diff --git a/_pipeline_data/configs/_include_project.yaml b/_pipeline_data/configs/_include_project.yaml new file mode 100644 index 0000000..d6328ad --- /dev/null +++ b/_pipeline_data/configs/_include_project.yaml @@ -0,0 +1,166 @@ +# This config file is required for running pipeline-utils and defines the necessary +# paths and configurations for the include_dbt_sandbox project. + + +paths: + pl_dir: + root: repo_root + template: dbt_project + + # Study input data (CSV + DD) + src_data_dir: + root: repo_root + template: "{study_data_dir}" + + # Static metadata root used for internal/export model generation + static_data_dir: + root: repo_root + template: "{pipeline_data_dir}/static" + + # static_int_metadata_dir is hardcoded since it is necessary prior to loading the paths from this file. This path is set in factory_functions.py + # static_exp_metadata_dir is hardcoded since it is necessary prior to loading the paths from this file. This path is set in factory_functions.py + + static_int_additions_dir: + root: repo_root + template: "{pipeline_data_dir}/static/common_data_models/internal/additions" + + static_sp_exp_dir: + root: repo_root + template: "{pipeline_data_dir}/static/common_data_models/export/{exp_model_name}" + + pl_exp_dir: + root: repo_root + template: dbt_project/models/export/{exp_model_name} + + pl_access_dir: + root: repo_root + template: dbt_project/models/access + + pl_combined_dir: + root: repo_root + template: dbt_project/models/combined + + pl_macros_dir: + root: repo_root + template: dbt_project/macros + + pl_profiles: + root: repo_root + template: dbt_project/profiles.yml + + utils_files_dir: + root: repo_root + template: . + + utils_macros_dir: + root: repo_root + template: dbt_project/macros + + pl_dag_dir: + base: repo_root + template: dags/{project_id} + +overridable_paths: + # Values come from the study YAML and are interpreted from repo root. + study_data_dir: + context_attr: study_data_dir + root: repo_root + template: _study_data/{study_id} + override_root: repo_root + + pipeline_data_dir: + context_attr: pipeline_data_dir + root: repo_root + template: _pipeline_data + override_root: repo_root + +derived_paths: + dbtp_src_study_dir: + base: pl_dir + template: models/include/{study_id}/src + + dbtp_ftdc_study_dir: + base: pl_dir + template: models/include/{study_id}/int + + dbtp_ftdc_study_docs_dir: + base: dbtp_ftdc_study_dir + template: docs + + dbtp_ftdc_dir: + base: pl_dir + template: models/include/{study_id} + + pl_scripts_dir: + base: pl_dir + template: scripts + + +stages: + sources: + models_dir: dbtp_src_study_dir + yml_dir: dbtp_src_study_dir + docs_dir: dbtp_src_study_dir + + intermediate: + models_dir: dbtp_ftdc_study_dir + yml_dir: dbtp_ftdc_study_dir + docs_dir: dbtp_ftdc_study_docs_dir + macros_dir: pl_macros_dir + + access: + models_dir: pl_access_dir + yml_dir: pl_access_dir + docs_dir: pl_access_dir + macros_dir: pl_macros_dir + + combined: + models_dir: pl_combined_dir + yml_dir: pl_combined_dir + docs_dir: pl_combined_dir + macros_dir: pl_macros_dir + + export: + models_dir: pl_exp_dir + yml_dir: pl_exp_dir + docs_dir: pl_exp_dir + +dbt_projects: + - dir_key: pl_dir + name: "include_dbt_sandbox" + +dbt_project_stages: + sources: + dir_key: pl_dir + dbtp_def: src + tables_attr: src_prefixed_tables + + intermediate: + dir_key: pl_dir + dbtp_def: stb + tables_attr: stb_prefixed_tables + + access: + dir_key: pl_dir + dbtp_def: access + tables_attr: int_prefixed_tables + + combined: + dir_key: pl_dir + dbtp_def: combined + tables_attr: combined_prefixed_tables + + export: + dir_key: pl_dir + dbtp_def: exp + tables_attr: exp_prefixed_tables + +run_script_dir: pl_scripts_dir + +study_sql_method: study_select_sql + +features: + copy_export_dir: false + copy_macros_dir: false + copy_profiles: false + copy_import_macros: false diff --git a/_pipeline_data/static/common_data_models/export/fhir/AccessPolicy-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/AccessPolicy-dd.csv new file mode 100644 index 0000000..77b277f --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/AccessPolicy-dd.csv @@ -0,0 +1,8 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +access_policy_id,Access policy communicates the limitations and/or requirements that define how a user may gain access to a particular set of data.,string,,,,, +description,More details associated with the given resource,string,,,,, +data_access_type,Type of access restrictions on file downloads ( open | registered | controlled ),enumeration,,,,open=Open Access;registered=Registered;controlled=Controlled;gsr_restricted=GSR Restricted;gsr_allowed=GSR Allowed, +website,"URL describing the entity this represents. This can include a formal website, such as the Entity's website, or to an online document describing the entity.",string,,,,, +consent_scope,Which of the four areas this resource covers (extensible),enumeration,,,,adr=Advanced Care Directive;research=Research;patient_privacy=Patient Privacy;treatment=Treatment, +disease_limitation,Disease Use Limitations,string,,,,, +status,Indicates the state of the consent.,enumeration,,,,draft=Draft;proposed=Proposed;active=Active;rejected=Rejected;inactive=Inactive;entered_in_error=Entered in Error, diff --git a/_pipeline_data/static/common_data_models/export/fhir/AccessPolicy_access_policy_code-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/AccessPolicy_access_policy_code-dd.csv new file mode 100644 index 0000000..bdd1e3a --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/AccessPolicy_access_policy_code-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +AccessPolicy_access_policy_id,Autocreated FK slot,string,,,,,Foreign Key: AccessPolicy.access_policy_id +access_policy_code,A classification of the type of consents found in a consent statement.,enumeration,,,,"gru=General Research Use;hmb=Health/Medical/Biomedical;ds=Disease-Specific (Disease/Trait/Exposure);irb=IRB Approval Required;pub=Publication Required;col=Collaboration Required;npu=Not-for-profit use only;mds=Methods;gso=Genetic Studies only;gsr=Genomic Summary Results;rd=Related Diseases;duo_0000004=This data use permission indicates there is no restriction on use.;duo_0000042=This data use permission indicates that use is allowed for general research use for any research purpose.;duo_0000006=This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.;duo_0000007=This data use permission indicates that use is allowed provided it is related to the specified disease.;duo_0000011=This data use permission indicates that use of the data is limited to the study of population origins or ancestry.;duo_0000012=This data use modifier indicates that use is limited to studies of a certain research type.;duo_0000015=This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).;duo_0000016=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);duo_0000018=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.;duo_0000019=This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.;duo_0000020=This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).;duo_0000021=This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.;duo_0000022=This data use modifier indicates that use is limited to within a specific geographic region.;duo_0000024=This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.;duo_0000025=This data use modifier indicates that use is approved for a specific number of months.;duo_0000026=This data use modifier indicates that use is limited to use by approved users.;duo_0000027=This data use modifier indicates that use is limited to use within an approved project.;duo_0000028=This data use modifier indicates that use is limited to use within an approved institution.;duo_0000029=This data use modifier indicates that the requestor must return derived/enriched data to the database/resource.;duo_0000043=This data use modifier indicates that use is allowed for clinical use and care.;duo_0000044=This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited.;duo_0000045=This data use modifier indicates that use of the data is limited to not-for-profit organisations.;duo_0000046=This data use modifier indicates that use of the data is limited to not-for-profit use.", diff --git a/_pipeline_data/static/common_data_models/export/fhir/AgeAt-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/AgeAt-dd.csv new file mode 100644 index 0000000..a3f3125 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/AgeAt-dd.csv @@ -0,0 +1,6 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +value_type,Age Value Type,enumeration,,,,"age=Age (must also be annotated with age units);code=Age as Code (ages will be provided as coded values);age_range=Age expressed as a range (relative date/time);date=Rather than an age, we have an actual date for the event's occurence", +relative_date_time_id,Age either numeric value or range,string,,,,,Foreign Key: RelativeDateTime.id +age_code,Age expressed as an enumerated value representing an age category,string,,,,, +as_date,Event Date (rather than age),string,,,,, +id,Unique Identifier for a table entry. This is probably not the Global ID,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/Aliquot-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Aliquot-dd.csv new file mode 100644 index 0000000..8bd7f28 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Aliquot-dd.csv @@ -0,0 +1,8 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +aliquot_id,Aliquot Global ID,string,,,,, +availability_status,Can this Sample be requested for further analysis?,enumeration,,,,available=Specimen is currently available;unavailable=Specimen is currently unavailable, +volume,What is the volume of the Aliquot?,number,,,,, +volume_units,Units associated with the volume (ucum),string,,,,, +concentration,What is the concentration of the analyte in the Aliquot?,string,,,,, +sample_id,Sample Global ID,string,,,,,Foreign Key: Sample.sample_id +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Aliquot_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Aliquot_external_id-dd.csv new file mode 100644 index 0000000..b50b96e --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Aliquot_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Aliquot_aliquot_id,Autocreated FK slot,string,,,,,Foreign Key: Aliquot.aliquot_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty-dd.csv new file mode 100644 index 0000000..260ce54 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty-dd.csv @@ -0,0 +1,7 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +name,Name of the entity.,string,,,,, +role,Research Study Party Role,enumeration,,,,sponsor=sponsor;lead_sponsor=lead-sponsor;sponsor_investigator;primary_investigator;collaborator;funding_source;general_contact;recruitment_contact;sub_investigator;study_director;study_chair;irb=Institutional Review Board, +associated_party_practitioner_id,Associated Party (is Practitioner).,string,,,,,Foreign Key: Practitioner.practitioner_id +associated_party_practitioner_role_id,Associated Party (is Practitioner Role),string,,,,,Foreign Key: PractitionerRole.practitioner_role_id +associated_party_institution_id,Associated Party (is Institution),string,,,,,Foreign Key: Institution.institution_id +id,Unique Identifier for a table entry. This is probably not the Global ID,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty_classifier-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty_classifier-dd.csv new file mode 100644 index 0000000..7751689 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty_classifier-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +AssociatedParty_id,Autocreated FK slot,string,,,,,Foreign Key: AssociatedParty.id +classifier,Research Study Party Organization Type (what type of institution is party),enumeration,,,,nih=NIH;fda=FDA;academic=Academic;government=Government;nonprofit=Nonprofit;industry=Industry, diff --git a/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty_period_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty_period_id-dd.csv new file mode 100644 index 0000000..638ae5d --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/AssociatedParty_period_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +AssociatedParty_id,Autocreated FK slot,string,,,,,Foreign Key: AssociatedParty.id +period_id_period_id,Reference to a time period which defines a Start and End datatime period.,string,,,,,Foreign Key: Period.period_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Family-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Family-dd.csv new file mode 100644 index 0000000..2bf5dca --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Family-dd.csv @@ -0,0 +1,8 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +family_global_id,Family Global ID,string,,,,, +family_id,External ID common to all family members,string,,,,, +family_type,"Describes the 'type' of study family, eg, trio.",enumeration,,,,control_only=Control Only;duo=Duo;trio=Trio;trioplus=Trio+;proband_only=Proband Only;other=Other, +description,More details associated with the given resource,string,,,,, +consanguinity,Is there known or suspected consanguinity in this study family?,enumeration,,,,not_suspected=Not suspected;suspected=Suspected;known_present=Known present;unknown=Unknown, +family_focus,"What is this study family investigating? EG, a specific condition",string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/FamilyRelationship-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/FamilyRelationship-dd.csv new file mode 100644 index 0000000..d13b2ab --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/FamilyRelationship-dd.csv @@ -0,0 +1,7 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +family_relationship_id,Family Relationship Global ID,string,,,,, +patient_id,The child from the parent-child relationship,string,,,,,Foreign Key: Participant.participant_id +relative_id,The parent from the parent-child relationship,string,,,,,Foreign Key: Participant.participant_id +relationship,The role the relative (parent) fills with respect to the patient (child) for this relationship.,enumeration,,,,"mother=The relative is the biological mother of the patient.;father=The relative is the biological father of the patient.;monozygotic_twin=The relative and patient are monozygotic twins;polyzygotic_twin=The relative and patient are polyzygotic twins;twin=The relative and patient are twins, but no further clarification is available (always use the more specific form when possible);full_sibling=The relative and child both share the same biological mother and father;half_sibling=The relative and child only share one biological parent;sibling=The relative share at least one biological parent, but there isn't enough information to confirm more then that.", +knowledge_source,The source for the reltionship term,enumeration,,,,"traditional=The knowledge comes from traditional sources like a form filled out by a patient or information copied from an external traditional source like government records.;inferred=The knowledge is inferred from indirect evidence. For example, the existence of one patient's mother can be inferred from the existence of the patient.", +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Family_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Family_external_id-dd.csv new file mode 100644 index 0000000..af0526b --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Family_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Family_family_global_id,Autocreated FK slot,string,,,,,Foreign Key: Family.family_global_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/FileLocation-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/FileLocation-dd.csv new file mode 100644 index 0000000..c6a80c3 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/FileLocation-dd.csv @@ -0,0 +1,5 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +file_location_id,Location details (this is not a global ID),string,,,,, +location_uri,The URI at which this data can be accessed,string,,,,, +file_name,The file's name (no path),string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/FileMetaData-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/FileMetaData-dd.csv new file mode 100644 index 0000000..97077fd --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/FileMetaData-dd.csv @@ -0,0 +1,15 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +file_meta_data_id,Representation of file metadata for NCPI,string,,,,, +meta_data_type,Clarify which type of meta data this file has recorded,enumeration,,,,bam_cram=Bam or Cram file;fastq=FASTQ File;maf=MAF (Somatic Mutation);proteomics=Proteomics file;vcf=GC or gVCF file, +assay_strategy,"e.g., Whole Genome Sequencing",string,,,,, +platform_instrument,"e.g., Illumina HiSeq2000",string,,,,, +library_prep,"e.g., polyA",string,,,,, +library_selection,...,string,,,,, +strandedness,"stranded, unstranded",string,,,,, +target_region,Target region,string,,,,, +is_paired_end,"True, False",string,,,,, +adaptor_trimmed,"True, False",string,,,,, +reference_genome,"GRCh37, GRCh38",string,,,,, +workflow_type,"e.g., alignment, somatic",string,,,,, +workflow_tool,"e.g., BAM-MEM, GATK-Haplotype Caller",string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/FileMetaData_samples-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/FileMetaData_samples-dd.csv new file mode 100644 index 0000000..1976f4e --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/FileMetaData_samples-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +FileMetaData_file_meta_data_id,Autocreated FK slot,string,,,,,Foreign Key: FileMetaData.file_meta_data_id +samples_sample_id,"e.g., Reference(sample)",string,,,,,Foreign Key: Sample.sample_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/HasExternalId_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/HasExternalId_external_id-dd.csv new file mode 100644 index 0000000..f951de1 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/HasExternalId_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +HasExternalId_id,Autocreated FK slot,integer,,,,,Foreign Key: HasExternalId.id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/Institution-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Institution-dd.csv new file mode 100644 index 0000000..d1e3c40 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Institution-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +institution_id,The institution this record is associated with.,string,,,,, +name,Name of the entity.,string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Institution_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Institution_external_id-dd.csv new file mode 100644 index 0000000..d7bfa23 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Institution_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Institution_institution_id,Autocreated FK slot,string,,,,,Foreign Key: Institution.institution_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/NCPIFile-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile-dd.csv new file mode 100644 index 0000000..a355765 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile-dd.csv @@ -0,0 +1,12 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +participant_id,The Global ID for the Participant,string,,,,,Foreign Key: Participant.participant_id +file_format,The file format used ([EDAM](http://edamontology.org) where possible),string,,,,, +file_size,"The size of the file, e.g., in bytes.",number,,,,, +file_size_unit,Units associated with the file_size value (ucum),string,,,,, +content_version,Version of the file content,string,,,,, +file_type,"The type of data contained in this file. Should be as detailed as possible, e.g., Whole Exome Variant Calls.",string,,,,, +file_hash,Value of hashing the file,string,,,,, +file_hash_type,"Algorithm used to calculate the hash (and size, where applicable)",string,,,,, +description,More details associated with the given resource,string,,,,, +file_global_id,File Global ID,string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_external_id-dd.csv new file mode 100644 index 0000000..419be24 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +NCPIFile_file_global_id,Autocreated FK slot,string,,,,,Foreign Key: NCPIFile.file_global_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_file_location_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_file_location_id-dd.csv new file mode 100644 index 0000000..ee38f9b --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_file_location_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +NCPIFile_file_global_id,Autocreated FK slot,string,,,,,Foreign Key: NCPIFile.file_global_id +file_location_id_file_location_id,Location details (this is not a global ID),string,,,,,Foreign Key: FileLocation.file_location_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_file_meta_data_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_file_meta_data_id-dd.csv new file mode 100644 index 0000000..e127f84 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/NCPIFile_file_meta_data_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +NCPIFile_file_global_id,Autocreated FK slot,string,,,,,Foreign Key: NCPIFile.file_global_id +file_meta_data_id_file_meta_data_id,Representation of file metadata for NCPI,string,,,,,Foreign Key: FileMetaData.file_meta_data_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Participant-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Participant-dd.csv new file mode 100644 index 0000000..4415132 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Participant-dd.csv @@ -0,0 +1,17 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +participant_id,The Global ID for the Participant,string,,,,, +birthsex,Sex assigned at birth (or pre-natal observed sex),enumeration,,,,"female=Female;male=Male;asku=Information was sought but not found (e.g., patient was asked but didn't know);oth=**Description:**The actual value is not a member of the set of permitted data values in the constrained value domain of a variable. (e.g., concept not provided by required code system). +Usage Notes: This flavor and its specializations are most commonly used with the CD datatype and its flavors. However, it may apply to *any* datatype where the constraints of the type are tighter than can be conveyed. For example, a PQ that is for a true measured amount whose units are not supported in UCUM, a need to convey a REAL when the type has been constrained to INT, etc. +With coded datatypes, this null flavor may only be used if the vocabulary binding has a coding strength of CNE. By definition, all local codes and original text are part of the value set if the coding strength is CWE.;unk=*Description:**A proper value is applicable, but not known. +Usage Notes: This means the actual value is not known. If the only thing that is unknown is how to properly express the value in the necessary constraints (value set, datatype, etc.), then the OTH or UNC flavor should be used. No properties should be included for a datatype with this property unless: +Those properties themselves directly translate to a semantic of 'unknown'. (E.g. a local code sent as a translation that conveys 'unknown') Those properties further qualify the nature of what is unknown. (E.g. specifying a use code of 'H' and a URL prefix of 'tel:' to convey that it is the home phone number that is unknown.)", +ethnicity,Reported ethnicity as defined by the 1997 OMB directives.,enumeration,,,,hispanic_or_latino=Hispanic or Latino;not_hispanic_or_latino=Not Hispanic or Latino;unknown=unknown;asked_but_unknown=asked but unknown, +population,"opulation, Race, and/or Ethnicity information.",enumeration,,,,,Code describing the population (CDC). This should be one of the codes from the [CDC Race codes](https://hl7.org/fhir/us/core/STU6.1/ValueSet-detailed-race.html). +dob,Date of Birth of the participant. Details of privacy method should be included in DOBMethod,string,,,,, +dob_method,Specifies method used to alter DOB for research sharing. Details should be available in the study protocols.,enumeration,,,,exact=Exact;year_only=Year Only;shifted=Shifted;decade_only=Decade Only;other=Other, +age_at_last_vital,Age or date of last vital status,string,,,,, +is_deceased,"Is the participant known to be Deceased, T, or Alive, F",string,,,,, +deceased_rel,Implementers can provide relativeDateTime if information is available.,string,,,,,Foreign Key: RelativeDateTime.id +patient_knowledge_source,The source of the knowledge represented by this Patient resource.,enumeration,,,,"traditional=The knowledge comes from traditional sources like a form filled out by a patient or information copied from an external traditional source like government records.;inferred=The knowledge is inferred from indirect evidence. For example, the existence of one patient's mother can be inferred from the existence of the patient.", +family_global_id,The family the participant is a part of,string,,,,,Foreign Key: Family.family_global_id +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/ParticipantAssertion-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ParticipantAssertion-dd.csv new file mode 100644 index 0000000..65a715b --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ParticipantAssertion-dd.csv @@ -0,0 +1,22 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +participant_assertion_id,Participant Assertion Global ID,string,,,,, +participant_id,The Global ID for the Participant,string,,,,,Foreign Key: Participant.participant_id +age_at_event,The date or age at which the event relating to this assertion occured.,string,,,,,Foreign Key: AgeAt.id +age_at_assertion,The date or age at which this condition is being asserted.,string,,,,,Foreign Key: AgeAt.id +age_at_onset,"The age of onset for this condition. Could be expressed with a term, an age, or an age range.",string,,,,,Foreign Key: AgeAt.id +age_at_resolution,"The age at which this condition was resolved, abated, or cured. Should be left empty in cases of current active status. Could be expressed with a term, an age, or an age range.",string,,,,,Foreign Key: AgeAt.id +entity_asserter,"Who recorded this assertion about the Participant? This can support understanding the differences between self-report, doctor, trained research staff.",enumeration,,,,self_report=The participant reported the assertion;doctor=Physician;staff=Trained research staff, +other_condition_modifiers,"Any additional modifiers for this condition, such as severity.",string,,,,, +assertion_type,Describe the type of assertion being made.,enumeration,,,,"phenotypic_feature=This is a phenotypic feature;disease=Disease;comorbidity=Comorbidity;histology=Histology;clinical_finding=Clinical Finding;ehr_billing_code=From an EHR billing record, which may indicate only investigation into a possible diagnosis.;measurement=A measurement of some feature, eg, height or glucose.", +assertion_code,The structured term defining the meaning of the assertion.,string,,,,, +assertion_text,Detailed description / free text about this assertion.,string,,,,, +assertion_source,"Where or how was this this assertion about the Participant recorded? This can support understanding the differences between surveys, automated EHR extraction, manual chart abstraction, etc.",string,,,,, +value_code,Value as code,string,,,,, +value_string,Value as string,string,,,,, +value_number,Value as numer,number,,,,, +value_units,The structured term defining the units of the value (ucum).,string,,,,, +body_site,"Location information for the observation, including site, laterality, and other qualifiers as appropriate. Multiple observations may be required if the same assertion is made in many locations, or complete location details can be provided in an NCPI Condition Summary.",string,,,,, +body_location,Any location qualifiers,string,,,,, +body_laterality,Laterality information for the condition site,string,,,,, +cancer_stage,Cancer staging information,string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Participant_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Participant_external_id-dd.csv new file mode 100644 index 0000000..719e642c --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Participant_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Participant_participant_id,Autocreated FK slot,string,,,,,Foreign Key: Participant.participant_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/Participant_race-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Participant_race-dd.csv new file mode 100644 index 0000000..19ed481 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Participant_race-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Participant_participant_id,Autocreated FK slot,string,,,,,Foreign Key: Participant.participant_id +race,Reported race as defined by the 1997 OMB directives.,enumeration,,,,american_indian_or_alaskan_native=American Indian or Alaskan Native;asian=Asian;black_or_african_american=Black or African American;native_hawaiian_or_pacific_islander=Native Hawaiian or Other Pacific Islander;white=White;other_race=Other Race;unknown=unknown;asked_but_unknown=asked but unknown, diff --git a/_pipeline_data/static/common_data_models/export/fhir/Participant_sample_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Participant_sample_id-dd.csv new file mode 100644 index 0000000..e977b00 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Participant_sample_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Participant_participant_id,Autocreated FK slot,string,,,,,Foreign Key: Participant.participant_id +sample_id_sample_id,Samples associated with this participant,string,,,,,Foreign Key: Sample.sample_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Period-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Period-dd.csv new file mode 100644 index 0000000..360b8b7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Period-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +period_id,ID for period (not a global ID),string,,,,, +start,Start attribute for a FHIR period data type.,string,,,,, +end,End attribute for a FHIR period data type.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/Person-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Person-dd.csv new file mode 100644 index 0000000..7b737e7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Person-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +person_id,Person Global ID (group),string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Person_participant_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Person_participant_id-dd.csv new file mode 100644 index 0000000..c91dd30 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Person_participant_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Person_person_id,Autocreated FK slot,string,,,,,Foreign Key: Person.person_id +participant_id_participant_id,The Global ID for the Participant,string,,,,,Foreign Key: Participant.participant_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Practitioner-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Practitioner-dd.csv new file mode 100644 index 0000000..54f18b3 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Practitioner-dd.csv @@ -0,0 +1,9 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +practitioner_id,The Global ID for the PractitionerRole that links a Practitioner to their Institution.,string,,,,, +name,Name of the entity.,string,,,,, +email,An email address to reach the entity.,string,,,,, +institution_id,The institution this record is associated with.,string,,,,,Foreign Key: Institution.institution_id +practitioner_role_id,Global ID for this record,string,,,,,Foreign Key: PractitionerRole.practitioner_role_id +description,More details associated with the given resource,string,,,,, +practitioner_title,"The title of the Investigator, eg, ""Assistant Professor""",string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Practitioner-dd.csv:Zone.Identifier b/_pipeline_data/static/common_data_models/export/fhir/Practitioner-dd.csv:Zone.Identifier new file mode 100644 index 0000000..55161c5 Binary files /dev/null and b/_pipeline_data/static/common_data_models/export/fhir/Practitioner-dd.csv:Zone.Identifier differ diff --git a/_pipeline_data/static/common_data_models/export/fhir/PractitionerRole-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/PractitionerRole-dd.csv new file mode 100644 index 0000000..d184d3b --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/PractitionerRole-dd.csv @@ -0,0 +1,5 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +practitioner_role_id,Global ID for this record,string,,,,, +institution_id,The institution this record is associated with.,string,,,,,Foreign Key: Institution.institution_id +practitioner_id,The Global ID for the PractitionerRole that links a Practitioner to their Institution.,string,,,,,Foreign Key: Practitioner.practitioner_id +period_id,Reference to a time period which defines a Start and End datatime period.,string,,,,,Foreign Key: Period.period_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/PractitionerRole-dd.csv:Zone.Identifier b/_pipeline_data/static/common_data_models/export/fhir/PractitionerRole-dd.csv:Zone.Identifier new file mode 100644 index 0000000..55161c5 Binary files /dev/null and b/_pipeline_data/static/common_data_models/export/fhir/PractitionerRole-dd.csv:Zone.Identifier differ diff --git a/_pipeline_data/static/common_data_models/export/fhir/Practitioner_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Practitioner_external_id-dd.csv new file mode 100644 index 0000000..6e1edda --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Practitioner_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Practitioner_practitioner_id,Autocreated FK slot,string,,,,,Foreign Key: Practitioner.practitioner_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/RelativeDateTime-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/RelativeDateTime-dd.csv new file mode 100644 index 0000000..4504a94 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/RelativeDateTime-dd.csv @@ -0,0 +1,5 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +offset,"The point after the target being described. For ranges, this can be used for the starting point",integer,,,,, +offset_end,The end of a relative date/time range,integer,,,,, +offset_type,"What is the datatype associated with the offset (days, years, etc)",enumeration,,,,days=The offset is represented in days;years=The offset is represented in Years, +id,Unique Identifier for a table entry. This is probably not the Global ID,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy-dd.csv new file mode 100644 index 0000000..24af669 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy-dd.csv @@ -0,0 +1,7 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +research_study_id,The Global ID for the Research Study.,string,,,,, +study_title,Research Study's formal title.,string,,,,, +parent_study_id,ID For Parent Study if this is a substudy,string,,,,,Foreign Key: ResearchStudy.research_study_id +description,More details associated with the given resource,string,,,,, +study_status,The current state of the study.,enumeration,,,,active=Study is opened for accrual.;administratively_completed=Study is completed prematurely and will not resume; patients are no longer examined nor treated.;approved=Approved;closed_to_accrual=Closed to Accrual;closed_to_accrual_and_intervention=Closed to Accrual and Intervention;completed=Completed;disapproved=Disapproved;in_review=In Review;temporarily_closed_to_accrual=Temporarily Closed to Accrual;temporarily_closed_to_accrual_and_intervention=Temporarily Closed to Accrual and Intervention;withdrawn=Withdrawn, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection-dd.csv new file mode 100644 index 0000000..b9c86bc --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection-dd.csv @@ -0,0 +1,8 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +research_study_collection_id,Global ID for this record,string,,,,, +description,More details associated with the given resource,string,,,,, +collection_title,The collection's title.,string,,,,, +research_study_collection_type,The type of collection being described.,enumeration,,,,consortium=Consortium;program=Program;user_defined=User Defined, +website,"URL describing the entity this represents. This can include a formal website, such as the Entity's website, or to an online document describing the entity.",string,,,,, +collection_status,The current state of the collection,enumeration,,,,current=Current;retired=Retired, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_external_id-dd.csv new file mode 100644 index 0000000..a79fb42 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudyCollection_research_study_collection_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudyCollection.research_study_collection_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_label-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_label-dd.csv new file mode 100644 index 0000000..e01986f --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_label-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudyCollection_research_study_collection_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudyCollection.research_study_collection_id +label,Alias such as acronym and alternate names.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_research_study_collection_member_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_research_study_collection_member_id-dd.csv new file mode 100644 index 0000000..ac42436 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudyCollection_research_study_collection_member_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudyCollection_research_study_collection_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudyCollection.research_study_collection_id +research_study_collection_member_id_research_study_id,"ID associated with a member of the collection (Research Study, Dataset, etc)",string,,,,,Foreign Key: ResearchStudy.research_study_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_external_id-dd.csv new file mode 100644 index 0000000..327e8cc --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudy_research_study_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudy.research_study_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_acknowledgement-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_acknowledgement-dd.csv new file mode 100644 index 0000000..622f4d7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_acknowledgement-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudy_research_study_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudy.research_study_id +study_acknowledgement,"Any attribution or acknowledgements relevant to the study. This can include but is not limited to funding sources, organizational affiliations or sponsors.",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_condition-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_condition-dd.csv new file mode 100644 index 0000000..8e67711 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_condition-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudy_research_study_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudy.research_study_id +study_condition,The primary focus(es) of the study. This is specific to the disease. MeSH terms are preferred.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_design-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_design-dd.csv new file mode 100644 index 0000000..54a5540 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_design-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudy_research_study_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudy.research_study_id +study_design,Study Design and Study Type ([example ValueSet can be found here](https://hl7.org/fhir/valueset-study-design.html)),string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_focus-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_focus-dd.csv new file mode 100644 index 0000000..061ff04 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_focus-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudy_research_study_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudy.research_study_id +study_focus,"The primary, non-disease focus(es) of the study. This can include terms related to intervention, drug, device, or other focus.",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_personnel-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_personnel-dd.csv new file mode 100644 index 0000000..dcf2b59 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchStudy_study_personnel-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +ResearchStudy_research_study_id,Autocreated FK slot,string,,,,,Foreign Key: ResearchStudy.research_study_id +study_personnel_id,"Every study must have at least one Primary Contact defined. Additional personnel such as Primary Investigator(s), Administrator(s), Collaborator(s) or other roles may also be included. If there are no appropriate individuals who can serve as primary contact for a study, an organization may be provided.",string,,,,,Foreign Key: AssociatedParty.id diff --git a/_pipeline_data/static/common_data_models/export/fhir/ResearchSubject-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/ResearchSubject-dd.csv new file mode 100644 index 0000000..b72b83e --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/ResearchSubject-dd.csv @@ -0,0 +1,5 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +research_subject_id,Research Subject Global ID (ResearchSubject),string,,,,, +participant_id,The Global ID for the Participant,string,,,,,Foreign Key: Participant.participant_id +study_membership_id,Study Membership Global ID (group),string,,,,,Foreign Key: StudyMembership.study_membership_id +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Sample-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Sample-dd.csv new file mode 100644 index 0000000..4409142 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Sample-dd.csv @@ -0,0 +1,15 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +sample_id,Sample Global ID,string,,,,, +parent_sample_id,Sample Global ID associated with the parent sample,string,,,,,Foreign Key: Sample.sample_id +participant_id,The Global ID for the Participant,string,,,,,Foreign Key: Participant.participant_id +sample_type,The type of material of which this Sample is comprised,string,,,,, +age_at_collection,"The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range.",string,,,,,Foreign Key: AgeAt.id +collection_method,The approach used to collect the biospecimen ([LOINC](https://loinc.org)),string,,,,, +collection_site,The location of the specimen collection,string,,,,, +spatial_qualifier,Any spatial/location qualifiers,string,,,,, +laterality,Laterality information for the site,string,,,,, +availability_status,Can this Sample be requested for further analysis?,enumeration,,,,available=Specimen is currently available;unavailable=Specimen is currently unavailable, +storage_method,"How is the Sample stored, eg, Frozen or with additives (e.g. https://terminology.hl7.org/5.3.0/ValueSet-v2-0493.html)",string,,,,, +quantity,The total quantity of the specimen,number,,,,, +quantity_units,Units associated with the quantity (ucum),string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/Sample_external_id-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Sample_external_id-dd.csv new file mode 100644 index 0000000..cec6554 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Sample_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Sample_sample_id,Autocreated FK slot,string,,,,,Foreign Key: Sample.sample_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/Sample_processing-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/Sample_processing-dd.csv new file mode 100644 index 0000000..12b2456 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/Sample_processing-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Sample_sample_id,Autocreated FK slot,string,,,,,Foreign Key: Sample.sample_id +processing,Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample,string,,,,, diff --git a/_pipeline_data/static/common_data_models/export/fhir/StudyMembership-dd.csv b/_pipeline_data/static/common_data_models/export/fhir/StudyMembership-dd.csv new file mode 100644 index 0000000..7ac91d0 --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/StudyMembership-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +study_membership_id,Study Membership Global ID (group),string,,,,, +access_policy_id,Access Policy Global ID,string,,,,,Foreign Key: AccessPolicy.access_policy_id +research_study_id,The Global ID for the Research Study.,string,,,,,Foreign Key: ResearchStudy.research_study_id diff --git a/_pipeline_data/static/common_data_models/export/fhir/_fhir_study.yaml b/_pipeline_data/static/common_data_models/export/fhir/_fhir_study.yaml new file mode 100644 index 0000000..c4d6ecf --- /dev/null +++ b/_pipeline_data/static/common_data_models/export/fhir/_fhir_study.yaml @@ -0,0 +1,102 @@ +model_name: fhir +model_prefix: fhir +format: ftd_dd +data_dictionary: + AccessPolicy: + identifier: AccessPolicy-dd.csv + AccessPolicy_access_policy_code: + identifier: AccessPolicy_access_policy_code-dd.csv + AgeAt: + identifier: AgeAt-dd.csv + Aliquot: + identifier: Aliquot-dd.csv + Aliquot_external_id: + identifier: Aliquot_external_id-dd.csv + AssociatedParty: + identifier: AssociatedParty-dd.csv + AssociatedParty_classifier: + identifier: AssociatedParty_classifier-dd.csv + AssociatedParty_period_id: + identifier: AssociatedParty_period_id-dd.csv + Family: + identifier: Family-dd.csv + FamilyRelationship: + identifier: FamilyRelationship-dd.csv + Family_external_id: + identifier: Family_external_id-dd.csv + FileLocation: + identifier: FileLocation-dd.csv + FileMetaData: + identifier: FileMetaData-dd.csv + FileMetaData_samples: + identifier: FileMetaData_samples-dd.csv + HasExternalId_external_id: + identifier: HasExternalId_external_id-dd.csv + Institution: + identifier: Institution-dd.csv + Institution_external_id: + identifier: Institution_external_id-dd.csv + NCPIFile: + identifier: NCPIFile-dd.csv + NCPIFile_external_id: + identifier: NCPIFile_external_id-dd.csv + NCPIFile_file_location_id: + identifier: NCPIFile_file_location_id-dd.csv + NCPIFile_file_meta_data_id: + identifier: NCPIFile_file_meta_data_id-dd.csv + Participant: + identifier: Participant-dd.csv + ParticipantAssertion: + identifier: ParticipantAssertion-dd.csv + Participant_external_id: + identifier: Participant_external_id-dd.csv + Participant_race: + identifier: Participant_race-dd.csv + Participant_sample_id: + identifier: Participant_sample_id-dd.csv + Period: + identifier: Period-dd.csv + Person: + identifier: Person-dd.csv + Person_participant_id: + identifier: Person_participant_id-dd.csv + Practitioner: + identifier: Practitioner-dd.csv + PractitionerRole: + identifier: PractitionerRole-dd.csv + Practitioner_external_id: + identifier: Practitioner_external_id-dd.csv + RelativeDateTime: + identifier: RelativeDateTime-dd.csv + ResearchStudy: + identifier: ResearchStudy-dd.csv + ResearchStudyCollection: + identifier: ResearchStudyCollection-dd.csv + ResearchStudyCollection_external_id: + identifier: ResearchStudyCollection_external_id-dd.csv + ResearchStudyCollection_label: + identifier: ResearchStudyCollection_label-dd.csv + ResearchStudyCollection_research_study_collection_member_id: + identifier: ResearchStudyCollection_research_study_collection_member_id-dd.csv + ResearchStudy_external_id: + identifier: ResearchStudy_external_id-dd.csv + ResearchStudy_study_acknowledgement: + identifier: ResearchStudy_study_acknowledgement-dd.csv + ResearchStudy_study_condition: + identifier: ResearchStudy_study_condition-dd.csv + ResearchStudy_study_design: + identifier: ResearchStudy_study_design-dd.csv + ResearchStudy_study_focus: + identifier: ResearchStudy_study_focus-dd.csv + ResearchStudy_study_personnel: + identifier: ResearchStudy_study_personnel-dd.csv + ResearchSubject: + identifier: ResearchSubject-dd.csv + Sample: + identifier: Sample-dd.csv + Sample_external_id: + identifier: Sample_external_id-dd.csv + Sample_processing: + identifier: Sample_processing-dd.csv + StudyMembership: + identifier: StudyMembership-dd.csv diff --git a/_pipeline_data/static/common_data_models/internal/access/Concept-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Concept-dd.csv new file mode 100644 index 0000000..d6bf3d0 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Concept-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +concept_curie,The standardized curie for the term.,string,,,,, +display,The friendly display string of the coded term.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/DOI-dd.csv b/_pipeline_data/static/common_data_models/internal/access/DOI-dd.csv new file mode 100644 index 0000000..d2a3da7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/DOI-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +doi,Digital Object Identifier (DOI) for this Record.,string,,,,, +bibliographic_reference,Text use to reference this Record.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/DOI_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/DOI_external_id-dd.csv new file mode 100644 index 0000000..ea5aa3d --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/DOI_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +DOI_doi,Autocreated FK slot,string,,,,,Foreign Key: DOI.doi +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Demographics-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Demographics-dd.csv new file mode 100644 index 0000000..371ee9b --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Demographics-dd.csv @@ -0,0 +1,8 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +subject_id,INLCUDE Global ID for the Subject,string,,,,, +sex,Sex of Participant,enumeration,,,,female=Female;male=Male;other=Other;unknown=Unknown, +ethnicity,Ethnicity of Participant,enumeration,,,,hispanic_or_latino=Hispanic or Latino;not_hispanic_or_latino=Not Hispanic or Latino;prefer_not_to_answer=Prefer not to answer;unknown=Unknown, +down_syndrome_status,Down Syndrome status of participant,enumeration,,,,d21=Disomy 21 (euploid);t21=Trisomy 21 (Down syndrome), +age_at_last_vital_status,Age in days when participant's vital status was last recorded,integer,,,UCUM:d,, +vital_status,Whether participant is alive or dead,enumeration,,,,dead=Dead;alive=Alive, +age_at_first_engagement,"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.",integer,,,UCUM:d,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Demographics_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Demographics_external_id-dd.csv new file mode 100644 index 0000000..90181ab --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Demographics_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Demographics_subject_id,Autocreated FK slot,string,,,,,Foreign Key: Demographics.subject_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Demographics_race-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Demographics_race-dd.csv new file mode 100644 index 0000000..63e5b43 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Demographics_race-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Demographics_subject_id,Autocreated FK slot,string,,,,,Foreign Key: Demographics.subject_id +race,Race of Participant,enumeration,,,,american_indian_or_alaska_native=American Indian or Alaska Native;asian=Asian;black_or_african_american=Black or African American;more_than_one_race=More than one race;native_hawaiian_or_other_pacific_islander=Native Hawaiian or Other Pacific Islander;other=Other;white=White;prefer_not_to_answer=Prefer not to answer;unknown=Unknown;east_asian=UK only; do not use for US data;latin_american=UK only; do not use for US data;middle_eastern_or_north_african=UK only; do not use for US data;south_asian=UK only; do not use for US data, diff --git a/_pipeline_data/static/common_data_models/internal/access/Investigator-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Investigator-dd.csv new file mode 100644 index 0000000..441ac8b --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Investigator-dd.csv @@ -0,0 +1,6 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +id,,integer,,,,, +name,Name of the entity.,string,,,,, +institution,Name of the institution this record is associated with.,string,,,,, +invesitgator_title,"The title of the Investigator, eg, ""Assistant Professor""",string,,,,, +email,An email address to reach the entity.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Investigator_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Investigator_external_id-dd.csv new file mode 100644 index 0000000..b0da466 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Investigator_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Investigator_id,Autocreated FK slot,integer,,,,,Foreign Key: Investigator.id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Publication-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Publication-dd.csv new file mode 100644 index 0000000..38790b5 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Publication-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +id,,integer,,,,, +bibliographic_reference,Text use to reference this Record.,string,,,,, +website,Website for the Record.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Publication_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Publication_external_id-dd.csv new file mode 100644 index 0000000..26f26d7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Publication_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Publication_id,Autocreated FK slot,integer,,,,,Foreign Key: Publication.id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Record_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Record_external_id-dd.csv new file mode 100644 index 0000000..ddd4e75 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Record_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Record_id,Autocreated FK slot,integer,,,,,Foreign Key: Record.id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study-dd.csv new file mode 100644 index 0000000..02ef8a4 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study-dd.csv @@ -0,0 +1,15 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +study_id,INLCUDE Global ID for the study,string,,,,, +parent_study,"The parent study for this study, if it is a nested study.",string,,,,,Foreign Key: Study.study_id +study_title,Full Study Title,string,,,,, +study_code,Unique identifier for the study (generally a short acronym),string,,,,, +study_short_name,Short name for the study,string,,,,, +study_description,Brief description of the study (2-4 sentences),string,,,,, +selection_criteria,Brief description of inclusion and/or exclusion criteria for the study,string,,,,, +website,Website for the Record.,string,,,,, +expected_number_of_participants,Total expected number of participants to be recruited.,integer,,,,, +actual_number_of_participants,Total participants included at this time.,integer,,,,, +acknowledgments,Funding statement and acknowledgments for this study,string,,,,, +citation_statement,"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 .""",string,,,,, +doi,Digital Object Identifier (DOI) for this Record.,string,,,,, +vbr_id,"Information about the study's Virtual Biorepository, if participating",integer,,,,,Foreign Key: VirtualBiorepository.id diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_clinical_data_source_type-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_clinical_data_source_type-dd.csv new file mode 100644 index 0000000..8a0e885 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_clinical_data_source_type-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +clinical_data_source_type,Source(s) of data collected from study participants,enumeration,,,,"medical_record=Data obtained directly from medical record;investigator_assessment=Data obtained by examination, interview, etc. with investigator;participant_or_caregiver_report=Data obtained from survey, questionnaire, etc. filled out by participant or caregiver;other=Data obtained from other source, such as tissue bank;unknown=Unknown", diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_contact-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_contact-dd.csv new file mode 100644 index 0000000..cd33900 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_contact-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +contact_id,The individual to contact with questions about this record.,integer,,,,,Foreign Key: Investigator.id diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_data_category-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_data_category-dd.csv new file mode 100644 index 0000000..0636026 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_data_category-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +data_category,"General category of data in this Record (e.g. Clinical, Genomics, etc)",enumeration,,,,unharmonized_demographic_clinical_data=Unharmonized Demographic/Clinical Data;harmonized_demographic_clinical_data=Harmonized Demographic/Clinical Data;genomics=Genomics;transcriptomics=Transcriptomics;epigenomics=Epigenomics;proteomics=Proteomics;metabolomics=Metabolomics;cognitive_behavioral=Cognitive/Behavioral;immune_profiling=Immune Profiling;imaging=Imaging;microbiome=Microbiome;fitness=Fitness;physical_activity=Physical Activity;other=Other;sleep_study=Sleep Study, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_external_id-dd.csv new file mode 100644 index 0000000..7d62253 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_funding_source-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_funding_source-dd.csv new file mode 100644 index 0000000..a0cbc7d --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_funding_source-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +funding_source,The funding source(s) of the study.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_participant_lifespan_stage-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_participant_lifespan_stage-dd.csv new file mode 100644 index 0000000..cf1a4d9 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_participant_lifespan_stage-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +participant_lifespan_stage,Focus age group(s) of the study population,enumeration,,,,fetal=Before birth;neonatal=0-28 days old;pediatric=Birth-17 years old;adult=18+ years old, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_principal_investigator-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_principal_investigator-dd.csv new file mode 100644 index 0000000..b8c210f --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_principal_investigator-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +principal_investigator_id,The Principal Investigator(s) responsible for the study.,integer,,,,,Foreign Key: Investigator.id diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_program-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_program-dd.csv new file mode 100644 index 0000000..333a677 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_program-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +program,Funding source(s) for the study,enumeration,,,,include=INCLUDE;kf=KF;other=Other, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_publication-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_publication-dd.csv new file mode 100644 index 0000000..89621b6 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_publication-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +publication_id,Publications associated with this Record.,integer,,,,,Foreign Key: Publication.id diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_research_domain-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_research_domain-dd.csv new file mode 100644 index 0000000..6290abb --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_research_domain-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +research_domain,"Main research domain(s) of the study, other than Down syndrome",enumeration,,,,behavior_and_behavior_mechanisms=Behavior and Behavior Mechanisms;congenital_heart_defects=Congenital Heart Defects;immune_system_diseases=Immune System Diseases;hematologic_diseases=Hematologic Diseases;neurodevelopment=Neurodevelopment;sleep_wake_disorders=Sleep Wake Disorders;all_co_occurring_conditions=All Co-occurring Conditions;physical_fitness=Physical Fitness;other=Other, diff --git a/_pipeline_data/static/common_data_models/internal/access/Study_study_design-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Study_study_design-dd.csv new file mode 100644 index 0000000..3f71991 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Study_study_design-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +study_design,"Overall design of study, including whether it is longitudinal and whether family members/unrelated controls are also enrolled",enumeration,,,,case_control=Case-Control;case_set=Case Set;control_set=Control Set;clinical_trial=Clinical Trial;cross_sectional=Cross-Sectional;family_twins_trios=Family/Twins/Trios;interventional=Interventional;longitudinal=Longitudinal;trial_readiness_study=Trial Readiness Study;tumor_vs_matched_normal=Tumor vs Matched Normal, diff --git a/_pipeline_data/static/common_data_models/internal/access/Subject-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Subject-dd.csv new file mode 100644 index 0000000..3d786f8 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Subject-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +subject_id,INLCUDE Global ID for the Subject,string,,,,, +subject_type,Type of entity this record represents,enumeration,,,,"participant=Study participant with consent, assent, or waiver of consent.;non_participant=An individual associated with a study who was not explictly consented, eg, the subject | of a reported family history.;cell_line=Cell Line;animal_model=Animal model;group=A group of individuals or entities.;other=A different entity type- ideally this will be resolved!", +organism_type,Organism Type,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion-dd.csv b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion-dd.csv new file mode 100644 index 0000000..148fa35 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion-dd.csv @@ -0,0 +1,12 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +assertion_id,INLCUDE Global ID for the Assertion,string,,,,, +subject_id,INLCUDE Global ID for the Subject,string,,,,, +assertion_provenance,The original source of this assertion,enumeration,,,,"medical_record=Data obtained from a medical record;investigator_assessment=Data obtained by examination, interview, etc. with investigator;participant_or_caregiver_report=Data obtained from survey, questionnaire, etc. filled out by participant or caregiver;other=Data obtained from other source, such as tissue bank", +age_at_assertion,The age in days of the Subject when the assertion was made.,integer,,,UCUM:d,, +age_at_event,"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.",integer,,,UCUM:d,, +age_at_resolution,The age in days of the Subject when the asserted state was resolved.,integer,,,UCUM:d,, +concept_source,The source text yielding the standardized concept.,string,,,,, +value_number,The numeric value of the assertion.,number,,,,, +value_source,The source text yielding the value.,string,,,,, +value_units,The structured term defining the units of the value.,string,,,,,Foreign Key: Concept.concept_curie +value_units_source,The source text yielding the value's units.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_concept-dd.csv b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_concept-dd.csv new file mode 100644 index 0000000..defa0b4 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_concept-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +SubjectAssertion_assertion_id,Autocreated FK slot,string,,,,,Foreign Key: SubjectAssertion.assertion_id +concept_concept_curie,The structured term defining the meaning of the assertion.,string,,,,,Foreign Key: Concept.concept_curie diff --git a/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_external_id-dd.csv new file mode 100644 index 0000000..b0d1095 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +SubjectAssertion_assertion_id,Autocreated FK slot,string,,,,,Foreign Key: SubjectAssertion.assertion_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_value_concept-dd.csv b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_value_concept-dd.csv new file mode 100644 index 0000000..d58a570 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/SubjectAssertion_value_concept-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +SubjectAssertion_assertion_id,Autocreated FK slot,string,,,,,Foreign Key: SubjectAssertion.assertion_id +value_concept_concept_curie,The structured term defining the value of the assertion.,string,,,,,Foreign Key: Concept.concept_curie diff --git a/_pipeline_data/static/common_data_models/internal/access/Subject_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/Subject_external_id-dd.csv new file mode 100644 index 0000000..1e383f7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/Subject_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Subject_subject_id,Autocreated FK slot,string,,,,,Foreign Key: Subject.subject_id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository-dd.csv b/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository-dd.csv new file mode 100644 index 0000000..553c821 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository-dd.csv @@ -0,0 +1,6 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +id,,integer,,,,, +name,Name of the entity.,string,,,,, +institution,Name of the institution this record is associated with.,string,,,,, +website,Website for the Record.,string,,,,, +vbr_readme,"Instructions for contacting or requesting samples from Virtual Biorepository, if participating",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository_contact-dd.csv b/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository_contact-dd.csv new file mode 100644 index 0000000..2a1a6d9 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository_contact-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +VirtualBiorepository_id,Autocreated FK slot,integer,,,,,Foreign Key: VirtualBiorepository.id +contact_id,The individual to contact with questions about this record.,integer,,,,,Foreign Key: Investigator.id diff --git a/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository_external_id-dd.csv b/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository_external_id-dd.csv new file mode 100644 index 0000000..a312eed --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/VirtualBiorepository_external_id-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +VirtualBiorepository_id,Autocreated FK slot,integer,,,,,Foreign Key: VirtualBiorepository.id +external_id,"Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/access/_access_study.yaml b/_pipeline_data/static/common_data_models/internal/access/_access_study.yaml new file mode 100644 index 0000000..26667e3 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/access/_access_study.yaml @@ -0,0 +1,142 @@ +model_name: access +model_prefix: access +format: ftd_dd +data_dictionary: + AccessPolicy: + identifier: AccessPolicy-dd.csv + ActivityDefinition: + identifier: ActivityDefinition-dd.csv + ActivityDefinition_external_id: + identifier: ActivityDefinition_external_id-dd.csv + Aliquot: + identifier: Aliquot-dd.csv + Aliquot_external_id: + identifier: Aliquot_external_id-dd.csv + BiospecimenCollection: + identifier: BiospecimenCollection-dd.csv + BiospecimenCollection_external_id: + identifier: BiospecimenCollection_external_id-dd.csv + Concept: + identifier: Concept-dd.csv + DOI: + identifier: DOI-dd.csv + DOI_external_id: + identifier: DOI_external_id-dd.csv + Dataset: + identifier: Dataset-dd.csv + Dataset_file_id: + identifier: Dataset_file_id-dd.csv + Dataset_publication: + identifier: Dataset_publication-dd.csv + Demographics: + identifier: Demographics-dd.csv + Demographics_external_id: + identifier: Demographics_external_id-dd.csv + Demographics_race: + identifier: Demographics_race-dd.csv + Encounter: + identifier: Encounter-dd.csv + EncounterDefinition: + identifier: EncounterDefinition-dd.csv + EncounterDefinition_activity_definition_id: + identifier: EncounterDefinition_activity_definition_id-dd.csv + EncounterDefinition_external_id: + identifier: EncounterDefinition_external_id-dd.csv + Encounter_external_id: + identifier: Encounter_external_id-dd.csv + Family: + identifier: Family-dd.csv + FamilyMember: + identifier: FamilyMember-dd.csv + FamilyMember_external_id: + identifier: FamilyMember_external_id-dd.csv + FamilyRelationship: + identifier: FamilyRelationship-dd.csv + FamilyRelationship_external_id: + identifier: FamilyRelationship_external_id-dd.csv + Family_external_id: + identifier: Family_external_id-dd.csv + File: + identifier: File-dd.csv + FileHash: + identifier: FileHash-dd.csv + File_external_id: + identifier: File_external_id-dd.csv + File_sample_id: + identifier: File_sample_id-dd.csv + File_subject_id: + identifier: File_subject_id-dd.csv + Investigator: + identifier: Investigator-dd.csv + Investigator_external_id: + identifier: Investigator_external_id-dd.csv + Publication: + identifier: Publication-dd.csv + Publication_external_id: + identifier: Publication_external_id-dd.csv + Record_external_id: + identifier: Record_external_id-dd.csv + Sample: + identifier: Sample-dd.csv + Sample_external_id: + identifier: Sample_external_id-dd.csv + Sample_processing: + identifier: Sample_processing-dd.csv + Sample_storage_method: + identifier: Sample_storage_method-dd.csv + Study: + identifier: Study-dd.csv + StudyMetadata: + identifier: StudyMetadata-dd.csv + StudyMetadata_clinical_data_source_type: + identifier: StudyMetadata_clinical_data_source_type-dd.csv + StudyMetadata_data_category: + identifier: StudyMetadata_data_category-dd.csv + StudyMetadata_external_id: + identifier: StudyMetadata_external_id-dd.csv + StudyMetadata_participant_lifespan_stage: + identifier: StudyMetadata_participant_lifespan_stage-dd.csv + StudyMetadata_research_domain: + identifier: StudyMetadata_research_domain-dd.csv + StudyMetadata_study_design: + identifier: StudyMetadata_study_design-dd.csv + Study_clinical_data_source_type: + identifier: Study_clinical_data_source_type-dd.csv + Study_contact: + identifier: Study_contact-dd.csv + Study_data_category: + identifier: Study_data_category-dd.csv + Study_external_id: + identifier: Study_external_id-dd.csv + Study_funding_source: + identifier: Study_funding_source-dd.csv + Study_participant_lifespan_stage: + identifier: Study_participant_lifespan_stage-dd.csv + Study_principal_investigator: + identifier: Study_principal_investigator-dd.csv + Study_program: + identifier: Study_program-dd.csv + Study_publication: + identifier: Study_publication-dd.csv + Study_research_domain: + identifier: Study_research_domain-dd.csv + Study_study_design: + identifier: Study_study_design-dd.csv + Subject: + identifier: Subject-dd.csv + SubjectAssertion: + identifier: SubjectAssertion-dd.csv + SubjectAssertion_concept: + identifier: SubjectAssertion_concept-dd.csv + SubjectAssertion_external_id: + identifier: SubjectAssertion_external_id-dd.csv + SubjectAssertion_value_concept: + identifier: SubjectAssertion_value_concept-dd.csv + Subject_external_id: + identifier: Subject_external_id-dd.csv + VirtualBiorepository: + identifier: VirtualBiorepository-dd.csv + VirtualBiorepository_contact: + identifier: VirtualBiorepository_contact-dd.csv + VirtualBiorepository_external_id: + identifier: VirtualBiorepository_external_id-dd.csv diff --git a/_pipeline_data/static/common_data_models/internal/stable/Concept-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Concept-dd.csv new file mode 100644 index 0000000..d6bf3d0 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Concept-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +concept_curie,The standardized curie for the term.,string,,,,, +display,The friendly display string of the coded term.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/DOI-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/DOI-dd.csv new file mode 100644 index 0000000..d2a3da7 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/DOI-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +doi,Digital Object Identifier (DOI) for this Record.,string,,,,, +bibliographic_reference,Text use to reference this Record.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Demographics-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Demographics-dd.csv new file mode 100644 index 0000000..371ee9b --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Demographics-dd.csv @@ -0,0 +1,8 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +subject_id,INLCUDE Global ID for the Subject,string,,,,, +sex,Sex of Participant,enumeration,,,,female=Female;male=Male;other=Other;unknown=Unknown, +ethnicity,Ethnicity of Participant,enumeration,,,,hispanic_or_latino=Hispanic or Latino;not_hispanic_or_latino=Not Hispanic or Latino;prefer_not_to_answer=Prefer not to answer;unknown=Unknown, +down_syndrome_status,Down Syndrome status of participant,enumeration,,,,d21=Disomy 21 (euploid);t21=Trisomy 21 (Down syndrome), +age_at_last_vital_status,Age in days when participant's vital status was last recorded,integer,,,UCUM:d,, +vital_status,Whether participant is alive or dead,enumeration,,,,dead=Dead;alive=Alive, +age_at_first_engagement,"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.",integer,,,UCUM:d,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Demographics_race-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Demographics_race-dd.csv new file mode 100644 index 0000000..63e5b43 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Demographics_race-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Demographics_subject_id,Autocreated FK slot,string,,,,,Foreign Key: Demographics.subject_id +race,Race of Participant,enumeration,,,,american_indian_or_alaska_native=American Indian or Alaska Native;asian=Asian;black_or_african_american=Black or African American;more_than_one_race=More than one race;native_hawaiian_or_other_pacific_islander=Native Hawaiian or Other Pacific Islander;other=Other;white=White;prefer_not_to_answer=Prefer not to answer;unknown=Unknown;east_asian=UK only; do not use for US data;latin_american=UK only; do not use for US data;middle_eastern_or_north_african=UK only; do not use for US data;south_asian=UK only; do not use for US data, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Investigator-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Investigator-dd.csv new file mode 100644 index 0000000..441ac8b --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Investigator-dd.csv @@ -0,0 +1,6 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +id,,integer,,,,, +name,Name of the entity.,string,,,,, +institution,Name of the institution this record is associated with.,string,,,,, +invesitgator_title,"The title of the Investigator, eg, ""Assistant Professor""",string,,,,, +email,An email address to reach the entity.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Publication-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Publication-dd.csv new file mode 100644 index 0000000..38790b5 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Publication-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +id,,integer,,,,, +bibliographic_reference,Text use to reference this Record.,string,,,,, +website,Website for the Record.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study-dd.csv new file mode 100644 index 0000000..02ef8a4 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study-dd.csv @@ -0,0 +1,15 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +study_id,INLCUDE Global ID for the study,string,,,,, +parent_study,"The parent study for this study, if it is a nested study.",string,,,,,Foreign Key: Study.study_id +study_title,Full Study Title,string,,,,, +study_code,Unique identifier for the study (generally a short acronym),string,,,,, +study_short_name,Short name for the study,string,,,,, +study_description,Brief description of the study (2-4 sentences),string,,,,, +selection_criteria,Brief description of inclusion and/or exclusion criteria for the study,string,,,,, +website,Website for the Record.,string,,,,, +expected_number_of_participants,Total expected number of participants to be recruited.,integer,,,,, +actual_number_of_participants,Total participants included at this time.,integer,,,,, +acknowledgments,Funding statement and acknowledgments for this study,string,,,,, +citation_statement,"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 .""",string,,,,, +doi,Digital Object Identifier (DOI) for this Record.,string,,,,, +vbr_id,"Information about the study's Virtual Biorepository, if participating",integer,,,,,Foreign Key: VirtualBiorepository.id diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_clinical_data_source_type-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_clinical_data_source_type-dd.csv new file mode 100644 index 0000000..8a0e885 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_clinical_data_source_type-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +clinical_data_source_type,Source(s) of data collected from study participants,enumeration,,,,"medical_record=Data obtained directly from medical record;investigator_assessment=Data obtained by examination, interview, etc. with investigator;participant_or_caregiver_report=Data obtained from survey, questionnaire, etc. filled out by participant or caregiver;other=Data obtained from other source, such as tissue bank;unknown=Unknown", diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_contact-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_contact-dd.csv new file mode 100644 index 0000000..cd33900 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_contact-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +contact_id,The individual to contact with questions about this record.,integer,,,,,Foreign Key: Investigator.id diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_data_category-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_data_category-dd.csv new file mode 100644 index 0000000..0636026 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_data_category-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +data_category,"General category of data in this Record (e.g. Clinical, Genomics, etc)",enumeration,,,,unharmonized_demographic_clinical_data=Unharmonized Demographic/Clinical Data;harmonized_demographic_clinical_data=Harmonized Demographic/Clinical Data;genomics=Genomics;transcriptomics=Transcriptomics;epigenomics=Epigenomics;proteomics=Proteomics;metabolomics=Metabolomics;cognitive_behavioral=Cognitive/Behavioral;immune_profiling=Immune Profiling;imaging=Imaging;microbiome=Microbiome;fitness=Fitness;physical_activity=Physical Activity;other=Other;sleep_study=Sleep Study, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_funding_source-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_funding_source-dd.csv new file mode 100644 index 0000000..a0cbc7d --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_funding_source-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +funding_source,The funding source(s) of the study.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_participant_lifespan_stage-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_participant_lifespan_stage-dd.csv new file mode 100644 index 0000000..cf1a4d9 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_participant_lifespan_stage-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +participant_lifespan_stage,Focus age group(s) of the study population,enumeration,,,,fetal=Before birth;neonatal=0-28 days old;pediatric=Birth-17 years old;adult=18+ years old, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_principal_investigator-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_principal_investigator-dd.csv new file mode 100644 index 0000000..b8c210f --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_principal_investigator-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +principal_investigator_id,The Principal Investigator(s) responsible for the study.,integer,,,,,Foreign Key: Investigator.id diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_program-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_program-dd.csv new file mode 100644 index 0000000..333a677 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_program-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +program,Funding source(s) for the study,enumeration,,,,include=INCLUDE;kf=KF;other=Other, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_publication-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_publication-dd.csv new file mode 100644 index 0000000..89621b6 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_publication-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +publication_id,Publications associated with this Record.,integer,,,,,Foreign Key: Publication.id diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_research_domain-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_research_domain-dd.csv new file mode 100644 index 0000000..6290abb --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_research_domain-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +research_domain,"Main research domain(s) of the study, other than Down syndrome",enumeration,,,,behavior_and_behavior_mechanisms=Behavior and Behavior Mechanisms;congenital_heart_defects=Congenital Heart Defects;immune_system_diseases=Immune System Diseases;hematologic_diseases=Hematologic Diseases;neurodevelopment=Neurodevelopment;sleep_wake_disorders=Sleep Wake Disorders;all_co_occurring_conditions=All Co-occurring Conditions;physical_fitness=Physical Fitness;other=Other, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Study_study_design-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Study_study_design-dd.csv new file mode 100644 index 0000000..3f71991 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Study_study_design-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +Study_study_id,Autocreated FK slot,string,,,,,Foreign Key: Study.study_id +study_design,"Overall design of study, including whether it is longitudinal and whether family members/unrelated controls are also enrolled",enumeration,,,,case_control=Case-Control;case_set=Case Set;control_set=Control Set;clinical_trial=Clinical Trial;cross_sectional=Cross-Sectional;family_twins_trios=Family/Twins/Trios;interventional=Interventional;longitudinal=Longitudinal;trial_readiness_study=Trial Readiness Study;tumor_vs_matched_normal=Tumor vs Matched Normal, diff --git a/_pipeline_data/static/common_data_models/internal/stable/Subject-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/Subject-dd.csv new file mode 100644 index 0000000..3d786f8 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/Subject-dd.csv @@ -0,0 +1,4 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +subject_id,INLCUDE Global ID for the Subject,string,,,,, +subject_type,Type of entity this record represents,enumeration,,,,"participant=Study participant with consent, assent, or waiver of consent.;non_participant=An individual associated with a study who was not explictly consented, eg, the subject | of a reported family history.;cell_line=Cell Line;animal_model=Animal model;group=A group of individuals or entities.;other=A different entity type- ideally this will be resolved!", +organism_type,Organism Type,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion-dd.csv new file mode 100644 index 0000000..148fa35 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion-dd.csv @@ -0,0 +1,12 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +assertion_id,INLCUDE Global ID for the Assertion,string,,,,, +subject_id,INLCUDE Global ID for the Subject,string,,,,, +assertion_provenance,The original source of this assertion,enumeration,,,,"medical_record=Data obtained from a medical record;investigator_assessment=Data obtained by examination, interview, etc. with investigator;participant_or_caregiver_report=Data obtained from survey, questionnaire, etc. filled out by participant or caregiver;other=Data obtained from other source, such as tissue bank", +age_at_assertion,The age in days of the Subject when the assertion was made.,integer,,,UCUM:d,, +age_at_event,"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.",integer,,,UCUM:d,, +age_at_resolution,The age in days of the Subject when the asserted state was resolved.,integer,,,UCUM:d,, +concept_source,The source text yielding the standardized concept.,string,,,,, +value_number,The numeric value of the assertion.,number,,,,, +value_source,The source text yielding the value.,string,,,,, +value_units,The structured term defining the units of the value.,string,,,,,Foreign Key: Concept.concept_curie +value_units_source,The source text yielding the value's units.,string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion_concept-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion_concept-dd.csv new file mode 100644 index 0000000..defa0b4 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion_concept-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +SubjectAssertion_assertion_id,Autocreated FK slot,string,,,,,Foreign Key: SubjectAssertion.assertion_id +concept_concept_curie,The structured term defining the meaning of the assertion.,string,,,,,Foreign Key: Concept.concept_curie diff --git a/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion_value_concept-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion_value_concept-dd.csv new file mode 100644 index 0000000..d58a570 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/SubjectAssertion_value_concept-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +SubjectAssertion_assertion_id,Autocreated FK slot,string,,,,,Foreign Key: SubjectAssertion.assertion_id +value_concept_concept_curie,The structured term defining the value of the assertion.,string,,,,,Foreign Key: Concept.concept_curie diff --git a/_pipeline_data/static/common_data_models/internal/stable/VirtualBiorepository-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/VirtualBiorepository-dd.csv new file mode 100644 index 0000000..553c821 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/VirtualBiorepository-dd.csv @@ -0,0 +1,6 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +id,,integer,,,,, +name,Name of the entity.,string,,,,, +institution,Name of the institution this record is associated with.,string,,,,, +website,Website for the Record.,string,,,,, +vbr_readme,"Instructions for contacting or requesting samples from Virtual Biorepository, if participating",string,,,,, diff --git a/_pipeline_data/static/common_data_models/internal/stable/VirtualBiorepository_contact-dd.csv b/_pipeline_data/static/common_data_models/internal/stable/VirtualBiorepository_contact-dd.csv new file mode 100644 index 0000000..2a1a6d9 --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/VirtualBiorepository_contact-dd.csv @@ -0,0 +1,3 @@ +variable_name,description,data_type,min,max,units,enumerations,comment +VirtualBiorepository_id,Autocreated FK slot,integer,,,,,Foreign Key: VirtualBiorepository.id +contact_id,The individual to contact with questions about this record.,integer,,,,,Foreign Key: Investigator.id diff --git a/_pipeline_data/static/common_data_models/internal/stable/_stable_study.yaml b/_pipeline_data/static/common_data_models/internal/stable/_stable_study.yaml new file mode 100644 index 0000000..097f73d --- /dev/null +++ b/_pipeline_data/static/common_data_models/internal/stable/_stable_study.yaml @@ -0,0 +1,103 @@ +model_name: access +model_prefix: access +format: ftd_dd +data_dictionary: + AccessPolicy: + identifier: AccessPolicy-dd.csv + ActivityDefinition: + identifier: ActivityDefinition-dd.csv + Aliquot: + identifier: Aliquot-dd.csv + + BiospecimenCollection: + identifier: BiospecimenCollection-dd.csv + Concept: + identifier: Concept-dd.csv + DOI: + identifier: DOI-dd.csv + Dataset: + identifier: Dataset-dd.csv + Dataset_file_id: + identifier: Dataset_file_id-dd.csv + Dataset_publication: + identifier: Dataset_publication-dd.csv + Demographics: + identifier: Demographics-dd.csv + Demographics_race: + identifier: Demographics_race-dd.csv + Encounter: + identifier: Encounter-dd.csv + EncounterDefinition: + identifier: EncounterDefinition-dd.csv + EncounterDefinition_activity_definition_id: + identifier: EncounterDefinition_activity_definition_id-dd.csv + Family: + identifier: Family-dd.csv + FamilyMember: + identifier: FamilyMember-dd.csv + FamilyRelationship: + identifier: FamilyRelationship-dd.csv + File: + identifier: File-dd.csv + FileHash: + identifier: FileHash-dd.csv + File_sample_id: + identifier: File_sample_id-dd.csv + File_subject_id: + identifier: File_subject_id-dd.csv + Investigator: + identifier: Investigator-dd.csv + Publication: + identifier: Publication-dd.csv + Sample: + identifier: Sample-dd.csv + Sample_processing: + identifier: Sample_processing-dd.csv + Sample_storage_method: + identifier: Sample_storage_method-dd.csv + Study: + identifier: Study-dd.csv + StudyMetadata: + identifier: StudyMetadata-dd.csv + StudyMetadata_clinical_data_source_type: + identifier: StudyMetadata_clinical_data_source_type-dd.csv + StudyMetadata_data_category: + identifier: StudyMetadata_data_category-dd.csv + StudyMetadata_participant_lifespan_stage: + identifier: StudyMetadata_participant_lifespan_stage-dd.csv + StudyMetadata_research_domain: + identifier: StudyMetadata_research_domain-dd.csv + StudyMetadata_study_design: + identifier: StudyMetadata_study_design-dd.csv + Study_clinical_data_source_type: + identifier: Study_clinical_data_source_type-dd.csv + Study_contact: + identifier: Study_contact-dd.csv + Study_data_category: + identifier: Study_data_category-dd.csv + Study_funding_source: + identifier: Study_funding_source-dd.csv + Study_participant_lifespan_stage: + identifier: Study_participant_lifespan_stage-dd.csv + Study_principal_investigator: + identifier: Study_principal_investigator-dd.csv + Study_program: + identifier: Study_program-dd.csv + Study_publication: + identifier: Study_publication-dd.csv + Study_research_domain: + identifier: Study_research_domain-dd.csv + Study_study_design: + identifier: Study_study_design-dd.csv + Subject: + identifier: Subject-dd.csv + SubjectAssertion: + identifier: SubjectAssertion-dd.csv + SubjectAssertion_concept: + identifier: SubjectAssertion_concept-dd.csv + SubjectAssertion_value_concept: + identifier: SubjectAssertion_value_concept-dd.csv + VirtualBiorepository: + identifier: VirtualBiorepository-dd.csv + VirtualBiorepository_contact: + identifier: VirtualBiorepository_contact-dd.csv