + text: SNOMED:68493006 + description: Gutter + title: Gutter + SNOMED:69320009: + text: SNOMED:69320009 + description: Extracellular + title: Extracellular + SNOMED:69389007: + text: SNOMED:69389007 + description: Saccular + title: Saccular + SNOMED:710097009: + text: SNOMED:710097009 + description: Incisal + title: Incisal + SNOMED:710098004: + text: SNOMED:710098004 + description: Occlusal + title: Occlusal + SNOMED:710099007: + text: SNOMED:710099007 + description: Mesial + title: Mesial + SNOMED:7771000: + text: SNOMED:7771000 + description: Left + title: Left + SNOMED:795002: + text: SNOMED:795002 + description: Deep + title: Deep + SNOMED:81654009: + text: SNOMED:81654009 + description: Coronal + title: Coronal + SNOMED:83167003: + text: SNOMED:83167003 + description: Intracellular + title: Intracellular + SNOMED:84177009: + text: SNOMED:84177009 + description: Straddling + title: Straddling + SNOMED:87687004: + text: SNOMED:87687004 + description: Extra-articular + title: Extra-articular + SNOMED:90069004: + text: SNOMED:90069004 + description: Posterolateral + title: Posterolateral + SNOMED:112233002: + text: SNOMED:112233002 + description: Marginal + title: Marginal + SNOMED:1197041002: + text: SNOMED:1197041002 + description: Intercostal + title: Intercostal + SNOMED:1285325005: + text: SNOMED:1285325005 + description: Intralobular + title: Intralobular + SNOMED:128590009: + text: SNOMED:128590009 + description: Anatomical reference point of right atrium + title: Anatomical reference point of right atrium + SNOMED:1362012009: + text: SNOMED:1362012009 + description: Inlet projection + title: Inlet projection + SNOMED:1363295008: + text: SNOMED:1363295008 + description: Unilobar + title: Unilobar + SNOMED:1363296009: + text: SNOMED:1363296009 + description: Ipsilateral multilobar + title: Ipsilateral multilobar + SNOMED:182353008: + text: SNOMED:182353008 + description: Side + title: Side + SNOMED:225780003: + text: SNOMED:225780003 + description: Sublingual + title: Sublingual + SNOMED:229801003: + text: SNOMED:229801003 + description: Intra-arterial + title: Intra-arterial + SNOMED:255208005: + text: SNOMED:255208005 + description: Ipsilateral + title: Ipsilateral + SNOMED:255209002: + text: SNOMED:255209002 + description: Contralateral + title: Contralateral + SNOMED:255348000: + text: SNOMED:255348000 + description: Inframammary + title: Inframammary + SNOMED:255472009: + text: SNOMED:255472009 + description: Panretinal + title: Panretinal + SNOMED:255482005: + text: SNOMED:255482005 + description: Left upper segment + title: Left upper segment + SNOMED:255486008: + text: SNOMED:255486008 + description: Lower segment + title: Lower segment + SNOMED:255496004: + text: SNOMED:255496004 + description: Right lower segment + title: Right lower segment + SNOMED:255499006: + text: SNOMED:255499006 + description: Right upper segment + title: Right upper segment + SNOMED:255501003: + text: SNOMED:255501003 + description: Upper segment + title: Upper segment + SNOMED:255546002: + text: SNOMED:255546002 + description: Underlay + title: Underlay + SNOMED:255547006: + text: SNOMED:255547006 + description: Overlay + title: Overlay + SNOMED:255548001: + text: SNOMED:255548001 + description: Sandwich graft + title: Sandwich graft + SNOMED:255549009: + text: SNOMED:255549009 + description: Anterior + title: Anterior + SNOMED:255550009: + text: SNOMED:255550009 + description: Anterior to epiglottis + title: Anterior to epiglottis + SNOMED:255551008: + text: SNOMED:255551008 + description: Posterior + title: Posterior + SNOMED:255552001: + text: SNOMED:255552001 + description: Posterior to epiglottis + title: Posterior to epiglottis + SNOMED:255554000: + text: SNOMED:255554000 + description: Dorsal + title: Dorsal + SNOMED:255557007: + text: SNOMED:255557007 + description: Intracerebral + title: Intracerebral + SNOMED:255558002: + text: SNOMED:255558002 + description: Intragastric + title: Intragastric + SNOMED:255559005: + text: SNOMED:255559005 + description: Intramuscular + title: Intramuscular + SNOMED:255560000: + text: SNOMED:255560000 + description: Intravenous + title: Intravenous + SNOMED:255561001: + text: SNOMED:255561001 + description: Medial + title: Medial + SNOMED:255562008: + text: SNOMED:255562008 + description: Mid + title: Mid + SNOMED:255563003: + text: SNOMED:255563003 + description: Mid-zone + title: Mid-zone + SNOMED:255564009: + text: SNOMED:255564009 + description: Perivascular + title: Perivascular + SNOMED:255565005: + text: SNOMED:255565005 + description: Peripapillary + title: Peripapillary + SNOMED:255567002: + text: SNOMED:255567002 + description: Postauricular + title: Postauricular + SNOMED:255568007: + text: SNOMED:255568007 + description: Retrosternal + title: Retrosternal + SNOMED:255569004: + text: SNOMED:255569004 + description: Suprasternal + title: Suprasternal + SNOMED:255579002: + text: SNOMED:255579002 + description: Palatal-lingual + title: Palatal-lingual + SNOMED:255584008: + text: SNOMED:255584008 + description: Septal + title: Septal + SNOMED:255690001: + text: SNOMED:255690001 + description: Drug in contact with skin + title: Drug in contact with skin + SNOMED:258186003: + text: SNOMED:258186003 + description: Via collaterals + title: Via collaterals + SNOMED:258187007: + text: SNOMED:258187007 + description: Via native vessel - graft impaired + title: Via native vessel - graft impaired + SNOMED:258188002: + text: SNOMED:258188002 + description: Via native vessel - graft occluded + title: Via native vessel - graft occluded + SNOMED:258189005: + text: SNOMED:258189005 + description: Via skip graft + title: Via skip graft + SNOMED:258329003: + text: SNOMED:258329003 + description: Supratentorial + title: Supratentorial + SNOMED:258330008: + text: SNOMED:258330008 + description: Infratentorial + title: Infratentorial + SNOMED:260240005: + text: SNOMED:260240005 + description: Interdental + title: Interdental + SNOMED:260318004: + text: SNOMED:260318004 + description: '["1 o''clock position"]' + title: 1 o'clock position + SNOMED:260319007: + text: SNOMED:260319007 + description: '["1.30 o''clock position"]' + title: 1.30 o'clock position + SNOMED:260322009: + text: SNOMED:260322009 + description: '["10 o''clock position"]' + title: 10 o'clock position + SNOMED:260323004: + text: SNOMED:260323004 + description: '["10.30 o''clock position"]' + title: 10.30 o'clock position + SNOMED:260324005: + text: SNOMED:260324005 + description: '["11 o''clock position"]' + title: 11 o'clock position + SNOMED:260325006: + text: SNOMED:260325006 + description: '["11.30 o''clock position"]' + title: 11.30 o'clock position + SNOMED:260326007: + text: SNOMED:260326007 + description: '["12 o''clock position"]' + title: 12 o'clock position + SNOMED:260327003: + text: SNOMED:260327003 + description: '["12.30 o''clock position"]' + title: 12.30 o'clock position + SNOMED:260328008: + text: SNOMED:260328008 + description: '["2 o''clock position"]' + title: 2 o'clock position + SNOMED:260329000: + text: SNOMED:260329000 + description: '["2.30 o''clock position"]' + title: 2.30 o'clock position + SNOMED:260330005: + text: SNOMED:260330005 + description: '["3 o''clock position"]' + title: 3 o'clock position + SNOMED:260331009: + text: SNOMED:260331009 + description: '["3.30 o''clock position"]' + title: 3.30 o'clock position + SNOMED:260333007: + text: SNOMED:260333007 + description: '["4 o''clock position"]' + title: 4 o'clock position + SNOMED:260334001: + text: SNOMED:260334001 + description: '["4.30 o''clock position"]' + title: 4.30 o'clock position + SNOMED:260335000: + text: SNOMED:260335000 + description: '["5 o''clock position"]' + title: 5 o'clock position + SNOMED:260336004: + text: SNOMED:260336004 + description: '["5.30 o''clock position"]' + title: 5.30 o'clock position + SNOMED:260337008: + text: SNOMED:260337008 + description: '["6 o''clock position"]' + title: 6 o'clock position + SNOMED:260338003: + text: SNOMED:260338003 + description: '["6.30 o''clock position"]' + title: 6.30 o'clock position + SNOMED:260339006: + text: SNOMED:260339006 + description: '["7 o''clock position"]' + title: 7 o'clock position + SNOMED:260340008: + text: SNOMED:260340008 + description: '["7.30 o''clock position"]' + title: 7.30 o'clock position + SNOMED:260341007: + text: SNOMED:260341007 + description: '["8 o''clock position"]' + title: 8 o'clock position + SNOMED:260342000: + text: SNOMED:260342000 + description: '["8.30 o''clock position"]' + title: 8.30 o'clock position + SNOMED:260343005: + text: SNOMED:260343005 + description: '["9 o''clock position"]' + title: 9 o'clock position + SNOMED:260344004: + text: SNOMED:260344004 + description: '["9.30 o''clock position"]' + title: 9.30 o'clock position + SNOMED:260419006: + text: SNOMED:260419006 + description: Projection + title: Projection + SNOMED:260421001: + text: SNOMED:260421001 + description: Left lateral oblique + title: Left lateral oblique + SNOMED:260422008: + text: SNOMED:260422008 + description: C1-C2 left oblique + title: C1-C2 left oblique + SNOMED:260424009: + text: SNOMED:260424009 + description: Right lateral oblique + title: Right lateral oblique + SNOMED:260425005: + text: SNOMED:260425005 + description: C1-C2 right oblique + title: C1-C2 right oblique + SNOMED:260426006: + text: SNOMED:260426006 + description: Medial oblique + title: Medial oblique + SNOMED:260427002: + text: SNOMED:260427002 + description: Oblique lateral + title: Oblique lateral + SNOMED:260428007: + text: SNOMED:260428007 + description: Mandible X-ray - lateral oblique + title: Mandible X-ray - lateral oblique + SNOMED:260430009: + text: SNOMED:260430009 + description: Anteroposterior left lateral decubitus + title: Anteroposterior left lateral decubitus + SNOMED:260431008: + text: SNOMED:260431008 + description: C1-C2 left lateral + title: C1-C2 left lateral + SNOMED:260432001: + text: SNOMED:260432001 + description: Left true lateral + title: Left true lateral + SNOMED:260434000: + text: SNOMED:260434000 + description: Anteroposterior right lateral decubitus + title: Anteroposterior right lateral decubitus + SNOMED:260435004: + text: SNOMED:260435004 + description: C1-C2 right lateral + title: C1-C2 right lateral + SNOMED:260436003: + text: SNOMED:260436003 + description: Right true lateral + title: Right true lateral + SNOMED:260437007: + text: SNOMED:260437007 + description: Lateral vertical beam + title: Lateral vertical beam + SNOMED:260438002: + text: SNOMED:260438002 + description: Lateral horizontal beam + title: Lateral horizontal beam + SNOMED:260439005: + text: SNOMED:260439005 + description: Lateral inverted + title: Lateral inverted + SNOMED:260440007: + text: SNOMED:260440007 + description: True lateral of mandible + title: True lateral of mandible + SNOMED:260441006: + text: SNOMED:260441006 + description: Frog lateral + title: Frog lateral + SNOMED:260442004: + text: SNOMED:260442004 + description: Erect lateral + title: Erect lateral + SNOMED:260443009: + text: SNOMED:260443009 + description: Anteroposterior inverted + title: Anteroposterior inverted + SNOMED:260444003: + text: SNOMED:260444003 + description: Rotated posteroanterior + title: Rotated posteroanterior + SNOMED:260445002: + text: SNOMED:260445002 + description: Posteroanterior 20 degree + title: Posteroanterior 20 degree + SNOMED:260446001: + text: SNOMED:260446001 + description: Posteroanterior in ulnar deviation + title: Posteroanterior in ulnar deviation + SNOMED:260447005: + text: SNOMED:260447005 + description: Penetrated posteroanterior + title: Penetrated posteroanterior + SNOMED:260450008: + text: SNOMED:260450008 + description: Lordotic projection + title: Lordotic projection + SNOMED:260451007: + text: SNOMED:260451007 + description: Supine decubitus + title: Supine decubitus + SNOMED:260452000: + text: SNOMED:260452000 + description: Decubitus + title: Decubitus + SNOMED:260453005: + text: SNOMED:260453005 + description: Internal/external rotation + title: Internal/external rotation + SNOMED:260454004: + text: SNOMED:260454004 + description: 45 degree projection + title: 45 degree projection + SNOMED:260455003: + text: SNOMED:260455003 + description: Head and neck projection + title: Head and neck projection + SNOMED:260458001: + text: SNOMED:260458001 + description: '["Slit Towne''s"]' + title: Slit Towne's + SNOMED:260459009: + text: SNOMED:260459009 + description: '["Reverse Towne''s"]' + title: Reverse Towne's + SNOMED:260460004: + text: SNOMED:260460004 + description: Slit 35 degree fronto-occipital + title: Slit 35 degree fronto-occipital + SNOMED:260461000: + text: SNOMED:260461000 + description: Vertex projection + title: Vertex projection + SNOMED:260463002: + text: SNOMED:260463002 + description: '["Left Stenver''s"]' + title: Left Stenver's + SNOMED:260464008: + text: SNOMED:260464008 + description: '["Right Stenver''s"]' + title: Right Stenver's + SNOMED:260465009: + text: SNOMED:260465009 + description: Occipitofrontal projection + title: Occipitofrontal projection + SNOMED:260466005: + text: SNOMED:260466005 + description: Occipitomental projection + title: Occipitomental projection + SNOMED:260467001: + text: SNOMED:260467001 + description: Occipitomental - erect + title: Occipitomental - erect + SNOMED:260468006: + text: SNOMED:260468006 + description: Occipitomental - tilted + title: Occipitomental - tilted + SNOMED:260469003: + text: SNOMED:260469003 + description: Occipitomental - prone + title: Occipitomental - prone + SNOMED:260470002: + text: SNOMED:260470002 + description: Occipitomental - 15 degree + title: Occipitomental - 15 degree + SNOMED:260471003: + text: SNOMED:260471003 + description: Occipitomental - 30 degree + title: Occipitomental - 30 degree + SNOMED:260472005: + text: SNOMED:260472005 + description: Occipitomental - 45 degree + title: Occipitomental - 45 degree + SNOMED:260473000: + text: SNOMED:260473000 + description: Waters - 35 degree tilt to radiographic baseline + title: Waters - 35 degree tilt to radiographic baseline + SNOMED:260475007: + text: SNOMED:260475007 + description: Submentovertical reduced exposure for zygomatic arches + title: Submentovertical reduced exposure for zygomatic arches + SNOMED:260476008: + text: SNOMED:260476008 + description: Slit submentovertical + title: Slit submentovertical + SNOMED:260477004: + text: SNOMED:260477004 + description: Dental/oral projection + title: Dental/oral projection + SNOMED:260478009: + text: SNOMED:260478009 + description: Body - molar + title: Body - molar + SNOMED:260479001: + text: SNOMED:260479001 + description: Body - premolar + title: Body - premolar + SNOMED:260481004: + text: SNOMED:260481004 + description: Ramus projection + title: Ramus projection + SNOMED:260482006: + text: SNOMED:260482006 + description: Bimolar projection + title: Bimolar projection + SNOMED:260483001: + text: SNOMED:260483001 + description: Transpharyngeal projection + title: Transpharyngeal projection + SNOMED:260484007: + text: SNOMED:260484007 + description: Transmaxillary projection + title: Transmaxillary projection + SNOMED:260485008: + text: SNOMED:260485008 + description: Temporomandibular joint setting + title: Temporomandibular joint setting + SNOMED:260486009: + text: SNOMED:260486009 + description: Maxillary sinus setting + title: Maxillary sinus setting + SNOMED:260487000: + text: SNOMED:260487000 + description: Dental panoramic + title: Dental panoramic + SNOMED:260489002: + text: SNOMED:260489002 + description: Implant setting projection + title: Implant setting projection + SNOMED:260490006: + text: SNOMED:260490006 + description: Segmental setting + title: Segmental setting + SNOMED:260491005: + text: SNOMED:260491005 + description: Axial view for sesamoid bones + title: Axial view for sesamoid bones + SNOMED:260492003: + text: SNOMED:260492003 + description: '["Brewerton''s projection"]' + title: Brewerton's projection + SNOMED:260493008: + text: SNOMED:260493008 + description: Harris Beath axial projection + title: Harris Beath axial projection + SNOMED:260494002: + text: SNOMED:260494002 + description: Intercondylar projection + title: Intercondylar projection + SNOMED:260496000: + text: SNOMED:260496000 + description: Judet projection + title: Judet projection + SNOMED:260497009: + text: SNOMED:260497009 + description: Mortice projection + title: Mortice projection + SNOMED:260499007: + text: SNOMED:260499007 + description: Occlusal projection + title: Occlusal projection + SNOMED:260500003: + text: SNOMED:260500003 + description: Projected oblique occlusal + title: Projected oblique occlusal + SNOMED:260501004: + text: SNOMED:260501004 + description: Lower true occlusal + title: Lower true occlusal + SNOMED:260502006: + text: SNOMED:260502006 + description: Power grip series + title: Power grip series + SNOMED:260503001: + text: SNOMED:260503001 + description: Radial head projection + title: Radial head projection + SNOMED:260504007: + text: SNOMED:260504007 + description: Skyline projection + title: Skyline projection + SNOMED:260506009: + text: SNOMED:260506009 + description: Van Rosen projection + title: Van Rosen projection + SNOMED:260514003: + text: SNOMED:260514003 + description: Via body reference line + title: Via body reference line + SNOMED:260520002: + text: SNOMED:260520002 + description: Extracorporeal + title: Extracorporeal + SNOMED:260521003: + text: SNOMED:260521003 + description: Internal + title: Internal + SNOMED:260528009: + text: SNOMED:260528009 + description: Median + title: Median + SNOMED:260529001: + text: SNOMED:260529001 + description: Vectors + title: Vectors + SNOMED:260530006: + text: SNOMED:260530006 + description: Via body region + title: Via body region + SNOMED:260532003: + text: SNOMED:260532003 + description: Thoracoabdominal + title: Thoracoabdominal + SNOMED:260535001: + text: SNOMED:260535001 + description: Lateral extrapleural + title: Lateral extrapleural + SNOMED:260541008: + text: SNOMED:260541008 + description: Nasopancreatic + title: Nasopancreatic + SNOMED:260544000: + text: SNOMED:260544000 + description: Endobronchial + title: Endobronchial + SNOMED:260549005: + text: SNOMED:260549005 + description: Orogastric + title: Orogastric + SNOMED:260568008: + text: SNOMED:260568008 + description: Via cardiovascular system + title: Via cardiovascular system + SNOMED:260602004: + text: SNOMED:260602004 + description: Via superficialized vessel (qualifier value) + title: Via superficialized vessel (qualifier value) + SNOMED:260620008: + text: SNOMED:260620008 + description: Postaural approach + title: Postaural approach + SNOMED:260637001: + text: SNOMED:260637001 + description: Sublabial transseptal + title: Sublabial transseptal + SNOMED:260641002: + text: SNOMED:260641002 + description: Extraperitoneal + title: Extraperitoneal + SNOMED:260642009: + text: SNOMED:260642009 + description: Retroperitoneal + title: Retroperitoneal + SNOMED:260668002: + text: SNOMED:260668002 + description: Venovenous + title: Venovenous + SNOMED:261045000: + text: SNOMED:261045000 + description: Anterior dorsal + title: Anterior dorsal + SNOMED:261052003: + text: SNOMED:261052003 + description: Aortocoronary + title: Aortocoronary + SNOMED:261054002: + text: SNOMED:261054002 + description: Arterio-arterial + title: Arterio-arterial + SNOMED:261055001: + text: SNOMED:261055001 + description: Arteriovenous + title: Arteriovenous + SNOMED:261057009: + text: SNOMED:261057009 + description: Between intestinal loops + title: Between intestinal loops + SNOMED:261059007: + text: SNOMED:261059007 + description: Bicoronal + title: Bicoronal + SNOMED:261065007: + text: SNOMED:261065007 + description: Circumareolar + title: Circumareolar + SNOMED:261067004: + text: SNOMED:261067004 + description: Dorsal part + title: Dorsal part + SNOMED:261073003: + text: SNOMED:261073003 + description: Epicardial + title: Epicardial + SNOMED:261074009: + text: SNOMED:261074009 + description: External + title: External + SNOMED:261075005: + text: SNOMED:261075005 + description: Extra-amniotic + title: Extra-amniotic + SNOMED:261076006: + text: SNOMED:261076006 + description: Extracoronal + title: Extracoronal + SNOMED:261089000: + text: SNOMED:261089000 + description: Inferior + title: Inferior + SNOMED:261094000: + text: SNOMED:261094000 + description: Into urinary bladder + title: Into urinary bladder + SNOMED:261095004: + text: SNOMED:261095004 + description: Into ureter + title: Into ureter + SNOMED:261097007: + text: SNOMED:261097007 + description: Intracoronal + title: Intracoronal + SNOMED:261100002: + text: SNOMED:261100002 + description: Intraperitoneal + title: Intraperitoneal + SNOMED:261101003: + text: SNOMED:261101003 + description: Intravascular + title: Intravascular + SNOMED:261117009: + text: SNOMED:261117009 + description: Laryngotracheal + title: Laryngotracheal + SNOMED:261119007: + text: SNOMED:261119007 + description: Lateral part + title: Lateral part + SNOMED:261122009: + text: SNOMED:261122009 + description: Lower + title: Lower + SNOMED:261123004: + text: SNOMED:261123004 + description: Lower anterior + title: Lower anterior + SNOMED:261128008: + text: SNOMED:261128008 + description: Medial part + title: Medial part + SNOMED:261131009: + text: SNOMED:261131009 + description: Midaxillary + title: Midaxillary + SNOMED:261132002: + text: SNOMED:261132002 + description: Midclavicular + title: Midclavicular + SNOMED:261133007: + text: SNOMED:261133007 + description: Middle third + title: Middle third + SNOMED:261136004: + text: SNOMED:261136004 + description: Mural + title: Mural + SNOMED:261137008: + text: SNOMED:261137008 + description: Musculocutaneous + title: Musculocutaneous + SNOMED:261146002: + text: SNOMED:261146002 + description: Para-aortic + title: Para-aortic + SNOMED:261147006: + text: SNOMED:261147006 + description: Paracolic + title: Paracolic + SNOMED:261148001: + text: SNOMED:261148001 + description: Paraspinal + title: Paraspinal + SNOMED:261149009: + text: SNOMED:261149009 + description: Parasternal + title: Parasternal + SNOMED:261154000: + text: SNOMED:261154000 + description: Penis and urinary bladder neck + title: Penis and urinary bladder neck + SNOMED:261156003: + text: SNOMED:261156003 + description: Periadrenal + title: Periadrenal + SNOMED:261165005: + text: SNOMED:261165005 + description: Posterior dorsal + title: Posterior dorsal + SNOMED:261172006: + text: SNOMED:261172006 + description: Proximal third + title: Proximal third + SNOMED:261174007: + text: SNOMED:261174007 + description: Retrocecal (qualifier value) + title: Retrocecal (qualifier value) + SNOMED:261175008: + text: SNOMED:261175008 + description: Retroduodenal + title: Retroduodenal + SNOMED:261181000: + text: SNOMED:261181000 + description: Tracheobronchial + title: Tracheobronchial + SNOMED:261183002: + text: SNOMED:261183002 + description: Upper + title: Upper + SNOMED:261184008: + text: SNOMED:261184008 + description: Upper anterior + title: Upper anterior + SNOMED:261185009: + text: SNOMED:261185009 + description: Venoarterial + title: Venoarterial + SNOMED:261186005: + text: SNOMED:261186005 + description: Ventral part + title: Ventral part + SNOMED:261411001: + text: SNOMED:261411001 + description: Distal third + title: Distal third + SNOMED:261446009: + text: SNOMED:261446009 + description: Transpulmonary annulus + title: Transpulmonary annulus + SNOMED:261466000: + text: SNOMED:261466000 + description: Via intrapulmonary trunk tunnel + title: Via intrapulmonary trunk tunnel + SNOMED:261469007: + text: SNOMED:261469007 + description: Via orbitotomy + title: Via orbitotomy + SNOMED:261760007: + text: SNOMED:261760007 + description: Deep to rectus abdominis + title: Deep to rectus abdominis + SNOMED:261788001: + text: SNOMED:261788001 + description: Exteriorized (qualifier value) + title: Exteriorized (qualifier value) + SNOMED:261799004: + text: SNOMED:261799004 + description: From existing graft to coronary artery + title: From existing graft to coronary artery + SNOMED:261847009: + text: SNOMED:261847009 + description: Intracervical + title: Intracervical + SNOMED:261851006: + text: SNOMED:261851006 + description: Internally to bladder + title: Internally to bladder + SNOMED:261945002: + text: SNOMED:261945002 + description: Mixed venoarterial and venovenous + title: Mixed venoarterial and venovenous + SNOMED:261964008: + text: SNOMED:261964008 + description: Muscle fibers only (qualifier value) + title: Muscle fibers only (qualifier value) + SNOMED:261980003: + text: SNOMED:261980003 + description: Neuromuscular junction only + title: Neuromuscular junction only + SNOMED:262379005: + text: SNOMED:262379005 + description: Dominant side + title: Dominant side + SNOMED:262458006: + text: SNOMED:262458006 + description: Non-dominant side + title: Non-dominant side + SNOMED:263672002: + text: SNOMED:263672002 + description: Anocutaneous + title: Anocutaneous + SNOMED:263674001: + text: SNOMED:263674001 + description: Anovestibular + title: Anovestibular + SNOMED:263759007: + text: SNOMED:263759007 + description: Foraminal + title: Foraminal + SNOMED:263794000: + text: SNOMED:263794000 + description: Left side-by-side + title: Left side-by-side + SNOMED:263795004: + text: SNOMED:263795004 + description: Left sided + title: Left sided + SNOMED:263830001: + text: SNOMED:263830001 + description: Panacinar + title: Panacinar + SNOMED:263831002: + text: SNOMED:263831002 + description: Panlobular + title: Panlobular + SNOMED:263838008: + text: SNOMED:263838008 + description: Periacinar + title: Periacinar + SNOMED:263846009: + text: SNOMED:263846009 + description: Prevascular + title: Prevascular + SNOMED:263848005: + text: SNOMED:263848005 + description: Proximal acinar + title: Proximal acinar + SNOMED:263869007: + text: SNOMED:263869007 + description: Separate + title: Separate + SNOMED:263887005: + text: SNOMED:263887005 + description: Subcutaneous + title: Subcutaneous + SNOMED:263938007: + text: SNOMED:263938007 + description: Above middle turbinate + title: Above middle turbinate + SNOMED:263942005: + text: SNOMED:263942005 + description: Anterior segment + title: Anterior segment + SNOMED:263943000: + text: SNOMED:263943000 + description: Anterior wall + title: Anterior wall + SNOMED:263952009: + text: SNOMED:263952009 + description: Periorbital + title: Periorbital + SNOMED:263953004: + text: SNOMED:263953004 + description: Perioral + title: Perioral + SNOMED:263955006: + text: SNOMED:263955006 + description: Atlantoaxial + title: Atlantoaxial + SNOMED:263958008: + text: SNOMED:263958008 + description: Between left common carotid and brachiocephalic arteries + title: Between left common carotid and brachiocephalic arteries + SNOMED:263959000: + text: SNOMED:263959000 + description: Between left subclavian and common carotid arteries + title: Between left subclavian and common carotid arteries + SNOMED:263965000: + text: SNOMED:263965000 + description: Bronchocutaneous + title: Bronchocutaneous + SNOMED:263966004: + text: SNOMED:263966004 + description: Bronchopleural + title: Bronchopleural + SNOMED:263969006: + text: SNOMED:263969006 + description: Centriacinar + title: Centriacinar + SNOMED:263970007: + text: SNOMED:263970007 + description: Centrilobular + title: Centrilobular + SNOMED:263974003: + text: SNOMED:263974003 + description: Cervicothoracic + title: Cervicothoracic + SNOMED:263975002: + text: SNOMED:263975002 + description: Cervicothoracolumbar + title: Cervicothoracolumbar + SNOMED:263981005: + text: SNOMED:263981005 + description: Distal to left subclavian artery + title: Distal to left subclavian artery + SNOMED:263990003: + text: SNOMED:263990003 + description: Duodenoduodenal + title: Duodenoduodenal + SNOMED:263991004: + text: SNOMED:263991004 + description: Duodenojejunal + title: Duodenojejunal + SNOMED:263996009: + text: SNOMED:263996009 + description: Extrafoveal + title: Extrafoveal + SNOMED:263997000: + text: SNOMED:263997000 + description: Extraureteric + title: Extraureteric + SNOMED:263998005: + text: SNOMED:263998005 + description: Extravaginal + title: Extravaginal + SNOMED:263999002: + text: SNOMED:263999002 + description: From anterosuperior-superior bridging leaflet commissure + title: From anterosuperior-superior bridging leaflet commissure + SNOMED:264000000: + text: SNOMED:264000000 + description: From left inferior bridging leaflet-lateral commissure + title: From left inferior bridging leaflet-lateral commissure + SNOMED:264001001: + text: SNOMED:264001001 + description: From left septal commissure + title: From left septal commissure + SNOMED:264002008: + text: SNOMED:264002008 + description: From left superior bridging leaflet-lateral commissure + title: From left superior bridging leaflet-lateral commissure + SNOMED:264004009: + text: SNOMED:264004009 + description: From left ventricular component + title: From left ventricular component + SNOMED:264005005: + text: SNOMED:264005005 + description: From right anterosuperior-inferior commissure + title: From right anterosuperior-inferior commissure + SNOMED:264006006: + text: SNOMED:264006006 + description: From right inferior bridging leaflet-inferior commissure + title: From right inferior bridging leaflet-inferior commissure + SNOMED:264007002: + text: SNOMED:264007002 + description: From right septal commissure + title: From right septal commissure + SNOMED:264008007: + text: SNOMED:264008007 + description: From right ventricular component + title: From right ventricular component + SNOMED:264011008: + text: SNOMED:264011008 + description: Gastroduodenal + title: Gastroduodenal + SNOMED:264012001: + text: SNOMED:264012001 + description: Gastrogastric + title: Gastrogastric + SNOMED:264015004: + text: SNOMED:264015004 + description: Hepatopleural + title: Hepatopleural + SNOMED:264023002: + text: SNOMED:264023002 + description: Ileocecal (qualifier value) + title: Ileocecal (qualifier value) + SNOMED:264024008: + text: SNOMED:264024008 + description: Ileocolic + title: Ileocolic + SNOMED:264025009: + text: SNOMED:264025009 + description: Iliofemoral vein zone + title: Iliofemoral vein zone + SNOMED:264026005: + text: SNOMED:264026005 + description: Ileo-ileal + title: Ileo-ileal + SNOMED:264027001: + text: SNOMED:264027001 + description: Ileorectal + title: Ileorectal + SNOMED:264030008: + text: SNOMED:264030008 + description: In joint + title: In joint + SNOMED:264031007: + text: SNOMED:264031007 + description: In situ + title: In situ + SNOMED:264034004: + text: SNOMED:264034004 + description: Infracardiac + title: Infracardiac + SNOMED:264035003: + text: SNOMED:264035003 + description: Infravesical + title: Infravesical + SNOMED:264040006: + text: SNOMED:264040006 + description: Interchordal + title: Interchordal + SNOMED:264041005: + text: SNOMED:264041005 + description: Interdigital + title: Interdigital + SNOMED:264042003: + text: SNOMED:264042003 + description: Intervertebral + title: Intervertebral + SNOMED:264043008: + text: SNOMED:264043008 + description: Intraligamentous + title: Intraligamentous + SNOMED:264044002: + text: SNOMED:264044002 + description: Intracardiac + title: Intracardiac + SNOMED:264045001: + text: SNOMED:264045001 + description: Intraluminal + title: Intraluminal + SNOMED:264046000: + text: SNOMED:264046000 + description: Intramammary + title: Intramammary + SNOMED:264047009: + text: SNOMED:264047009 + description: Intrapulmonary + title: Intrapulmonary + SNOMED:264049007: + text: SNOMED:264049007 + description: Intravaginal + title: Intravaginal + SNOMED:264056001: + text: SNOMED:264056001 + description: Lateral column + title: Lateral column + SNOMED:264060003: + text: SNOMED:264060003 + description: Lateral segment + title: Lateral segment + SNOMED:264065008: + text: SNOMED:264065008 + description: Left anterior + title: Left anterior + SNOMED:264067000: + text: SNOMED:264067000 + description: Left lateral wall + title: Left lateral wall + SNOMED:264068005: + text: SNOMED:264068005 + description: Left lower segment + title: Left lower segment + SNOMED:264076007: + text: SNOMED:264076007 + description: Lower left parasternal + title: Lower left parasternal + SNOMED:264081003: + text: SNOMED:264081003 + description: Lower third + title: Lower third + SNOMED:264083000: + text: SNOMED:264083000 + description: Lumbosacral + title: Lumbosacral + SNOMED:264096004: + text: SNOMED:264096004 + description: Medial segment + title: Medial segment + SNOMED:264103001: + text: SNOMED:264103001 + description: Midtarsal + title: Midtarsal + SNOMED:264107000: + text: SNOMED:264107000 + description: Paravertebral + title: Paravertebral + SNOMED:264110007: + text: SNOMED:264110007 + description: Esophagocolonic (qualifier value) + title: Esophagocolonic (qualifier value) + SNOMED:264111006: + text: SNOMED:264111006 + description: Esophagogastric (qualifier value) + title: Esophagogastric (qualifier value) + SNOMED:264112004: + text: SNOMED:264112004 + description: Esophagojejunal (qualifier value) + title: Esophagojejunal (qualifier value) + SNOMED:264114003: + text: SNOMED:264114003 + description: Ostium + title: Ostium + SNOMED:264117005: + text: SNOMED:264117005 + description: Paraesophageal (qualifier value) + title: Paraesophageal (qualifier value) + SNOMED:264118000: + text: SNOMED:264118000 + description: Paraduodenal + title: Paraduodenal + SNOMED:264119008: + text: SNOMED:264119008 + description: Parafoveal + title: Parafoveal + SNOMED:264121003: + text: SNOMED:264121003 + description: Paramacular + title: Paramacular + SNOMED:264123000: + text: SNOMED:264123000 + description: Paraseptal + title: Paraseptal + SNOMED:264124006: + text: SNOMED:264124006 + description: Paraumbilical + title: Paraumbilical + SNOMED:264126008: + text: SNOMED:264126008 + description: Paravascular + title: Paravascular + SNOMED:264127004: + text: SNOMED:264127004 + description: Paraovarian + title: Paraovarian + SNOMED:264128009: + text: SNOMED:264128009 + description: Paratracheal + title: Paratracheal + SNOMED:264131005: + text: SNOMED:264131005 + description: Peri-intestinal + title: Peri-intestinal + SNOMED:264133008: + text: SNOMED:264133008 + description: Perianal + title: Perianal + SNOMED:264136000: + text: SNOMED:264136000 + description: Perihepatic + title: Perihepatic + SNOMED:264137009: + text: SNOMED:264137009 + description: Perinephric + title: Perinephric + SNOMED:264139007: + text: SNOMED:264139007 + description: Peripancreatic + title: Peripancreatic + SNOMED:264142001: + text: SNOMED:264142001 + description: Perisplenic + title: Perisplenic + SNOMED:264153007: + text: SNOMED:264153007 + description: Posterior pole + title: Posterior pole + SNOMED:264154001: + text: SNOMED:264154001 + description: Posterior segment + title: Posterior segment + SNOMED:264159006: + text: SNOMED:264159006 + description: Posterior wall + title: Posterior wall + SNOMED:264168008: + text: SNOMED:264168008 + description: Rectocloacal + title: Rectocloacal + SNOMED:264169000: + text: SNOMED:264169000 + description: Rectocutaneous + title: Rectocutaneous + SNOMED:264170004: + text: SNOMED:264170004 + description: Rectourethral + title: Rectourethral + SNOMED:264171000: + text: SNOMED:264171000 + description: Rectovaginal + title: Rectovaginal + SNOMED:264172007: + text: SNOMED:264172007 + description: Rectovesical + title: Rectovesical + SNOMED:264173002: + text: SNOMED:264173002 + description: Rectovulval + title: Rectovulval + SNOMED:264174008: + text: SNOMED:264174008 + description: Retromammary + title: Retromammary + SNOMED:264175009: + text: SNOMED:264175009 + description: Retrocolumellar + title: Retrocolumellar + SNOMED:264176005: + text: SNOMED:264176005 + description: Right anterior + title: Right anterior + SNOMED:264178006: + text: SNOMED:264178006 + description: Right lateral wall + title: Right lateral wall + SNOMED:264179003: + text: SNOMED:264179003 + description: Right side-by-side + title: Right side-by-side + SNOMED:264180000: + text: SNOMED:264180000 + description: Right sided + title: Right sided + SNOMED:264193005: + text: SNOMED:264193005 + description: Segment + title: Segment + SNOMED:264201006: + text: SNOMED:264201006 + description: Sternocostal + title: Sternocostal + SNOMED:264202004: + text: SNOMED:264202004 + description: Subaortic + title: Subaortic + SNOMED:264205002: + text: SNOMED:264205002 + description: Subareolar + title: Subareolar + SNOMED:264206001: + text: SNOMED:264206001 + description: Subconjunctival + title: Subconjunctival + SNOMED:264208000: + text: SNOMED:264208000 + description: Subcostal + title: Subcostal + SNOMED:264209008: + text: SNOMED:264209008 + description: Subfoveal + title: Subfoveal + SNOMED:264216009: + text: SNOMED:264216009 + description: Superficial to rectus abdominis + title: Superficial to rectus abdominis + SNOMED:264217000: + text: SNOMED:264217000 + description: Superior + title: Superior + SNOMED:264221007: + text: SNOMED:264221007 + description: Supraumbilical + title: Supraumbilical + SNOMED:264222000: + text: SNOMED:264222000 + description: Supracardiac + title: Supracardiac + SNOMED:264224004: + text: SNOMED:264224004 + description: Supraglottic + title: Supraglottic + SNOMED:264225003: + text: SNOMED:264225003 + description: Suprahepatic + title: Suprahepatic + SNOMED:264227006: + text: SNOMED:264227006 + description: Tarsometatarsal + title: Tarsometatarsal + SNOMED:264232007: + text: SNOMED:264232007 + description: Thoracolumbar + title: Thoracolumbar + SNOMED:264245006: + text: SNOMED:264245006 + description: Upper left parasternal + title: Upper left parasternal + SNOMED:264253003: + text: SNOMED:264253003 + description: Upper third + title: Upper third + SNOMED:264261008: + text: SNOMED:264261008 + description: Cholecystoduodenal + title: Cholecystoduodenal + SNOMED:264262001: + text: SNOMED:264262001 + description: Cholecystenteric (qualifier value) + title: Cholecystenteric (qualifier value) + SNOMED:264263006: + text: SNOMED:264263006 + description: Cholecystogastric + title: Cholecystogastric + SNOMED:264264000: + text: SNOMED:264264000 + description: Choledochoduodenal + title: Choledochoduodenal + SNOMED:264266003: + text: SNOMED:264266003 + description: Colocolic + title: Colocolic + SNOMED:264267007: + text: SNOMED:264267007 + description: Colorectal + title: Colorectal + SNOMED:264463009: + text: SNOMED:264463009 + description: Epitrochlear + title: Epitrochlear + SNOMED:264940008: + text: SNOMED:264940008 + description: Under inferior bridging leaflet + title: Under inferior bridging leaflet + SNOMED:264941007: + text: SNOMED:264941007 + description: Under superior bridging leaflet + title: Under superior bridging leaflet + SNOMED:272288000: + text: SNOMED:272288000 + description: Onlay + title: Onlay + SNOMED:272425003: + text: SNOMED:272425003 + description: General site descriptor + title: General site descriptor + SNOMED:272427006: + text: SNOMED:272427006 + description: Anatomical part descriptor + title: Anatomical part descriptor + SNOMED:272428001: + text: SNOMED:272428001 + description: Anatomical third + title: Anatomical third + SNOMED:272429009: + text: SNOMED:272429009 + description: Part structure + title: Part structure + SNOMED:272430004: + text: SNOMED:272430004 + description: Column structure + title: Column structure + SNOMED:272431000: + text: SNOMED:272431000 + description: Segment structure + title: Segment structure + SNOMED:272432007: + text: SNOMED:272432007 + description: Wall structure + title: Wall structure + SNOMED:272434008: + text: SNOMED:272434008 + description: Anatomical relationship descriptor + title: Anatomical relationship descriptor + SNOMED:272435009: + text: SNOMED:272435009 + description: Centri-location + title: Centri-location + SNOMED:272436005: + text: SNOMED:272436005 + description: Circum-location + title: Circum-location + SNOMED:272437001: + text: SNOMED:272437001 + description: Extra-location + title: Extra-location + SNOMED:272438006: + text: SNOMED:272438006 + description: Extrapleural + title: Extrapleural + SNOMED:272439003: + text: SNOMED:272439003 + description: Infra-location + title: Infra-location + SNOMED:272440001: + text: SNOMED:272440001 + description: Inter-location + title: Inter-location + SNOMED:272441002: + text: SNOMED:272441002 + description: Intra-location + title: Intra-location + SNOMED:272442009: + text: SNOMED:272442009 + description: Mid-location + title: Mid-location + SNOMED:272443004: + text: SNOMED:272443004 + description: Pan-location + title: Pan-location + SNOMED:272444005: + text: SNOMED:272444005 + description: Para-location + title: Para-location + SNOMED:272446007: + text: SNOMED:272446007 + description: Per-location + title: Per-location + SNOMED:272447003: + text: SNOMED:272447003 + description: Peri-location + title: Peri-location + SNOMED:272448008: + text: SNOMED:272448008 + description: Post-location + title: Post-location + SNOMED:272449000: + text: SNOMED:272449000 + description: Pre-location + title: Pre-location + SNOMED:272450000: + text: SNOMED:272450000 + description: Retro-location + title: Retro-location + SNOMED:272451001: + text: SNOMED:272451001 + description: Sub-location + title: Sub-location + SNOMED:272452008: + text: SNOMED:272452008 + description: Supra-location + title: Supra-location + SNOMED:272455005: + text: SNOMED:272455005 + description: Inferosuperior projection + title: Inferosuperior projection + SNOMED:272456006: + text: SNOMED:272456006 + description: Apical projection + title: Apical projection + SNOMED:272457002: + text: SNOMED:272457002 + description: Vertical projection + title: Vertical projection + SNOMED:272458007: + text: SNOMED:272458007 + description: Prone projection + title: Prone projection + SNOMED:272459004: + text: SNOMED:272459004 + description: Supine projection + title: Supine projection + SNOMED:272460009: + text: SNOMED:272460009 + description: Anterior projection + title: Anterior projection + SNOMED:272461008: + text: SNOMED:272461008 + description: Right posterior projection + title: Right posterior projection + SNOMED:272462001: + text: SNOMED:272462001 + description: Left posterior projection + title: Left posterior projection + SNOMED:272464000: + text: SNOMED:272464000 + description: Perorbital projection + title: Perorbital projection + SNOMED:272465004: + text: SNOMED:272465004 + description: Temporomandibular joint projection + title: Temporomandibular joint projection + SNOMED:272466003: + text: SNOMED:272466003 + description: Optic foramen projection + title: Optic foramen projection + SNOMED:272467007: + text: SNOMED:272467007 + description: Lateral facial skeleton projection + title: Lateral facial skeleton projection + SNOMED:272468002: + text: SNOMED:272468002 + description: Ear projection + title: Ear projection + SNOMED:272469005: + text: SNOMED:272469005 + description: Mid face projection + title: Mid face projection + SNOMED:272470006: + text: SNOMED:272470006 + description: Cervical spine projection + title: Cervical spine projection + SNOMED:272472003: + text: SNOMED:272472003 + description: Macro projection + title: Macro projection + SNOMED:272473008: + text: SNOMED:272473008 + description: Outlet projection + title: Outlet projection + SNOMED:272474002: + text: SNOMED:272474002 + description: '["Swimmer''s projection"]' + title: Swimmer's projection + SNOMED:272475001: + text: SNOMED:272475001 + description: Tibial tuberosity projection + title: Tibial tuberosity projection + SNOMED:272476000: + text: SNOMED:272476000 + description: Transthoracic projection + title: Transthoracic projection + SNOMED:272478004: + text: SNOMED:272478004 + description: Transcranial projection + title: Transcranial projection + SNOMED:272479007: + text: SNOMED:272479007 + description: Posteroanterior projection + title: Posteroanterior projection + SNOMED:272480005: + text: SNOMED:272480005 + description: Horizontal projection + title: Horizontal projection + SNOMED:272481009: + text: SNOMED:272481009 + description: Erect projection + title: Erect projection + SNOMED:272482002: + text: SNOMED:272482002 + description: Adduction projection + title: Adduction projection + SNOMED:272483007: + text: SNOMED:272483007 + description: True projection + title: True projection + SNOMED:272484001: + text: SNOMED:272484001 + description: Contralateral projection + title: Contralateral projection + SNOMED:272485000: + text: SNOMED:272485000 + description: Clockface position + title: Clockface position + SNOMED:272486004: + text: SNOMED:272486004 + description: Trans-direction + title: Trans-direction + SNOMED:272487008: + text: SNOMED:272487008 + description: Into-structure + title: Into-structure + SNOMED:272488003: + text: SNOMED:272488003 + description: From-structure + title: From-structure + SNOMED:272489006: + text: SNOMED:272489006 + description: Via values + title: Via values + SNOMED:272496008: + text: SNOMED:272496008 + description: Via incision + title: Via incision + SNOMED:276749003: + text: SNOMED:276749003 + description: Epi-location + title: Epi-location + SNOMED:276825009: + text: SNOMED:276825009 + description: Overlapping sites + title: Overlapping sites + SNOMED:276979001: + text: SNOMED:276979001 + description: Aortoiliac + title: Aortoiliac + SNOMED:277292000: + text: SNOMED:277292000 + description: Endo-location + title: Endo-location + SNOMED:277407002: + text: SNOMED:277407002 + description: Deep locations + title: Deep locations + SNOMED:277409004: + text: SNOMED:277409004 + description: Superficial locations + title: Superficial locations + SNOMED:277410009: + text: SNOMED:277410009 + description: Anterior locations + title: Anterior locations + SNOMED:277411008: + text: SNOMED:277411008 + description: Posterior locations + title: Posterior locations + SNOMED:277412001: + text: SNOMED:277412001 + description: Proximal locations + title: Proximal locations + SNOMED:277413006: + text: SNOMED:277413006 + description: Distal locations + title: Distal locations + SNOMED:277414000: + text: SNOMED:277414000 + description: Between locations + title: Between locations + SNOMED:277415004: + text: SNOMED:277415004 + description: Above locations + title: Above locations + SNOMED:277593009: + text: SNOMED:277593009 + description: Right posterior + title: Right posterior + SNOMED:277594003: + text: SNOMED:277594003 + description: Left posterior + title: Left posterior + SNOMED:277681008: + text: SNOMED:277681008 + description: Intrastomal + title: Intrastomal + SNOMED:277685004: + text: SNOMED:277685004 + description: Tubo-ovarian + title: Tubo-ovarian + SNOMED:277686003: + text: SNOMED:277686003 + description: Peritubular + title: Peritubular + SNOMED:277806003: + text: SNOMED:277806003 + description: Sidedness + title: Sidedness + SNOMED:278227002: + text: SNOMED:278227002 + description: Limited structures + title: Limited structures + SNOMED:278255003: + text: SNOMED:278255003 + description: Posterior projection + title: Posterior projection + SNOMED:278267001: + text: SNOMED:278267001 + description: Abduction projection + title: Abduction projection + SNOMED:278318001: + text: SNOMED:278318001 + description: Transorbital projection + title: Transorbital projection + SNOMED:278701003: + text: SNOMED:278701003 + description: Periumbilical + title: Periumbilical + SNOMED:278702005: + text: SNOMED:278702005 + description: Transumbilical + title: Transumbilical + SNOMED:285418008: + text: SNOMED:285418008 + description: Subcuticular + title: Subcuticular + SNOMED:298107004: + text: SNOMED:298107004 + description: Orthotopic + title: Orthotopic + SNOMED:298108009: + text: SNOMED:298108009 + description: Heterotopic + title: Heterotopic + SNOMED:298109001: + text: SNOMED:298109001 + description: Ectopic + title: Ectopic + SNOMED:303218009: + text: SNOMED:303218009 + description: Subfascial + title: Subfascial + SNOMED:303231004: + text: SNOMED:303231004 + description: Intracranial + title: Intracranial + SNOMED:303232006: + text: SNOMED:303232006 + description: Extracranial + title: Extracranial + SNOMED:303483009: + text: SNOMED:303483009 + description: Subcranial + title: Subcranial + SNOMED:304047000: + text: SNOMED:304047000 + description: Transannular + title: Transannular + SNOMED:304059001: + text: SNOMED:304059001 + description: Endocardial + title: Endocardial + SNOMED:306766009: + text: SNOMED:306766009 + description: Low - site descriptor + title: Low - site descriptor + SNOMED:306767000: + text: SNOMED:306767000 + description: High - site descriptor + title: High - site descriptor + SNOMED:312206004: + text: SNOMED:312206004 + description: Periapical + title: Periapical + SNOMED:3583002: + text: SNOMED:3583002 + description: Caudal + title: Caudal + SNOMED:373863008: + text: SNOMED:373863008 + description: Intracavitary + title: Intracavitary + SNOMED:397406000: + text: SNOMED:397406000 + description: Collateral branch of vessel + title: Collateral branch of vessel + SNOMED:397421006: + text: SNOMED:397421006 + description: Vessel origin + title: Vessel origin + SNOMED:398236008: + text: SNOMED:398236008 + description: Intrauterine + title: Intrauterine + SNOMED:398994001: + text: SNOMED:398994001 + description: Five chamber view + title: Five chamber view + SNOMED:398996004: + text: SNOMED:398996004 + description: Leonard-George projection + title: Leonard-George projection + SNOMED:398998003: + text: SNOMED:398998003 + description: Right ventricular inflow tract view + title: Right ventricular inflow tract view + SNOMED:399000008: + text: SNOMED:399000008 + description: Mayer projection + title: Mayer projection + SNOMED:399001007: + text: SNOMED:399001007 + description: Posterior emissive projection + title: Posterior emissive projection + SNOMED:399002000: + text: SNOMED:399002000 + description: Nolke projection + title: Nolke projection + SNOMED:399003005: + text: SNOMED:399003005 + description: Hughston projection + title: Hughston projection + SNOMED:399004004: + text: SNOMED:399004004 + description: Oblique axial projection + title: Oblique axial projection + SNOMED:399005003: + text: SNOMED:399005003 + description: Miller projection + title: Miller projection + SNOMED:399006002: + text: SNOMED:399006002 + description: Left posterior oblique projection + title: Left posterior oblique projection + SNOMED:399011000: + text: SNOMED:399011000 + description: Axillary tail mammography view + title: Axillary tail mammography view + SNOMED:399012007: + text: SNOMED:399012007 + description: Medial-lateral emissive projection + title: Medial-lateral emissive projection + SNOMED:399013002: + text: SNOMED:399013002 + description: Chassard-Lapin projection + title: Chassard-Lapin projection + SNOMED:399022001: + text: SNOMED:399022001 + description: Pirie projection + title: Pirie projection + SNOMED:399024000: + text: SNOMED:399024000 + description: May projection + title: May projection + SNOMED:399025004: + text: SNOMED:399025004 + description: Ischerwood projection + title: Ischerwood projection + SNOMED:399026003: + text: SNOMED:399026003 + description: Zanelli projection + title: Zanelli projection + SNOMED:399028002: + text: SNOMED:399028002 + description: Clements projection + title: Clements projection + SNOMED:399033003: + text: SNOMED:399033003 + description: Frontal projection + title: Frontal projection + SNOMED:399036006: + text: SNOMED:399036006 + description: Parasternal short axis view at the mitral valve level + title: Parasternal short axis view at the mitral valve level + SNOMED:399037002: + text: SNOMED:399037002 + description: Lewis projection + title: Lewis projection + SNOMED:399038007: + text: SNOMED:399038007 + description: Right posterior oblique projection + title: Right posterior oblique projection + SNOMED:399043000: + text: SNOMED:399043000 + description: Cardiac imaging views + title: Cardiac imaging views + SNOMED:399059000: + text: SNOMED:399059000 + description: Postero-anterior oblique projection + title: Postero-anterior oblique projection + SNOMED:399061009: + text: SNOMED:399061009 + description: Axial projection + title: Axial projection + SNOMED:399065000: + text: SNOMED:399065000 + description: Causton projection + title: Causton projection + SNOMED:399067008: + text: SNOMED:399067008 + description: Lateral projection + title: Lateral projection + SNOMED:399071006: + text: SNOMED:399071006 + description: Plantodorsal projection + title: Plantodorsal projection + SNOMED:399073009: + text: SNOMED:399073009 + description: Fuchs projection + title: Fuchs projection + SNOMED:399074003: + text: SNOMED:399074003 + description: Left anterior oblique emissive projection + title: Left anterior oblique emissive projection + SNOMED:399075002: + text: SNOMED:399075002 + description: Right posterior oblique emissive projection + title: Right posterior oblique emissive projection + SNOMED:399080006: + text: SNOMED:399080006 + description: Kuchendorf projection + title: Kuchendorf projection + SNOMED:399082003: + text: SNOMED:399082003 + description: Gaynor-Hart projection + title: Gaynor-Hart projection + SNOMED:399083008: + text: SNOMED:399083008 + description: Hsieh projection + title: Hsieh projection + SNOMED:399089007: + text: SNOMED:399089007 + description: Oblique axial emissive projection + title: Oblique axial emissive projection + SNOMED:399098005: + text: SNOMED:399098005 + description: Staunig projection + title: Staunig projection + SNOMED:399099002: + text: SNOMED:399099002 + description: Latero-medial oblique projection + title: Latero-medial oblique projection + SNOMED:399101009: + text: SNOMED:399101009 + description: Cranio-caudal projection exaggerated medially + title: Cranio-caudal projection exaggerated medially + SNOMED:399103007: + text: SNOMED:399103007 + description: Friedman projection + title: Friedman projection + SNOMED:399106004: + text: SNOMED:399106004 + description: Suprasternal long axis view + title: Suprasternal long axis view + SNOMED:399108003: + text: SNOMED:399108003 + description: Right anterior oblique emissive projection + title: Right anterior oblique emissive projection + SNOMED:399110001: + text: SNOMED:399110001 + description: Tangential projection + title: Tangential projection + SNOMED:399113004: + text: SNOMED:399113004 + description: Eponymous projection + title: Eponymous projection + SNOMED:399118008: + text: SNOMED:399118008 + description: Left lateral emissive projection + title: Left lateral emissive projection + SNOMED:399125001: + text: SNOMED:399125001 + description: Twining projection + title: Twining projection + SNOMED:399127009: + text: SNOMED:399127009 + description: Teufel projection + title: Teufel projection + SNOMED:399129007: + text: SNOMED:399129007 + description: Holly projection + title: Holly projection + SNOMED:399130002: + text: SNOMED:399130002 + description: West Point projection + title: West Point projection + SNOMED:399132005: + text: SNOMED:399132005 + description: Frontal-oblique axial projection + title: Frontal-oblique axial projection + SNOMED:399135007: + text: SNOMED:399135007 + description: Left anterior oblique projection + title: Left anterior oblique projection + SNOMED:399136008: + text: SNOMED:399136008 + description: Left posterior oblique emissive projection + title: Left posterior oblique emissive projection + SNOMED:399138009: + text: SNOMED:399138009 + description: Penner projection + title: Penner projection + SNOMED:399139001: + text: SNOMED:399139001 + description: Parasternal long axis view + title: Parasternal long axis view + SNOMED:399142007: + text: SNOMED:399142007 + description: Albers-Schönberg projection + title: Albers-Schönberg projection + SNOMED:399145009: + text: SNOMED:399145009 + description: Suprasternal short axis view + title: Suprasternal short axis view + SNOMED:399146005: + text: SNOMED:399146005 + description: Grashey projection + title: Grashey projection + SNOMED:399148006: + text: SNOMED:399148006 + description: Chamberlain projection + title: Chamberlain projection + SNOMED:399152006: + text: SNOMED:399152006 + description: Kandel projection + title: Kandel projection + SNOMED:399156009: + text: SNOMED:399156009 + description: Laquerriere-Pierquin projection + title: Laquerriere-Pierquin projection + SNOMED:399157000: + text: SNOMED:399157000 + description: '["Norgaard''s projection"]' + title: Norgaard's projection + SNOMED:399159002: + text: SNOMED:399159002 + description: Latero-medial oblique emissive projection + title: Latero-medial oblique emissive projection + SNOMED:399160007: + text: SNOMED:399160007 + description: Frontal oblique projection + title: Frontal oblique projection + SNOMED:399161006: + text: SNOMED:399161006 + description: Cleavage mammography view + title: Cleavage mammography view + SNOMED:399162004: + text: SNOMED:399162004 + description: Cranio-caudal projection + title: Cranio-caudal projection + SNOMED:399163009: + text: SNOMED:399163009 + description: Magnified projection + title: Magnified projection + SNOMED:399168000: + text: SNOMED:399168000 + description: Hough projection + title: Hough projection + SNOMED:399169008: + text: SNOMED:399169008 + description: Lauenstein projection + title: Lauenstein projection + SNOMED:399171008: + text: SNOMED:399171008 + description: Ottonello projection + title: Ottonello projection + SNOMED:399173006: + text: SNOMED:399173006 + description: Left lateral projection + title: Left lateral projection + SNOMED:399179005: + text: SNOMED:399179005 + description: Lawrence projection + title: Lawrence projection + SNOMED:399181007: + text: SNOMED:399181007 + description: Pawlow projection + title: Pawlow projection + SNOMED:399182000: + text: SNOMED:399182000 + description: Oblique projection + title: Oblique projection + SNOMED:399184004: + text: SNOMED:399184004 + description: Left oblique projection + title: Left oblique projection + SNOMED:399188001: + text: SNOMED:399188001 + description: Superolateral to inferomedial oblique projection + title: Superolateral to inferomedial oblique projection + SNOMED:399192008: + text: SNOMED:399192008 + description: Cranio-caudal projection exaggerated laterally + title: Cranio-caudal projection exaggerated laterally + SNOMED:399195005: + text: SNOMED:399195005 + description: Right ventricular outflow tract view + title: Right ventricular outflow tract view + SNOMED:399196006: + text: SNOMED:399196006 + description: Caudo-cranial projection + title: Caudo-cranial projection + SNOMED:399198007: + text: SNOMED:399198007 + description: Right lateral projection + title: Right lateral projection + SNOMED:399199004: + text: SNOMED:399199004 + description: Henschen projection + title: Henschen projection + SNOMED:399200001: + text: SNOMED:399200001 + description: Subcostal short axis view + title: Subcostal short axis view + SNOMED:399201002: + text: SNOMED:399201002 + description: Judd projection + title: Judd projection + SNOMED:399206007: + text: SNOMED:399206007 + description: Law projection + title: Law projection + SNOMED:399212002: + text: SNOMED:399212002 + description: Camp-Coventry projection + title: Camp-Coventry projection + SNOMED:399214001: + text: SNOMED:399214001 + description: Apical four chamber view + title: Apical four chamber view + SNOMED:399215000: + text: SNOMED:399215000 + description: Wigby-Taylor projection + title: Wigby-Taylor projection + SNOMED:399218003: + text: SNOMED:399218003 + description: Arcelin projection + title: Arcelin projection + SNOMED:399225005: + text: SNOMED:399225005 + description: Oblique caudo-cranial projection + title: Oblique caudo-cranial projection + SNOMED:399227002: + text: SNOMED:399227002 + description: Kemp Harper projection + title: Kemp Harper projection + SNOMED:399232001: + text: SNOMED:399232001 + description: Apical two chamber view + title: Apical two chamber view + SNOMED:399234000: + text: SNOMED:399234000 + description: Rhese projection + title: Rhese projection + SNOMED:399236003: + text: SNOMED:399236003 + description: Right oblique projection + title: Right oblique projection + SNOMED:399237007: + text: SNOMED:399237007 + description: Alexander projection + title: Alexander projection + SNOMED:399239005: + text: SNOMED:399239005 + description: Parasternal short axis view at the aortic valve level + title: Parasternal short axis view at the aortic valve level + SNOMED:399241006: + text: SNOMED:399241006 + description: Titterington projection + title: Titterington projection + SNOMED:399242004: + text: SNOMED:399242004 + description: Acanthioparietal projection + title: Acanthioparietal projection + SNOMED:399243009: + text: SNOMED:399243009 + description: Settegast projection + title: Settegast projection + SNOMED:399245002: + text: SNOMED:399245002 + description: Cleaves projection + title: Cleaves projection + SNOMED:399246001: + text: SNOMED:399246001 + description: Blackett-Healy projection + title: Blackett-Healy projection + SNOMED:399247005: + text: SNOMED:399247005 + description: Tarrant projection + title: Tarrant projection + SNOMED:399251007: + text: SNOMED:399251007 + description: Lorenz projection + title: Lorenz projection + SNOMED:399255003: + text: SNOMED:399255003 + description: Submentovertical projection + title: Submentovertical projection + SNOMED:399260004: + text: SNOMED:399260004 + description: Mediolateral projection + title: Mediolateral projection + SNOMED:399263002: + text: SNOMED:399263002 + description: Beclere projection + title: Beclere projection + SNOMED:399265009: + text: SNOMED:399265009 + description: Exaggerated cranio-caudal projection + title: Exaggerated cranio-caudal projection + SNOMED:399268006: + text: SNOMED:399268006 + description: Medio-lateral oblique emissive projection + title: Medio-lateral oblique emissive projection + SNOMED:399270002: + text: SNOMED:399270002 + description: '["Towne''s projection"]' + title: Towne's projection + SNOMED:399271003: + text: SNOMED:399271003 + description: Parasternal short axis view at the papillary muscle level + title: Parasternal short axis view at the papillary muscle level + SNOMED:399272005: + text: SNOMED:399272005 + description: Parietoacanthial projection + title: Parietoacanthial projection + SNOMED:399273000: + text: SNOMED:399273000 + description: Sagittal-oblique axial emissive projection + title: Sagittal-oblique axial emissive projection + SNOMED:399277004: + text: SNOMED:399277004 + description: Hickey projection + title: Hickey projection + SNOMED:399278009: + text: SNOMED:399278009 + description: Cahoon projection + title: Cahoon projection + SNOMED:399280003: + text: SNOMED:399280003 + description: Kasabach projection + title: Kasabach projection + SNOMED:399281004: + text: SNOMED:399281004 + description: Fleischner projection + title: Fleischner projection + SNOMED:399284007: + text: SNOMED:399284007 + description: Merchant projection + title: Merchant projection + SNOMED:399285008: + text: SNOMED:399285008 + description: Holmblad projection + title: Holmblad projection + SNOMED:399288005: + text: SNOMED:399288005 + description: Oblique cranio-caudal projection + title: Oblique cranio-caudal projection + SNOMED:399290006: + text: SNOMED:399290006 + description: Schüller projection + title: Schüller projection + SNOMED:399292003: + text: SNOMED:399292003 + description: Stecher projection + title: Stecher projection + SNOMED:399296000: + text: SNOMED:399296000 + description: Taylor projection + title: Taylor projection + SNOMED:399297009: + text: SNOMED:399297009 + description: Right lateral emissive projection + title: Right lateral emissive projection + SNOMED:399300004: + text: SNOMED:399300004 + description: Lateral-medial emissive projection + title: Lateral-medial emissive projection + SNOMED:399303002: + text: SNOMED:399303002 + description: Dunlap projection + title: Dunlap projection + SNOMED:399306005: + text: SNOMED:399306005 + description: Parasternal short axis view + title: Parasternal short axis view + SNOMED:399308006: + text: SNOMED:399308006 + description: Lindblom projection + title: Lindblom projection + SNOMED:399310008: + text: SNOMED:399310008 + description: Subcostal long axis view + title: Subcostal long axis view + SNOMED:399311007: + text: SNOMED:399311007 + description: Grandy projection + title: Grandy projection + SNOMED:399312000: + text: SNOMED:399312000 + description: Antero-posterior oblique projection + title: Antero-posterior oblique projection + SNOMED:399313005: + text: SNOMED:399313005 + description: Swanson projection + title: Swanson projection + SNOMED:399316002: + text: SNOMED:399316002 + description: Parieto-orbital projection + title: Parieto-orbital projection + SNOMED:399318001: + text: SNOMED:399318001 + description: Kovacs projection + title: Kovacs projection + SNOMED:399320003: + text: SNOMED:399320003 + description: Clements-Nakayama projection + title: Clements-Nakayama projection + SNOMED:399321004: + text: SNOMED:399321004 + description: Anterior emissive projection + title: Anterior emissive projection + SNOMED:399325008: + text: SNOMED:399325008 + description: Sagittal-oblique axial projection + title: Sagittal-oblique axial projection + SNOMED:399327000: + text: SNOMED:399327000 + description: Low-Beer projection + title: Low-Beer projection + SNOMED:399330007: + text: SNOMED:399330007 + description: Valdini projection + title: Valdini projection + SNOMED:399332004: + text: SNOMED:399332004 + description: Kurzbauer projection + title: Kurzbauer projection + SNOMED:399335002: + text: SNOMED:399335002 + description: Dorsoplantar projection + title: Dorsoplantar projection + SNOMED:399339008: + text: SNOMED:399339008 + description: Apical long axis + title: Apical long axis + SNOMED:399341009: + text: SNOMED:399341009 + description: Haas projection + title: Haas projection + SNOMED:399342002: + text: SNOMED:399342002 + description: Lilienfeld projection + title: Lilienfeld projection + SNOMED:399344001: + text: SNOMED:399344001 + description: Broden projection + title: Broden projection + SNOMED:399348003: + text: SNOMED:399348003 + description: Antero-posterior projection + title: Antero-posterior projection + SNOMED:399349006: + text: SNOMED:399349006 + description: '["Stenver''s projection"]' + title: Stenver's projection + SNOMED:399351005: + text: SNOMED:399351005 + description: Orbito-parietal projection + title: Orbito-parietal projection + SNOMED:399352003: + text: SNOMED:399352003 + description: Lateral-medial projection + title: Lateral-medial projection + SNOMED:399355001: + text: SNOMED:399355001 + description: Chausse projection + title: Chausse projection + SNOMED:399356000: + text: SNOMED:399356000 + description: Right anterior oblique projection + title: Right anterior oblique projection + SNOMED:399358004: + text: SNOMED:399358004 + description: Caldwell projection + title: Caldwell projection + SNOMED:399360002: + text: SNOMED:399360002 + description: Verticosubmental projection + title: Verticosubmental projection + SNOMED:399361003: + text: SNOMED:399361003 + description: Nuclear medicine projection + title: Nuclear medicine projection + SNOMED:399362005: + text: SNOMED:399362005 + description: Bertel projection + title: Bertel projection + SNOMED:399365007: + text: SNOMED:399365007 + description: Pearson projection + title: Pearson projection + SNOMED:399368009: + text: SNOMED:399368009 + description: Medio-lateral oblique projection + title: Medio-lateral oblique projection + SNOMED:399370000: + text: SNOMED:399370000 + description: Lysholm projection + title: Lysholm projection + SNOMED:399371001: + text: SNOMED:399371001 + description: Parasternal short axis view at the level of the mitral chords + title: Parasternal short axis view at the level of the mitral chords + SNOMED:399372008: + text: SNOMED:399372008 + description: Ferguson projection + title: Ferguson projection + SNOMED:399488007: + text: SNOMED:399488007 + description: Midline + title: Midline + SNOMED:408723005: + text: SNOMED:408723005 + description: Cranial LAO + title: Cranial LAO + SNOMED:408724004: + text: SNOMED:408724004 + description: Caudal LAO + title: Caudal LAO + SNOMED:408725003: + text: SNOMED:408725003 + description: Cranial RAO + title: Cranial RAO + SNOMED:408726002: + text: SNOMED:408726002 + description: Caudal RAO + title: Caudal RAO + SNOMED:421610009: + text: SNOMED:421610009 + description: Bottom + title: Bottom + SNOMED:421812003: + text: SNOMED:421812003 + description: Top + title: Top + SNOMED:422534007: + text: SNOMED:422534007 + description: Rafert-Long projection + title: Rafert-Long projection + SNOMED:422568001: + text: SNOMED:422568001 + description: Moore projection + title: Moore projection + SNOMED:422670003: + text: SNOMED:422670003 + description: Apple projection + title: Apple projection + SNOMED:422795009: + text: SNOMED:422795009 + description: Neer projection + title: Neer projection + SNOMED:422861003: + text: SNOMED:422861003 + description: Burman projection + title: Burman projection + SNOMED:422954003: + text: SNOMED:422954003 + description: Stryker projection + title: Stryker projection + SNOMED:422996004: + text: SNOMED:422996004 + description: Wolf projection + title: Wolf projection + SNOMED:423091003: + text: SNOMED:423091003 + description: Colcher-Sussman projection + title: Colcher-Sussman projection + SNOMED:423720000: + text: SNOMED:423720000 + description: Rafer projection + title: Rafer projection + SNOMED:424086005: + text: SNOMED:424086005 + description: Hirtz Modification projection + title: Hirtz Modification projection + SNOMED:424655003: + text: SNOMED:424655003 + description: Eraso Modification projection + title: Eraso Modification projection + SNOMED:424811006: + text: SNOMED:424811006 + description: Danelius-Miller projection + title: Danelius-Miller projection + SNOMED:424962005: + text: SNOMED:424962005 + description: Fisk projection + title: Fisk projection + SNOMED:425030002: + text: SNOMED:425030002 + description: Kite projection + title: Kite projection + SNOMED:425035007: + text: SNOMED:425035007 + description: Robert projection + title: Robert projection + SNOMED:425042007: + text: SNOMED:425042007 + description: Rosenberg projection + title: Rosenberg projection + SNOMED:425157002: + text: SNOMED:425157002 + description: Folio projection + title: Folio projection + SNOMED:425188003: + text: SNOMED:425188003 + description: Garth projection + title: Garth projection + SNOMED:441505008: + text: SNOMED:441505008 + description: Dorsopalmar projection + title: Dorsopalmar projection + SNOMED:441555000: + text: SNOMED:441555000 + description: Inferomedial to superolateral oblique view + title: Inferomedial to superolateral oblique view + SNOMED:441672003: + text: SNOMED:441672003 + description: Dorso-ventral projection + title: Dorso-ventral projection + SNOMED:441753009: + text: SNOMED:441753009 + description: Mammography view + title: Mammography view + SNOMED:442361004: + text: SNOMED:442361004 + description: Stereoscopic view + title: Stereoscopic view + SNOMED:442441009: + text: SNOMED:442441009 + description: Ventro-dorsal projection + title: Ventro-dorsal projection + SNOMED:442580003: + text: SNOMED:442580003 + description: Axillary tissue mammography view + title: Axillary tissue mammography view + SNOMED:442581004: + text: SNOMED:442581004 + description: Nipple in profile mammography view + title: Nipple in profile mammography view + SNOMED:442593008: + text: SNOMED:442593008 + description: Infra-mammary fold mammography view + title: Infra-mammary fold mammography view + SNOMED:442594002: + text: SNOMED:442594002 + description: Right stereoscopic view + title: Right stereoscopic view + SNOMED:442640004: + text: SNOMED:442640004 + description: Left stereoscopic view + title: Left stereoscopic view + SNOMED:442653001: + text: SNOMED:442653001 + description: Stereoscopic view incremented from baseline + title: Stereoscopic view incremented from baseline + SNOMED:442667005: + text: SNOMED:442667005 + description: Stereoscopic view decremented from baseline + title: Stereoscopic view decremented from baseline + SNOMED:443082005: + text: SNOMED:443082005 + description: Parasternal long axis view of right ventricular inflow tract + title: Parasternal long axis view of right ventricular inflow tract + SNOMED:443083000: + text: SNOMED:443083000 + description: Parasternal long axis view of right ventricular outflow tract + title: Parasternal long axis view of right ventricular outflow tract + SNOMED:443100003: + text: SNOMED:443100003 + description: Subcostal view of cardiac outlets directed anteriorly + title: Subcostal view of cardiac outlets directed anteriorly + SNOMED:443160001: + text: SNOMED:443160001 + description: Subcostal short axis view at papillary muscle level + title: Subcostal short axis view at papillary muscle level + SNOMED:443162009: + text: SNOMED:443162009 + description: Suprasternal coronal view + title: Suprasternal coronal view + SNOMED:443163004: + text: SNOMED:443163004 + description: Suprasternal sagittal view + title: Suprasternal sagittal view + SNOMED:443293000: + text: SNOMED:443293000 + description: Transgastric short axis view + title: Transgastric short axis view + SNOMED:443459002: + text: SNOMED:443459002 + description: Intramedullary + title: Intramedullary + SNOMED:443499004: + text: SNOMED:443499004 + description: Subcostal short axis view at mitral valve level + title: Subcostal short axis view at mitral valve level + SNOMED:443500008: + text: SNOMED:443500008 + description: Subcostal short axis view at venous inflow level + title: Subcostal short axis view at venous inflow level + SNOMED:443562002: + text: SNOMED:443562002 + description: Suprasternal long axis view of aortic arch + title: Suprasternal long axis view of aortic arch + SNOMED:443609003: + text: SNOMED:443609003 + description: Subcostal short axis view at aortic valve level + title: Subcostal short axis view at aortic valve level + SNOMED:443640005: + text: SNOMED:443640005 + description: Subcostal oblique coronal view + title: Subcostal oblique coronal view + SNOMED:443662005: + text: SNOMED:443662005 + description: Transesophageal four chamber view (qualifier value) + title: Transesophageal four chamber view (qualifier value) + SNOMED:443698002: + text: SNOMED:443698002 + description: Transesophageal short axis view (qualifier value) + title: Transesophageal short axis view (qualifier value) + SNOMED:65424008: + text: SNOMED:65424008 + description: Contiguous + title: Contiguous + SNOMED:66459002: + text: SNOMED:66459002 + description: Unilateral + title: Unilateral + SNOMED:72906007: + text: SNOMED:72906007 + description: Common + title: Common + SNOMED:741000124103: + text: SNOMED:741000124103 + description: Dorsoventral + title: Dorsoventral + SNOMED:761000124104: + text: SNOMED:761000124104 + description: Dorsolateral + title: Dorsolateral + SNOMED:771000124106: + text: SNOMED:771000124106 + description: Ventrolateral + title: Ventrolateral + SNOMED:781000124109: + text: SNOMED:781000124109 + description: Palmar + title: Palmar diff --git a/src/cam_expanded_enums/schema/EnumStudyDesign.yaml b/src/cam_expanded_enums/schema/EnumStudyDesign.yaml new file mode 100644 index 0000000..6941216 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumStudyDesign.yaml @@ -0,0 +1,29 @@ +--- +id: https://includedcc.org/common-access-model/EnumStudyDesign +name: EnumStudyDesign +enums: + EnumStudyDesign: + title: Study Design + description: Approaches for collecting data, investigating interventions, and/or + analyzing data. + permissible_values: + case_control: + title: Case-Control + case_set: + title: Case Set + control_set: + title: Control Set + clinical_trial: + title: Clinical Trial + cross_sectional: + title: Cross-Sectional + family_twins_trios: + title: Family/Twins/Trios + interventional: + title: Interventional + longitudinal: + title: Longitudinal + trial_readiness_study: + title: Trial Readiness Study + tumor_vs_matched_normal: + title: Tumor vs Matched Normal diff --git a/src/cam_expanded_enums/schema/EnumSubjectType.yaml b/src/cam_expanded_enums/schema/EnumSubjectType.yaml new file mode 100644 index 0000000..f3aa2da --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumSubjectType.yaml @@ -0,0 +1,20 @@ +--- +id: https://includedcc.org/common-access-model/EnumSubjectType +name: EnumSubjectType +enums: + EnumSubjectType: + description: Types of Subject entities + permissible_values: + participant: + description: Study participant with consent, assent, or waiver of consent. + non_participant: + description: An individual associated with a study who was not explictly consented, + eg, the subject of a reported family history. + cell_line: + description: Cell Line + animal_model: + description: Animal model + group: + description: A group of individuals or entities. + other: + description: A different entity type- ideally this will be resolved! diff --git a/src/cam_expanded_enums/schema/EnumVitalStatus.yaml b/src/cam_expanded_enums/schema/EnumVitalStatus.yaml new file mode 100644 index 0000000..3e6ba19 --- /dev/null +++ b/src/cam_expanded_enums/schema/EnumVitalStatus.yaml @@ -0,0 +1,14 @@ +--- +id: https://includedcc.org/common-access-model/EnumVitalStatus +name: EnumVitalStatus +enums: + EnumVitalStatus: + description: Descriptions of a Subject's vital status + is_a: EnumNull + permissible_values: + dead: + title: Dead + meaning: NCIT:C28554 + alive: + title: Alive + meaning: NCIT:C37987 diff --git a/src/cam_expanded_enums/schema/README.md b/src/cam_expanded_enums/schema/README.md new file mode 100644 index 0000000..46c29fd --- /dev/null +++ b/src/cam_expanded_enums/schema/README.md @@ -0,0 +1,3 @@ +# Schema Directory + +This folder contains the LinkML schema yaml files. diff --git a/src/cam_expanded_enums/schema/cam-expanded-enums.yaml b/src/cam_expanded_enums/schema/cam-expanded-enums.yaml new file mode 100644 index 0000000..78dc8d1 --- /dev/null +++ b/src/cam_expanded_enums/schema/cam-expanded-enums.yaml @@ -0,0 +1,74 @@ +--- +id: https://includedcc.org/cam-expanded-enums +name: cam-expanded-enums +title: Common Access Model Expanded Enums +description: LinkML Schema for the Common Access Model Expanded Enums +license: MIT +see_also: + - https://includedcc.github.io/common-access-model + +prefixes: + cam: https://includedcc.org/common-access-model/ + linkml: https://w3id.org/linkml/ + schema: http://schema.org/ + # subset of CDC Race and Ethnicity Code Set Version 1.0 + cdc_race_eth: urn:oid:2.16.840.1.113883.6.238/ + hl7_null: http://terminology.hl7.org/CodeSystem/v3-NullFlavor/ + ig_dob_method: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/ + igcondtype: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/ + ig2dac: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/ + ig2dat: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/ + ig2_biospecimen_availability: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/ + snomed_ct: http://snomed.info/id/ + MONDO: http://purl.obolibrary.org/obo/MONDO_ + HP: http://purl.obolibrary.org/obo/HP_ + mesh: http://id.nlm.nih.gov/mesh/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + PATO: http://purl.obolibrary.org/obo/PATO_ + DUO: http://purl.obolibrary.org/obo/DUO_ + +default_prefix: cam +default_range: string + +imports: + - linkml:types + - EnumDataUsePermission + - EnumDataUseModifier + - EnumProgram + - EnumResearchDomain + - EnumParticipantLifespanStage + - EnumStudyDesign + - EnumClinicalDataSourceType + - EnumDataCategory + - EnumSubjectType + - EnumSex + - EnumRace + - EnumEthnicity + - EnumVitalStatus + - EnumNull + - EnumFamilyType + - EnumConsanguinityAssertion + - EnumAssertionProvenance + - EnumAvailabilityStatus + - EnumSampleCollectionMethod + - EnumSite + - EnumSpatialQualifiers + - EnumLaterality + - EnumEDAMFormats + - EnumEDAMDataTypes + - EnumFileHashType + +classes: + RequiredClass: + description: "This is a placeholder class to satisfy the LinkML requirement of at least one class and is not otherwise used." + attributes: + id: + description: "Unique identifier" + full_name: + description: "Full name" + aliases: + description: "Aliases" + phone: + description: "Phone number" + age: + description: "Age" diff --git a/src/tweaver/_version.py b/src/tweaver/_version.py index 68f437f..9cdfe55 100644 --- a/src/tweaver/_version.py +++ b/src/tweaver/_version.py @@ -18,7 +18,7 @@ commit_id: str | None __commit_id__: str | None -__version__ = version = '0.1.dev2+gd224cbbae.d20260513' -__version_tuple__ = version_tuple = (0, 1, 'dev2', 'gd224cbbae.d20260513') +__version__ = version = '0.1.dev8+g109c86ff3.d20260609' +__version_tuple__ = version_tuple = (0, 1, 'dev8', 'g109c86ff3.d20260609') -__commit_id__ = commit_id = 'gd224cbbae' +__commit_id__ = commit_id = 'g109c86ff3' diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..4ff3ce3 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1 @@ +"""Tests for cam-expanded-enums.""" diff --git a/tests/data/README.md b/tests/data/README.md new file mode 100644 index 0000000..ef4c9fc --- /dev/null +++ b/tests/data/README.md @@ -0,0 +1,14 @@ +# Example data for cam_expanded_enums + +This folder contains example data for testing and demonstrating the datamodel` +sorted in subfolders: + +- `valid` for data conforming to the datamodel. Used to verify the datamodel. +- `invalid` for data not conforming to the datamodel. Used to verify the validation. +- `problem` for data which are not yet handled correctly in the current schema version, + again separated into valid/invalid. + +The filenames of all example data must conform to the scheme `classname-###.yaml` +where classname must be a the name of a class from the schema. "###" can be a number +or one or more other characters allowed in filenames. 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883cb1f85ed064e3e7636ed49145e980c5a19376 Mon Sep 17 00:00:00 2001 From: yelenacox Date: Wed, 10 Jun 2026 13:54:43 -0500 Subject: [PATCH 7/7] Automatically copy enums that don't have a source_ontology --- scripts/expand_enums.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/scripts/expand_enums.py b/scripts/expand_enums.py index 323bfb4..8aa61ea 100644 --- a/scripts/expand_enums.py +++ b/scripts/expand_enums.py @@ -60,9 +60,15 @@ def expand( for name, enum in enums.items(): expanded_enum = output_filepath / f"{name}.yaml" - if "permissible_values" in (enum) and enum["permissible_values"]: + has_permissible = ( + "permissible_values" in (enum) and enum["permissible_values"] + ) + has_ontology = enum.get("reachable_from") and enum["reachable_from"].get( + "source_ontology" + ) + if has_permissible or not has_ontology: expanded_enum.write_text(raw_enum) - logging.info(f"Copied {name} (permissible_values already exists)") + logging.info(f"Copied {name} (does not require expansion)") enum_count += 1 expanded_count += 1 continue