From f42d42098323da4bb98d662cc5271be332346208 Mon Sep 17 00:00:00 2001 From: Dan Berrios Date: Tue, 23 Dec 2025 10:29:39 -0800 Subject: [PATCH 1/4] Correction Annotation Props definitions --- src/templates/RBO_classes.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/templates/RBO_classes.tsv b/src/templates/RBO_classes.tsv index dcd0d89..46edaf2 100644 --- a/src/templates/RBO_classes.tsv +++ b/src/templates/RBO_classes.tsv @@ -1,5 +1,5 @@ Ontology ID Label editor preferred term has curation status alternative term definition definition source example of usage editor note term editor curator note ontology term requester term tracker item Logical Type Class Type Parent exact synonym broad synonym Has Subset Member of superset db xref deprecated -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A IAO:0000115 A definition source SPLIT=| A example of usage SPLIT=| A editor note SPLIT=| A term editor SPLIT=| A rdfs:comment SPLIT=| A ontology term requester A term tracker item TYPE CLASS_TYPE C % SPLIT=| A oboInOwl:hasExactSynonym SPLIT=| A oboInOwl:hasBroadSynonym SPLIT=| C 'has subset some % SPLIT=| C 'part of' superset % A http://www.geneontology.org/formats/oboInOwl#hasDbXref AT deprecated^^xsd:boolean +ID LABEL A IAO:0000115 AI IAO:0000114 A IAO:0000118 SPLIT=| A IAO:0000115 A IAO:0000119 SPLIT=| A IAO:0000112 SPLIT=| A editor note SPLIT=| A term editor SPLIT=| A rdfs:comment SPLIT=| A ontology term requester A term tracker item TYPE CLASS_TYPE C % SPLIT=| A oboInOwl:hasExactSynonym SPLIT=| A oboInOwl:hasBroadSynonym SPLIT=| C 'has subset some % SPLIT=| C 'part of' superset % A http://www.geneontology.org/formats/oboInOwl#hasDbXref AT deprecated^^xsd:boolean obo:RBO_00000001 ionizing radiation categorized by source Ionizing radiation classified by the material entity which generates or emits it. obo:RBO_00000116 obo:RBO_00000002 space radiation Radiation originating outside the Earth's atmosphere. http://purl.obolibrary.org/obo/RBO_00000001 obo:RBO_00000003 ground radiation Radiation produced on Earth or on another planetary body by natural or artificial means. One of the principal sources of ground radiation is radon gas. http://purl.obolibrary.org/obo/RBO_00000001 From 216c5e2175efa02abe0e7ce3f4be51bfe37f92de Mon Sep 17 00:00:00 2001 From: Dan Berrios Date: Tue, 23 Dec 2025 10:50:51 -0800 Subject: [PATCH 2/4] Correct template definition --- src/templates/RBO_classes.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/templates/RBO_classes.tsv b/src/templates/RBO_classes.tsv index 46edaf2..f3d19ec 100644 --- a/src/templates/RBO_classes.tsv +++ b/src/templates/RBO_classes.tsv @@ -1,5 +1,5 @@ Ontology ID Label editor preferred term has curation status alternative term definition definition source example of usage editor note term editor curator note ontology term requester term tracker item Logical Type Class Type Parent exact synonym broad synonym Has Subset Member of superset db xref deprecated -ID LABEL A IAO:0000115 AI IAO:0000114 A IAO:0000118 SPLIT=| A IAO:0000115 A IAO:0000119 SPLIT=| A IAO:0000112 SPLIT=| A editor note SPLIT=| A term editor SPLIT=| A rdfs:comment SPLIT=| A ontology term requester A term tracker item TYPE CLASS_TYPE C % SPLIT=| A oboInOwl:hasExactSynonym SPLIT=| A oboInOwl:hasBroadSynonym SPLIT=| C 'has subset some % SPLIT=| C 'part of' superset % A http://www.geneontology.org/formats/oboInOwl#hasDbXref AT deprecated^^xsd:boolean +ID LABEL A IAO:0000111 AI IAO:0000114 A IAO:0000118 SPLIT=| A IAO:0000115 A IAO:0000119 SPLIT=| A IAO:0000112 SPLIT=| A editor note SPLIT=| A term editor SPLIT=| A rdfs:comment SPLIT=| A ontology term requester A term tracker item TYPE CLASS_TYPE C % SPLIT=| A oboInOwl:hasExactSynonym SPLIT=| A oboInOwl:hasBroadSynonym SPLIT=| C 'has subset some % SPLIT=| C 'part of' superset % A http://www.geneontology.org/formats/oboInOwl#hasDbXref AT deprecated^^xsd:boolean obo:RBO_00000001 ionizing radiation categorized by source Ionizing radiation classified by the material entity which generates or emits it. obo:RBO_00000116 obo:RBO_00000002 space radiation Radiation originating outside the Earth's atmosphere. http://purl.obolibrary.org/obo/RBO_00000001 obo:RBO_00000003 ground radiation Radiation produced on Earth or on another planetary body by natural or artificial means. One of the principal sources of ground radiation is radon gas. http://purl.obolibrary.org/obo/RBO_00000001 From e8ee28f5615349174c863f453ac3d3979d1cd5cd Mon Sep 17 00:00:00 2001 From: Dan Berrios Date: Thu, 15 Jan 2026 15:15:58 -0800 Subject: [PATCH 3/4] NTR for ionization cluster concepts --- src/templates/RBO_classes.tsv | 39 +++++++++++++++-------------------- 1 file changed, 17 insertions(+), 22 deletions(-) diff --git a/src/templates/RBO_classes.tsv b/src/templates/RBO_classes.tsv index f3d19ec..8e70e01 100644 --- a/src/templates/RBO_classes.tsv +++ b/src/templates/RBO_classes.tsv @@ -47,9 +47,9 @@ obo:RBO_00000070 radioprotectant radioprotector A substance present at the tim obo:RBO_00000071 radionuclide chelator Radionuclide chelators are small organic molecules or in some cases larger peptides that chemically sequester the radionuclide ion by forming a complex that determines the thermodynamic stability and kinetic inertness of the radionuclide. CHEBI:24432 obo:RBO_00000072 co-carcinogen A co-carcinogen is generally a chemical that promotes the effects of a carcinogen in the production of cancer. In some circumstances exposure to radiation or physical trauma is considered to be co-carcinogenic. CHEBI:24432 obo:RBO_00000073 radiation response modifier "Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors. " "Citrin DE, Mitchell JB. Altering the response to radiation: sensitizers and protectors. Semin Oncol. 2014 Dec;41(6):848-59. doi: 10.1053/j.seminoncol.2014.09.013. Epub 2014 Oct 7. PMID: 25499642; PMCID: PMC4270009." CHEBI:24432 -obo:RBO_00000074 peptide radiation response modifier Radiation response modifiers that are peptides. "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" radiation response modifier +obo:RBO_00000074 peptide radiation response modifier Radiation response modifiers that are peptides. "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" radiation response modifier obo:RBO_00000075 small molecule radiation response modifier Radiation response modifiers that are small molecules. radiation response modifier -obo:RBO_00000076 nuclear industry worker "A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers." "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" occupational role +obo:RBO_00000076 nuclear industry worker "A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers." "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" occupational role obo:RBO_00000077 astronaut occupational role obo:RBO_00000078 military occupational role obo:RBO_00000079 medical professional occupational role @@ -84,7 +84,7 @@ obo:RBO_00000107 toxicity study A study of the toxicity of chemical or biolog obo:RBO_00000108 endocrine study A study of the effects of radiation on the endocrine system or of endocrine hormones on the effects of radiation. obo:RBO_00000089 obo:RBO_00000109 offspring study transgenerational study A study of the effects of radiation on the offspring of an irradiated animal or plant. radiobiology study type obo:RBO_00000110 biokinetics study pharmacokinetics A study of the distribution and metabolism orf drugs or biologicals used for therapeutic purposes. radiobiology study type -obo:RBO_00000111 occupational role "A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society." BFO:0000023 +obo:RBO_00000111 occupational role "A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society." BFO:0000023 obo:RBO_00000112 high linear energy transfer radiation "Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1]." NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf obo:RBO_00000116 NCIT:C17052 obo:RBO_00000113 low linear energy transfer radiation X and gamma rays or light charged particles such as electrons that produce sparse ionizing events far apart on a molecular scale. NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf obo:RBO_00000116 low LET|low-LET NCIT:C17052 obo:RBO_00000114 ionizing electromagnetic radiation Electromagnetic radiation having sufficient energy to remove one or more electrons from an atom obo:RBO_00000116 @@ -98,15 +98,7 @@ obo:RBO_00000121 particle accelerator A device used to impart kinetic energy obo:RBO_00000122 nuclear reactor A device in which nuclear fission may be initiated and controlled in a self-sustaining chain reaction to generate energy or produce useful radiation. COB:0001300|obo:RBO_00005014 MESH:D009688 obo:RBO_00000123 biological process BFO:0000015 GO:0008150 true obo:RBO_00000124 cellular process obo:RBO_00000123 GO:0009987 true -obo:RBO_00005001 heavy ion radiation "A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles." "Heavy ion radiation has several notable characteristics and contexts: - -High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. - -Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. - -Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. - -In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, ""heavy"" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." obo:RBO_00000117 +obo:RBO_00005001 heavy ion radiation "A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles." "Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, ""heavy"" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." obo:RBO_00000117 obo:RBO_00005002 light ion radiation "Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means" obo:RBO_00000117 obo:RBO_00005003 charged particle A particle with a positive or negative electric charge BFO:0000040 obo:RBO_00005009 space flight space flight spaceflight Activity carried out by crewed or robotic vehicles outside the Earth's atmmosphere. ENVO:03000010 Space flight true @@ -165,7 +157,7 @@ obo:RBO_00005042 microbeam "A microbeam is a narrow beam of radiation, of mic UO:0000127 IAO:0000003 obo:RBO_00005066 miligray per second mGy/sec mGy/sec A derived absorbed dose unit which is equal to one milligray absorbed per second UO:0000129 UO:0010065 true obo:RBO_00005067 indirect cellular response to stimulus Indirect cellular response to stimulus "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell" Paul Schofield "This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen." GO:0051716 -obo:RBO_00005068 indirect cellular response to radiation "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells." Paul Schofield "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" obo:RBO_00005067 +obo:RBO_00005068 indirect cellular response to radiation "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells." Paul Schofield "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" obo:RBO_00005067 obo:RBO_00005069 indirect cellular response to ionising radiation "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells." Paul Schofield "Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component." obo:RBO_00005068 obo:RBO_00005070 ionizing radiation device A device for exposing materials or biological organisms to ionizing radiation for research or therapeutic purposes. radiation source obo:RBO_00005071 high-altitude balloon "High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level." Wikipedia Jack Miller aircraft @@ -300,8 +292,8 @@ obo:RBO_00002125 anthropogenic environment radiation monitoring Monitoring fo obo:RBO_00002126 natural environment radiation monitoring Monitoring for radiation dose or quality within a natural environment. obo:RBO_00002122|obo:RBO_00002123 obo:RBO_00015000 radiation That energy which is transferred in space and time as part of the process of radiation (ENVO:01001023). obo:BFO_0000040 obo:RBO_00015001 neutral particle radiation Uncharged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator) obo:RBO_00015000 -obo:RBO_00015002 nanodosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." Usually a track structure assay at nm scale obo:RBO_00005041 -obo:RBO_00015003 microdosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." Usually a track structure assay at micrometre scale obo:RBO_00005041 +obo:RBO_00015002 nanodosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." Usually a track structure assay at nm scale obo:RBO_00005041 +obo:RBO_00015003 microdosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." Usually a track structure assay at micrometre scale obo:RBO_00005041 obo:RBO_00015004 alpha decay Nuclear decay in which an alpha particle is emitted. https://goldbook.iupac.org/terms/view/A00005 obo:RBO_00002118 alpha-decay http://purl.obolibrary.org/obo/REX_0000017 obo:RBO_00015005 beta decay Radioactive decay in which a beta particle is emitted or in which orbital electron capture occurs. http://goldbook.iupac.org/B00572.html obo:RBO_00002118 beta-decay http://purl.obolibrary.org/obo/REX_0000007 obo:RBO_00015006 subatomic process Processes in which electrons or components of the atomic nucleus are participants. BFO:0000015 @@ -342,7 +334,7 @@ obo:RBO_00015040 anthropogenic non-ionizing background radiation anthropogenic n obo:RBO_00015041 natural non-ionizing background radiation natural non-ionizing background radiation Non-ionizing background radiation that is not the result of a human planned process. "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" obo:RBO_00015039 obo:RBO_00015042 Van Allen belts "The toroidal zones surrounding the Earth, comprised of charged particles trapped by the Earth's magnetic field. There are two permanent belts, an inner and an outer belt. A transient third belt may form during periods of high solar activity." https://doi.org/10.1029/2018JA025940 "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" obo:RBO_00000016 obo:RBO_00015043 solar particle event SPE "The emission and acceleration of large numbers of energetic charged particles, mainly protons, from the Sun. Sources include solar flares and coronal mass ejections (CME)." https://three.jsc.nasa.gov/articles/Hu-SPEs.pdf "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" ENVO:03000010 -obo:RBO_00015044 geomagnetosphere "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earths magnetic field." https://www.swpc.noaa.gov/phenomena/earths-magnetosphere "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" ENVO:01000951 +obo:RBO_00015044 geomagnetosphere "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field." https://www.swpc.noaa.gov/phenomena/earths-magnetosphere "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" ENVO:01000951 obo:RBO_00015045 high dose rate irradiation "A radiation exposure in which the delivery of energy to the target is considered to be ""high dose rate"" in a given context." The context here is determined by the type of radiation and application of the exposure. radiation exposure obo:RBO_00015046 space radiation environment A radiation environment outside a commonly defined boundary marking the beginning of space (frequently the Karman line). radiation environment true obo:RBO_00015047 radiation-induced senescence "Senescence caused by radiation and associated with the dismantling of a cell as a response to oxidative stress, e.g. high levels of reactive oxygen species, such as superoxide anions, hydrogen peroxide, and hydroxyl radicals." cellular senescence @@ -368,7 +360,7 @@ obo:RBO_00010016 radiation dose "A measurement datum of the quantity of radia obo:RBO_00010018 radiation weighting factor A factor used to allow for differences in the biological effectiveness between different radiations when calculating equivalent dose (H_T) (see equivalent dose). These factors are independent of the tissue or organ irradiated. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Radiation weighting factors may change as more data on biological effects are obtained. Jack Miller OBI:0001909 obo:RBO_00010019 relative biological effectiveness RBE "Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Neutrons have been found to have a higher RBE than electrons. Jack Miller IAO:0000109 RBE obo:RBO_00010020 tissue equivalence Denotes a substance with absorbing and scattering properties for a given radiation that sufficiently match those of a particular biological tissue. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Tissue equivalent materials can be used to study radiation effects at depth in the human body. Jack Miller PATO:0001018 -obo:RBO_00015052 senolytic "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cellscells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" "Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies." "http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670" obo:RBO_00000073 +obo:RBO_00015052 senolytic "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" "Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies." "http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670" obo:RBO_00000073 obo:RBO_00010021 radon dosimeter radon detector "Radon dosimeters are radiation dosimeters used to measure the presence and concentration of radon gas (Rn-222), a radioactive noble gas that can accumulate in buildings and pose health risks. Different types of radon detectors use various detection methods, based on the radioactive decay products of radon." obo:RBO_00000115 obo:RBO_00010022 active radon dosimeter An active dosimeter for radon. obo:RBO_00000011 obo:RBO_00010023 passive radon dosimeter An passive dosimeter for radon. obo:RBO_00000012 @@ -376,9 +368,9 @@ obo:RBO_00010024 scintillation radon dosimeter "An active radon dosimeter tha obo:RBO_00010025 continuous working level radon dosimeter CWLM "An active radon dosimeter that measure the concentration of radon decay products (polonium-218, lead-214, and bismuth-214) using alpha spectroscopy or particle collection on a filter. They provide working level (WL) values, which indicate the potential radiation dose from radon decay products." "Provides direct measurement of biologically relevant radiation exposure. Expensive, mainly used in occupational settings." obo:RBO_00010026 obo:RBO_00010026 continuous radon monitor CRM "An active radon dosimeter that uses various sensors (e.g., scintillation detectors, ion chambers, or solid-state silicon detectors) to measure radon decay in real-time. They typically record radon levels at hourly intervals." "Provides near real-time results, detects fluctuations over time, useful for home inspections." obo:RBO_00010022 obo:RBO_00010027 electret ion chamber radon dosimeter "A passive radon dosimeter that contain an electret (a charged Teflon disc) inside an ionization chamber. Radon decay ionizes the air, causing a measurable voltage drop in the electret, which correlates with radon concentration." "Can be read without a lab, provides both short- and long-term measurements." obo:RBO_00010023 -obo:RBO_00010028 charcoal cannister radon dosimeter "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 27 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." obo:RBO_00010023 +obo:RBO_00010028 charcoal cannister radon dosimeter "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." obo:RBO_00010023 obo:RBO_00010029 alpha track radon dosimeter alpha track detector "A passive radon dosimeter in which a small plastic film or polycarbonate chip is exposed to radon gas. When radon decays, it emits alpha particles that leave microscopic tracks on the film. After exposure, the film is chemically etched to reveal the tracks, which are counted under a microscope to determine radon levels." Alpha track radon dosimeters are used domestically for radon monitoring over long periods of time. obo:RBO_00010023 -obo:RBO_00010030 research nuclear reactor research reactor "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects internal structure." Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development obo:RBO_00000122 +obo:RBO_00010030 research nuclear reactor research reactor "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure." Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development obo:RBO_00000122 obo:RBO_00010031 nuclear power reactor power reactor A nuclear reactor primarily used to generate and supply power. "This conceptualization of nuclear power reactor emphasizes its role as a radiation source. For use to emphasize its roles in energy production, recommend use of identically named concept ENVO:02000137" obo:RBO_00000122 obo:RBO_00010032 military nuclear reactor A nuclear reactor used for military purposes such as plutonium production. obo:RBO_00000122 obo:RBO_00010033 multi-purpose nuclear reactor A nuclear reactor used for more than one purpose. obo:RBO_00000122 @@ -395,8 +387,7 @@ obo:RBO_00010043 passive radiation shielding role "The role of materials used obo:RBO_00010044 radiation intensity The power per unit solid angle delivered by radiation incident on a given location. PATO:0001018 obo:RBO_00010045 radiation shielding role "The role of a material in reducing radiation intensity by modifying the composition, and/or energy of incident radiation." BFO:0000023 obo:RBO_00010046 passive radiation shielding "Radiation shielding using materials such as concrete, lead, or polyethylene, with no requirement for external power or operator intervention" obo:RBO_00010041 -obo:RBO_00010047 acute radiation syndrome "acute radiation sickness, ARS" "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiationtypically more than 1 Gray (Gy)over a short period (minutes to hours). -Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (110 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (520 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." "Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome" http://purl.obolibrary.org/obo/DOID_4 +obo:RBO_00010047 acute radiation syndrome "acute radiation sickness, ARS" "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." "Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome" http://purl.obolibrary.org/obo/DOID_4 obo:RBO_00010048 anthropogenic radiation environment An environment in which there is human-created radiation. "Includes terrestrial and non-terrestrial environments. Includes environments created for investigations, and those used for other purposes including those created by humans for habitation, manufacture, storage, clinical practice and transport. Will include mines and other environments actively created by humans by the manipulation of natural materials" RBO:00000016 obo:RBO_00010049 natural radiation environment A radiation environment resulting from natural processes. RBO:00000016 obo:RBO_00010050 earth subsurface radiation environment "The radiation environment below the surface of the Earth, consisting of radiation from naturally occurring radioactive elements; particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field, atmosphere and materials in the Earth's crust to enable them to penetrate below the Earth's surface; particles produced by interactions of primary radiation with the Earth's crust; and anthropogenic sources of radiation such as buried nuclear waste. The composition and strength of the radiation at a given point under the Earth's surface depends strongly on depth below the surface and composition of the surrounding crustal material." obo:RBO_00000016 terrestrial subsurface radiation environment @@ -406,5 +397,9 @@ obo:RBO_00010053 high linear energy transfer "The quality of neutrons or char obo:RBO_00010054 low linear energy transfer The quality of X and gamma rays or light charged particles such as electrons such that they can only produce sparse ionizing events far apart on a molecular scale. PATO:0001739 obo:RBO_00010055 microdosimetry study type Microdosimetry is a radiobiology study type that deals with the study of the distribution of energy deposition on a micrometer scale in biological systems exposed to ionizing radiation. It focuses on understanding how radiation interacts with cellular and sub-cellular structures and the resulting effects on biological systems. RBO:00000082 obo:RBO_00010056 low dose radiation study type "A study of the biological effects of low acute or protracted doses of ionising radiation defined as being below 500 mSv, less than 100mGy, or at dose rates less than 5mGy per hour. ( https://www.nationalacademies.org/our-work/developing-a-long-term-strategy-for-low-dose-radiation-research-in-the-united-states)" RBO:00000082 -obo:RBO_00010057 earth hydrosphere radiation environment "The radiation environment consisting of the water at the surface of the Earth, including all of Earths water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." obo:RBO_00010051 +obo:RBO_00010057 earth hydrosphere radiation environment "The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." obo:RBO_00010051 obo:RBO_00010058 lineal energy measurement datum A measurement of the amount of energy deposited by ionizing radiation per unit length of a medium. . It represents the average energy transferred to the material per unit length along the path of the particle in a specified micrometric ( or smaller) site divided by the mean chord length of the site volume. Lineal energy is typically expressed in units of keV/?m (kilo-electron volts per micrometer) or MeV/cm (mega-electron volts per centimeter) IAO:0000109 +obo:RBO_00010059 ionization cluster size ionisation cluster size The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. "In the case of ionization cluster size per unit length, the common unit is ""ion pairs per micrometer"" (ion pairs/µm) or ""ion pairs per millimeter"" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be ""ion pairs per cubic micrometer"" (ion pairs/µm³) or ""ion pairs per cubic millimeter"" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.""" PATO:0001241 +obo:RBO_00010060 ionization cluster size measurement datum ionisation cluster size measurement datum A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. "In the case of ionization cluster size per unit length, the common unit is ""ion pairs per micrometer"" (ion pairs/µm) or ""ion pairs per millimeter"" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be ""ion pairs per cubic micrometer"" (ion pairs/µm³) or ""ion pairs per cubic millimeter"" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.""" IAO:0000032 +obo:RBO_00010061 particle track penumbra "The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium."" Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity." "Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf" BFO:0000006 +obo:RBO_00010062 particle track core "In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle." BFO:0000006 From 5ea62c776f84d0e1daa5ad4684ca91df4282594e Mon Sep 17 00:00:00 2001 From: DanBerrios Date: Thu, 15 Jan 2026 23:28:53 +0000 Subject: [PATCH 4/4] Build with NTR for microdosimetry --- rbo-base.json | 112 +- rbo-base.owl | 83 +- rbo-full.json | 106 +- rbo-full.owl | 71 +- rbo.json | 106 +- rbo.owl | 71 +- src/ontology/components/all_templates.owl | 96 +- src/ontology/reports/basic-report.tsv | 115 +- .../reports/class-count-by-prefix.tsv | 2 +- src/ontology/reports/edges.tsv | 21946 ++++++++-------- .../reports/rbo-edit.owl-obo-report.tsv | 2 +- src/ontology/reports/rbo.owl-obo-report.tsv | 26 +- src/ontology/reports/synonyms.tsv | 476 +- src/ontology/reports/xrefs.tsv | 216 +- src/templates/RBO_classes.owl | 94 +- 15 files changed, 12034 insertions(+), 11488 deletions(-) diff --git a/rbo-base.json b/rbo-base.json index e4d8bed..d65d48c 100644 --- a/rbo-base.json +++ b/rbo-base.json @@ -16,11 +16,14 @@ "val" : "http://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2025-12-11" + "val" : "2026-01-15" } ], - "version" : "http://purl.obolibrary.org/obo/rbo/releases/2025-12-11/rbo-base.json" + "version" : "http://purl.obolibrary.org/obo/rbo/releases/2026-01-15/rbo-base.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "type" : "CLASS" + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "type" : "CLASS" }, { @@ -101,6 +104,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000030", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000032", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000104", "type" : "CLASS" @@ -829,6 +835,9 @@ "val" : "Radiation response modifiers that are peptides." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" } ] @@ -851,6 +860,9 @@ "val" : "A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" } ] @@ -3155,6 +3167,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Heavy ion radiation has several notable characteristics and contexts:\n\nHigh Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues.\n\nEnhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.\n\nSpace Radiation: Heavy ions are a component of the galactic cosmic radiation present in space.\n\nIn common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, \"heavy\" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, \"heavy\" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." } ] } }, { @@ -3995,6 +4010,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Paul Schofield" @@ -4524,7 +4542,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." + "val" : "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." } } }, { @@ -4549,7 +4567,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure." + "val" : "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -4728,7 +4746,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours).\nKey features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." + "val" : "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -4841,7 +4859,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." + "val" : "The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." } } }, { @@ -4853,6 +4871,60 @@ "val" : "A measurement of the amount of energy deposited by ionizing radiation per unit length of a medium. . It represents the average energy transferred to the material per unit length along the path of the particle in a specified micrometric ( or smaller) site divided by the mean chord length of the site volume. Lineal energy is typically expressed in units of keV/?m (kilo-electron volts per micrometer) or MeV/cm (mega-electron volts per centimeter)" } } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010059", + "lbl" : "ionization cluster size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the case of ionization cluster size per unit length, the common unit is \"ion pairs per micrometer\" (ion pairs/µm) or \"ion pairs per millimeter\" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be \"ion pairs per cubic micrometer\" (ion pairs/µm³) or \"ion pairs per cubic millimeter\" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ionisation cluster size" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010060", + "lbl" : "ionization cluster size measurement datum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the case of ionization cluster size per unit length, the common unit is \"ion pairs per micrometer\" (ion pairs/µm) or \"ion pairs per millimeter\" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be \"ion pairs per cubic micrometer\" (ion pairs/µm³) or \"ion pairs per cubic millimeter\" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ionisation cluster size measurement datum" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010061", + "lbl" : "particle track penumbra", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium.\" Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010062", + "lbl" : "particle track core", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle." + } + } }, { "id" : "http://purl.obolibrary.org/obo/RBO_00015000", "lbl" : "radiation", @@ -4881,6 +4953,9 @@ }, "comments" : [ "Usually a track structure assay at nm scale" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." } ] @@ -4895,6 +4970,9 @@ }, "comments" : [ "Usually a track structure assay at micrometre scale" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." } ] @@ -5500,7 +5578,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field." + "val" : "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -5599,7 +5677,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " + "val" : "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -5609,7 +5687,7 @@ "val" : "http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" + "val" : "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" } ] } }, { @@ -8082,6 +8160,22 @@ "sub" : "http://purl.obolibrary.org/obo/RBO_00010058", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000109" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010060", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010061", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/RBO_00015000", "pred" : "is_a", diff --git a/rbo-base.owl b/rbo-base.owl index cb52576..eccc3f7 100644 --- a/rbo-base.owl +++ b/rbo-base.owl @@ -13,12 +13,12 @@ xmlns:dcterms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology - 2025-12-11 + 2026-01-15 @@ -184,6 +184,12 @@ + + + + + + @@ -346,6 +352,12 @@ + + + + + + @@ -1023,6 +1035,7 @@ Radiation response modifiers that are peptides. + Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 peptide radiation response modifier @@ -1044,6 +1057,7 @@ A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. + Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 nuclear industry worker @@ -1400,6 +1414,7 @@ + A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. occupational role @@ -3097,6 +3112,7 @@ Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in m Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. + Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -3749,6 +3765,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 + The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to radiation @@ -4127,7 +4144,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. + A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. charcoal cannister radon dosimeter @@ -4149,7 +4166,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure. + Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure. research reactor Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development research nuclear reactor @@ -4327,8 +4344,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours). -Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. + A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. acute radiation sickness, ARS Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome acute radiation syndrome @@ -4434,7 +4450,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. + The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. earth hydrosphere radiation environment @@ -4450,6 +4466,51 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati + + + + + The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size + ionization cluster size + + + + + + + + + A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size measurement datum + ionization cluster size measurement datum + + + + + + + + + The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium." Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity. + Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf + particle track penumbra + + + + + + + + + In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle. + particle track core + + + + @@ -4475,6 +4536,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale nanodosimetry assay @@ -4487,6 +4549,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale microdosimetry assay @@ -4996,7 +5059,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field. + The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field. http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 https://www.swpc.noaa.gov/phenomena/earths-magnetosphere geomagnetosphere @@ -5084,10 +5147,10 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. + A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies. http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 - See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 + See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 senolytic diff --git a/rbo-full.json b/rbo-full.json index c472858..7ca35ab 100644 --- a/rbo-full.json +++ b/rbo-full.json @@ -13,9 +13,9 @@ "val" : "http://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2025-12-11" + "val" : "2026-01-15" } ], - "version" : "http://purl.obolibrary.org/obo/rbo/releases/2025-12-11/rbo-full.json" + "version" : "http://purl.obolibrary.org/obo/rbo/releases/2026-01-15/rbo-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", @@ -167549,6 +167549,9 @@ "val" : "Radiation response modifiers that are peptides." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" } ] @@ -167571,6 +167574,9 @@ "val" : "A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" } ] @@ -169875,6 +169881,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Heavy ion radiation has several notable characteristics and contexts:\n\nHigh Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues.\n\nEnhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.\n\nSpace Radiation: Heavy ions are a component of the galactic cosmic radiation present in space.\n\nIn common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, \"heavy\" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, \"heavy\" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." } ] } }, { @@ -170715,6 +170724,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Paul Schofield" @@ -171244,7 +171256,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." + "val" : "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." } } }, { @@ -171269,7 +171281,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure." + "val" : "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -171448,7 +171460,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours).\nKey features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." + "val" : "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -171561,7 +171573,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." + "val" : "The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." } } }, { @@ -171573,6 +171585,60 @@ "val" : "A measurement of the amount of energy deposited by ionizing radiation per unit length of a medium. . It represents the average energy transferred to the material per unit length along the path of the particle in a specified micrometric ( or smaller) site divided by the mean chord length of the site volume. Lineal energy is typically expressed in units of keV/?m (kilo-electron volts per micrometer) or MeV/cm (mega-electron volts per centimeter)" } } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010059", + "lbl" : "ionization cluster size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the case of ionization cluster size per unit length, the common unit is \"ion pairs per micrometer\" (ion pairs/µm) or \"ion pairs per millimeter\" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be \"ion pairs per cubic micrometer\" (ion pairs/µm³) or \"ion pairs per cubic millimeter\" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ionisation cluster size" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010060", + "lbl" : "ionization cluster size measurement datum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the case of ionization cluster size per unit length, the common unit is \"ion pairs per micrometer\" (ion pairs/µm) or \"ion pairs per millimeter\" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be \"ion pairs per cubic micrometer\" (ion pairs/µm³) or \"ion pairs per cubic millimeter\" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ionisation cluster size measurement datum" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010061", + "lbl" : "particle track penumbra", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium.\" Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010062", + "lbl" : "particle track core", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle." + } + } }, { "id" : "http://purl.obolibrary.org/obo/RBO_00015000", "lbl" : "radiation", @@ -171601,6 +171667,9 @@ }, "comments" : [ "Usually a track structure assay at nm scale" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." } ] @@ -171615,6 +171684,9 @@ }, "comments" : [ "Usually a track structure assay at micrometre scale" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." } ] @@ -172220,7 +172292,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field." + "val" : "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -172319,7 +172391,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " + "val" : "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -172329,7 +172401,7 @@ "val" : "http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" + "val" : "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" } ] } }, { @@ -354159,6 +354231,22 @@ "sub" : "http://purl.obolibrary.org/obo/RBO_00010058", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000109" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010060", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010061", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/RBO_00015000", "pred" : "is_a", diff --git a/rbo-full.owl b/rbo-full.owl index 8153e37..6841a64 100644 --- a/rbo-full.owl +++ b/rbo-full.owl @@ -39,11 +39,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology - 2025-12-11 + 2026-01-15 @@ -278962,6 +278962,7 @@ Classes for population already exist in IDO ('organism population', I Radiation response modifiers that are peptides. + Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 peptide radiation response modifier @@ -278983,6 +278984,7 @@ Classes for population already exist in IDO ('organism population', I A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. + Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 nuclear industry worker @@ -279339,6 +279341,7 @@ Classes for population already exist in IDO ('organism population', I + A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. occupational role @@ -281036,6 +281039,7 @@ Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in m Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. + Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -281688,6 +281692,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 + The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to radiation @@ -282066,7 +282071,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. + A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. charcoal cannister radon dosimeter @@ -282088,7 +282093,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure. + Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure. research reactor Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development research nuclear reactor @@ -282266,8 +282271,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours). -Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. + A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. acute radiation sickness, ARS Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome acute radiation syndrome @@ -282373,7 +282377,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. + The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. earth hydrosphere radiation environment @@ -282389,6 +282393,51 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati + + + + + The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size + ionization cluster size + + + + + + + + + A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size measurement datum + ionization cluster size measurement datum + + + + + + + + + The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium." Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity. + Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf + particle track penumbra + + + + + + + + + In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle. + particle track core + + + + @@ -282414,6 +282463,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale nanodosimetry assay @@ -282426,6 +282476,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale microdosimetry assay @@ -282935,7 +282986,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field. + The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field. http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 https://www.swpc.noaa.gov/phenomena/earths-magnetosphere geomagnetosphere @@ -283023,10 +283074,10 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. + A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies. http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 - See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 + See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 senolytic diff --git a/rbo.json b/rbo.json index 11ab175..967dcc4 100644 --- a/rbo.json +++ b/rbo.json @@ -13,9 +13,9 @@ "val" : "http://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2025-12-11" + "val" : "2026-01-15" } ], - "version" : "http://purl.obolibrary.org/obo/rbo/releases/2025-12-11/rbo.json" + "version" : "http://purl.obolibrary.org/obo/rbo/releases/2026-01-15/rbo.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", @@ -167549,6 +167549,9 @@ "val" : "Radiation response modifiers that are peptides." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" } ] @@ -167571,6 +167574,9 @@ "val" : "A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" } ] @@ -169875,6 +169881,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Heavy ion radiation has several notable characteristics and contexts:\n\nHigh Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues.\n\nEnhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.\n\nSpace Radiation: Heavy ions are a component of the galactic cosmic radiation present in space.\n\nIn common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, \"heavy\" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, \"heavy\" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." } ] } }, { @@ -170715,6 +170724,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Paul Schofield" @@ -171244,7 +171256,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." + "val" : "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." } } }, { @@ -171269,7 +171281,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure." + "val" : "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -171448,7 +171460,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours).\nKey features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." + "val" : "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", @@ -171561,7 +171573,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." + "val" : "The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." } } }, { @@ -171573,6 +171585,60 @@ "val" : "A measurement of the amount of energy deposited by ionizing radiation per unit length of a medium. . It represents the average energy transferred to the material per unit length along the path of the particle in a specified micrometric ( or smaller) site divided by the mean chord length of the site volume. Lineal energy is typically expressed in units of keV/?m (kilo-electron volts per micrometer) or MeV/cm (mega-electron volts per centimeter)" } } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010059", + "lbl" : "ionization cluster size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the case of ionization cluster size per unit length, the common unit is \"ion pairs per micrometer\" (ion pairs/µm) or \"ion pairs per millimeter\" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be \"ion pairs per cubic micrometer\" (ion pairs/µm³) or \"ion pairs per cubic millimeter\" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ionisation cluster size" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010060", + "lbl" : "ionization cluster size measurement datum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the case of ionization cluster size per unit length, the common unit is \"ion pairs per micrometer\" (ion pairs/µm) or \"ion pairs per millimeter\" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be \"ion pairs per cubic micrometer\" (ion pairs/µm³) or \"ion pairs per cubic millimeter\" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ionisation cluster size measurement datum" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010061", + "lbl" : "particle track penumbra", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium.\" Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RBO_00010062", + "lbl" : "particle track core", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle." + } + } }, { "id" : "http://purl.obolibrary.org/obo/RBO_00015000", "lbl" : "radiation", @@ -171601,6 +171667,9 @@ }, "comments" : [ "Usually a track structure assay at nm scale" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." } ] @@ -171615,6 +171684,9 @@ }, "comments" : [ "Usually a track structure assay at micrometre scale" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." } ] @@ -172220,7 +172292,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field." + "val" : "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -172319,7 +172391,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " + "val" : "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -172329,7 +172401,7 @@ "val" : "http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" + "val" : "See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4" } ] } }, { @@ -354159,6 +354231,22 @@ "sub" : "http://purl.obolibrary.org/obo/RBO_00010058", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000109" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010060", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010061", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/RBO_00010062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/RBO_00015000", "pred" : "is_a", diff --git a/rbo.owl b/rbo.owl index 4d2b126..67e03b8 100644 --- a/rbo.owl +++ b/rbo.owl @@ -39,11 +39,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology - 2025-12-11 + 2026-01-15 @@ -278962,6 +278962,7 @@ Classes for population already exist in IDO ('organism population', I Radiation response modifiers that are peptides. + Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 peptide radiation response modifier @@ -278983,6 +278984,7 @@ Classes for population already exist in IDO ('organism population', I A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. + Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 nuclear industry worker @@ -279339,6 +279341,7 @@ Classes for population already exist in IDO ('organism population', I + A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. occupational role @@ -281036,6 +281039,7 @@ Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in m Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. + Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -281688,6 +281692,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 + The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to radiation @@ -282066,7 +282071,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. + A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. charcoal cannister radon dosimeter @@ -282088,7 +282093,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure. + Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure. research reactor Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development research nuclear reactor @@ -282266,8 +282271,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours). -Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. + A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. acute radiation sickness, ARS Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome acute radiation syndrome @@ -282373,7 +282377,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. + The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. earth hydrosphere radiation environment @@ -282389,6 +282393,51 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati + + + + + The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size + ionization cluster size + + + + + + + + + A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size measurement datum + ionization cluster size measurement datum + + + + + + + + + The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium." Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity. + Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf + particle track penumbra + + + + + + + + + In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle. + particle track core + + + + @@ -282414,6 +282463,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale nanodosimetry assay @@ -282426,6 +282476,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale microdosimetry assay @@ -282935,7 +282986,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field. + The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field. http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 https://www.swpc.noaa.gov/phenomena/earths-magnetosphere geomagnetosphere @@ -283023,10 +283074,10 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. + A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies. http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 - See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 + See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 senolytic diff --git a/src/ontology/components/all_templates.owl b/src/ontology/components/all_templates.owl index fc9b5f9..8e86351 100644 --- a/src/ontology/components/all_templates.owl +++ b/src/ontology/components/all_templates.owl @@ -9,7 +9,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -125,6 +125,12 @@ + + + + + + @@ -275,6 +281,12 @@ + + + + + + @@ -952,7 +964,7 @@ Radiation response modifiers that are peptides. - Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 + Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 peptide radiation response modifier @@ -973,7 +985,7 @@ A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. - Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 + Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 nuclear industry worker @@ -1325,7 +1337,7 @@ - A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. + A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. occupational role @@ -2997,15 +3009,7 @@ A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. - Heavy ion radiation has several notable characteristics and contexts: - -High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. - -Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. - -Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. - -In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. + Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -3650,7 +3654,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 + The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to radiation @@ -4029,7 +4033,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. + A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. charcoal cannister radon dosimeter @@ -4051,7 +4055,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure. + Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure. research reactor Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development research nuclear reactor @@ -4228,8 +4232,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours). -Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. + A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. acute radiation sickness, ARS Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome acute radiation syndrome @@ -4335,7 +4338,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. + The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. earth hydrosphere radiation environment @@ -4351,6 +4354,51 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati + + + + + The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size + ionization cluster size + + + + + + + + + A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size measurement datum + ionization cluster size measurement datum + + + + + + + + + The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium." Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity. + Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf + particle track penumbra + + + + + + + + + In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle. + particle track core + + + + @@ -4376,7 +4424,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers - See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale nanodosimetry assay @@ -4388,7 +4436,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers - See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale microdosimetry assay @@ -4873,7 +4921,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field. + The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field. http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 https://www.swpc.noaa.gov/phenomena/earths-magnetosphere geomagnetosphere @@ -4961,10 +5009,10 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. + A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies. http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 - See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 + See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 senolytic diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index 419a257..bd54d68 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -332,7 +332,6 @@ "Any process that modulates the frequency, rate or extent of small intestine smooth muscle contraction." "Any muscle organ that is part of a cloaca." - "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours).\nKey features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." "A submucosa that is part of a cystic duct [Automatically generated definition]." "FMA:18013" "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." "MESH:D001854 FMA:83621 BTO:0004850" "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." @@ -555,7 +554,7 @@ "The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles." "A stable isotope of selenium with relative atomic mass 81.91670, 8.82 atom percent natural abundance and nuclear spin 0." "PMID:31386478 PMID:33576665 PMID:16028633 Chemspider:4892236 CAS:14687-58-2 PMID:31951429 PMID:18781022 PMID:6337549 PMID:30881205 PMID:23575454 PMID:29932707 PMID:22258472 PMID:21139275" "PO_GIT:466" - "The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct." "galen:CommonBileDuct UMLS:C0009437 EMAPA:17201 http://www.snomedbrowser.com/Codes/Details/362199009 MESH:D003135 NCIT:C12698 TAO:0005165 http://linkedlifedata.com/resource/umls/id/C0009437 ZFA:0005165 GAID:282 EHDAA2:0000303 MA:0001631 http://en.wikipedia.org/wiki/Common_bile_duct VHOG:0000214 FMA:14667 EHDAA:3981" + "The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct." "galen:CommonBileDuct UMLS:C0009437 EMAPA:17201 http://www.snomedbrowser.com/Codes/Details/362199009 MESH:D003135 TAO:0005165 NCIT:C12698 http://linkedlifedata.com/resource/umls/id/C0009437 ZFA:0005165 GAID:282 EHDAA2:0000303 MA:0001631 http://en.wikipedia.org/wiki/Common_bile_duct VHOG:0000214 FMA:14667 EHDAA:3981" "A role played by the molecular entity or part thereof which causes the development of a pathological process." "Any meiotic cell cycle process that is involved in oocyte maturation." "A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition]." "MA:0002833 FMA:84428 EMAPA:36573" @@ -607,7 +606,6 @@ "Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." "The dorsal region of the optic cup that gives rise to the dorsal part of the retina." "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs." "FMA:74562 EMAPA:18765 EHDAA2:0004615 CALOHA:TS-2018 MA:0000013" - "The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." "Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death." @@ -765,6 +763,7 @@ "The pulmonary artery that supplies the left lung." "NCIT:C32971 MA:0002032 FMA:50873 http://www.snomedbrowser.com/Codes/Details/244234004 galen:LeftPulmonaryArtery http://en.wikipedia.org/wiki/Left_pulmonary_artery EMAPA:37097 http://linkedlifedata.com/resource/umls/id/C0923925 UMLS:C0923925" + "In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle." "Mesenchyme that develops_from a trunk neural crest." "ZFA:0000999 EMAPA:16182 TAO:0000999 EHDAA2:0002093" "SWEETRealm:Wood LTER:637 EcoLexicon:wood https://en.wikipedia.org/wiki/Wood" "https://en.wikipedia.org/wiki/Hospital" @@ -1325,7 +1324,7 @@ "Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism." - "The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs." "EMAPA:16777 EHDAA2:0002205 NCIT:C33881 UMLS:C0225776 http://www.snomedbrowser.com/Codes/Details/361997008 VHOG:0001496 FMA:9734 MA:0002489 http://linkedlifedata.com/resource/umls/id/C0225776" + "The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs." "EMAPA:16777 EHDAA2:0002205 NCIT:C33881 http://www.snomedbrowser.com/Codes/Details/361997008 UMLS:C0225776 VHOG:0001496 FMA:9734 MA:0002489 http://linkedlifedata.com/resource/umls/id/C0225776" "GC_ID:1" "The chemical reactions and pathways resulting in the breakdown of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, as carried out by individual cells." "Any process that activates or increases the frequency, rate or extent of lipid binding." @@ -1366,7 +1365,7 @@ "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures." "MESH:D002988 ZFA:0005781 http://www.snomedbrowser.com/Codes/Details/362857006 http://www.snomedbrowser.com/Codes/Details/370631000 http://linkedlifedata.com/resource/umls/id/C0008987 XAO:0000244 GAID:1206 VHOG:0001186 UMLS:C0008987 AAO:0000095 NCIT:C34127 http://en.wikipedia.org/wiki/Cloaca" "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal." "FMA:14543 BTO:0000269 EMAPA:18939 galen:Colon CALOHA:TS-0158 MESH:D003106 VHOG:0000648 ZFA:0000706 NCIT:C12382 UMLS:C0009368 MA:0000335 http://www.snomedbrowser.com/Codes/Details/302508007 TAO:0000706 AAO:0010400 XAO:0000243 http://en.wikipedia.org/wiki/Colon_(anatomy) MAP:0000001 http://linkedlifedata.com/resource/umls/id/C0009368 GAID:309 MAT:0000526 EFO:0000361 EV:0100079" - "A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve." "UMLS:C0225844 FMA:7096 EHDAA2:0000290 http://linkedlifedata.com/resource/umls/id/C0225844 VHOG:0000328 NCIT:C12868 EMAPA:17321 http://en.wikipedia.org/wiki/Right_atrium galen:RightAtrium XAO:0003192 MA:0000075 BTO:0001703 AAO:0010248 http://www.snomedbrowser.com/Codes/Details/244383003" + "A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve." "UMLS:C0225844 FMA:7096 EHDAA2:0000290 http://linkedlifedata.com/resource/umls/id/C0225844 VHOG:0000328 NCIT:C12868 EMAPA:17321 galen:RightAtrium http://en.wikipedia.org/wiki/Right_atrium XAO:0003192 MA:0000075 BTO:0001703 AAO:0010248 http://www.snomedbrowser.com/Codes/Details/244383003" "Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements." "http://www.snomedbrowser.com/Codes/Details/272627002 EMAPA:37843" "The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." @@ -1441,7 +1440,7 @@ "A fourteen-membered heterodetic cyclic peptide comprising the sequence Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys cyclised by a disulfide bridge between the two Cys residues at positions 3 and 14." "PMID:22147011 Drug_Central:2997 LINCS:LSM-5326 Wikipedia:Somatostatin KEGG:D07431 Reaxys:10148626 KEGG:C16022 CAS:38916-34-6 PMID:21922516 PMID:22483686 PMID:22129035 PMID:22251942 PMID:22509294 HMDB:HMDB0013072" "A muscle layer that is part of a large intestine." "NCIT:C32927 UMLS:C0734205 FMA:14971 http://linkedlifedata.com/resource/umls/id/C0734205" - "An epithelium that is part of a lower jaw [Automatically generated definition]." "VHOG:0000802 EHDAA:7999 EMAPA:35516 EHDAA2:0001019" + "An epithelium that is part of a lower jaw [Automatically generated definition]." "EHDAA2:0001019 VHOG:0000802 EHDAA:7999 EMAPA:35516" "An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage." @@ -1594,7 +1593,7 @@ "A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay."@en "A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development." "Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly." - "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles)." "EHDAA:5978 EHDAA:5035 EHDAA:5043 TAO:0005277 EV:0100377 VHOG:0000319 EFO:0000888 MESH:D018482 GAID:141 AAO:0011099 MIAA:0000302 EMAPA:35988 CALOHA:TS-0933 XAO:0000174 BTO:0001103 ZFA:0005277 MA:0003148 EHDAA:5984 MAT:0000302" + "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles)." "EHDAA:5978 EHDAA:5035 EHDAA:5043 TAO:0005277 EV:0100377 VHOG:0000319 EFO:0000888 MESH:D018482 GAID:141 MIAA:0000302 AAO:0011099 EMAPA:35988 CALOHA:TS-0933 XAO:0000174 BTO:0001103 ZFA:0005277 MA:0003148 EHDAA:5984 MAT:0000302" "Any process that modulates the frequency, rate or extent of protein localization to cilium." "Any process that modulates the frequency, rate or extent of protein localization to microtubule." "PMID:9727836 PMID:11557979 GC_ID:1" @@ -1891,7 +1890,7 @@ "The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle." "The outermost solid or liquid area of a planet" "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." "CALOHA:TS-0866 BTO:0001036 FMA:67748" - "The part of the retina that contains neurons and photoreceptor cells[GO]." "EMAPA:17171 EHDAA:4763 EHDAA2:0001253 AAO:0011095 MA:0000277 TAO:0000046 VHOG:0000535 FMA:58628 CALOHA:TS-0685 XAO:0003216 NCIT:C33166 http://linkedlifedata.com/resource/umls/id/C1518263 EMAPA:18590 BTO:0000929 ZFA:0000046 UMLS:C1518263" + "The part of the retina that contains neurons and photoreceptor cells[GO]." "UMLS:C1518263 EMAPA:17171 EHDAA:4763 EHDAA2:0001253 AAO:0011095 MA:0000277 TAO:0000046 VHOG:0000535 FMA:58628 CALOHA:TS-0685 XAO:0003216 NCIT:C33166 http://linkedlifedata.com/resource/umls/id/C1518263 EMAPA:18590 BTO:0000929 ZFA:0000046" "A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid." "Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." @@ -2008,6 +2007,7 @@ "Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means" "A developmental process, independent of morphogenetic (shape) change, that is required for the trigeminal nerve to attain its fully functional state. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae." + "A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis." "Energy possessed by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors."@en "WebElements:S KEGG:C00087 KEGG:D06527 CAS:7704-34-9 PPDB:605" "Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins." @@ -2109,7 +2109,7 @@ "A mixed forest which is subject to tropical climatic conditions." "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]." "NCIT:C34236 FMA:293357 http://www.snomedbrowser.com/Codes/Details/362864008 http://linkedlifedata.com/resource/umls/id/C0231106 TAO:0000050 UMLS:C0231106 EMAPA:16540 XAO:0000228 ZFA:0000050 AAO:0011039 http://en.wikipedia.org/wiki/Optic_vesicles VHOG:0000165 EHDAA2:0001320" "Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]." "EMAPA:17071 UMLS:C1516904 EHDAA2:0001149 BIRNLEX:965 http://linkedlifedata.com/resource/umls/id/C0376353 NCIT:C32741 DHBA:10655 HBA:4833 UMLS:C0376353 http://en.wikipedia.org/wiki/Metencephalon MA:0000197 MESH:D020540 neuronames:543 BAMS:Met FMA:62003 BTO:0000673 http://linkedlifedata.com/resource/umls/id/C1516904 VHOG:0000741 EHDAA:5498 CALOHA:TS-2029 GAID:594" - "A vertebra that is located in the cervical region of the vertebral column." "MA:0000311 XAO:0003076 http://en.wikipedia.org/wiki/Cervical_vertebrae MESH:D002574 galen:CervicalVertebra NCIT:C12693 FMA:9915 EMAPA:17674 http://www.snomedbrowser.com/Codes/Details/181820005 GAID:235" + "A vertebra that is located in the cervical region of the vertebral column." "XAO:0003076 MA:0000311 http://en.wikipedia.org/wiki/Cervical_vertebrae MESH:D002574 galen:CervicalVertebra NCIT:C12693 FMA:9915 EMAPA:17674 http://www.snomedbrowser.com/Codes/Details/181820005 GAID:235" "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." "A sclerophyllous forest which is subject to temperate climate patterns." @@ -2140,7 +2140,7 @@ "Organism at the cleavage stage." "BILA:0000058" "The deposition or aggregation of coloring matter in a cell." "Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium." - "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." "AEO:0001017 EHDAA:1719 UMLS:C0180383 http://linkedlifedata.com/resource/umls/id/C0180383 AAO:0011028 EHDAA:1731 EHDAA:1737 EHDAA:1725 NCIT:C61572 XAO:0000220 http://en.wikipedia.org/wiki/Dermatome_(embryology) EMAPA:32838 FMA:295656 EHDAA2_RETIRED:0003428" + "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." "AEO:0001017 EHDAA:1719 UMLS:C0180383 http://linkedlifedata.com/resource/umls/id/C0180383 EHDAA:1731 AAO:0011028 EHDAA:1737 EHDAA:1725 NCIT:C61572 XAO:0000220 http://en.wikipedia.org/wiki/Dermatome_(embryology) EMAPA:32838 FMA:295656 EHDAA2_RETIRED:0003428" "A myeloid leukemia that is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells." "KEGG:05221 MESH:D015470 ICDO:9861/3 ICD9CM:205.0 SNOMEDCT_US_2021_09_01:91861009 UMLS_CUI:C0023467 NCI:C3171 OMIM:601626 GARD:12757 ICD10CM:C92.0" "A facility located below the earth's surface in order to minimize natural background radiation" "A piece of apparatus that is used to measure a physical quantity." @@ -2183,6 +2183,7 @@ "A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere." "Any fibroblast that is part of a cardiac ventricle." "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." + "The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." "An ionic polymer is a polymer, composed of ionic macromolecules." "A hydrological process in which irregular aggregates of snow fall to the surface of an astronomical body." "http://sweetontology.net/phenAtmoPrecipitation/Snowfall" "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." @@ -2224,7 +2225,7 @@ "Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process." "Binding to a vascular endothelial growth factor receptor 2." "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration." - "A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel." "MA:0002499 NCIT:C33342 FMA:17523 http://www.snomedbrowser.com/Codes/Details/362192000 http://linkedlifedata.com/resource/umls/id/C0227514 http://en.wikipedia.org/wiki/Portal_triad UMLS:C0227514" + "A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel." "MA:0002499 NCIT:C33342 http://www.snomedbrowser.com/Codes/Details/362192000 FMA:17523 http://linkedlifedata.com/resource/umls/id/C0227514 http://en.wikipedia.org/wiki/Portal_triad UMLS:C0227514" "The stage of being a sexually mature adult animal." "OGES:000027 XAO:1000093 BILS:0000113 ZFS:0000044 OGES:000026 EV:0300064 MmusDv:0000110 EV:0300070 MIAA:0000403" "A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation." "EMAPA:18045" "A cell that specializes in controlled release of one or more substances." "FMA:86916 BTO:0003659" @@ -2347,7 +2348,7 @@ "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." "Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle." "Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement." - "Enables the transfer of a protein from one side of a membrane to the other." "Reactome:R-HSA-184269 Reactome:R-HSA-9698930 Reactome:R-HSA-1299475 Reactome:R-HSA-5244404 Reactome:R-HSA-9636375 Reactome:R-HSA-5336420 Reactome:R-HSA-5244428 Reactome:R-HSA-5250616 Reactome:R-HSA-5246514 Reactome:R-HSA-5205661 Reactome:R-HSA-5250884 Reactome:R-HSA-5210943 Reactome:R-HSA-5250972 Reactome:R-HSA-5210947 Reactome:R-HSA-5229111 Reactome:R-HSA-3149434 Reactome:R-HSA-5228406 Reactome:R-HSA-5244506 Reactome:R-HSA-9698933 Reactome:R-HSA-1268022" + "Enables the transfer of a protein from one side of a membrane to the other." "Reactome:R-HSA-184269 Reactome:R-HSA-9698930 Reactome:R-HSA-1299475 Reactome:R-HSA-5244404 Reactome:R-HSA-9636375 Reactome:R-HSA-5244428 Reactome:R-HSA-5336420 Reactome:R-HSA-5250616 Reactome:R-HSA-5246514 Reactome:R-HSA-5205661 Reactome:R-HSA-5250884 Reactome:R-HSA-5210943 Reactome:R-HSA-5250972 Reactome:R-HSA-5210947 Reactome:R-HSA-5229111 Reactome:R-HSA-3149434 Reactome:R-HSA-5228406 Reactome:R-HSA-5244506 Reactome:R-HSA-9698933 Reactome:R-HSA-1268022" @@ -2464,7 +2465,7 @@ "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates." "Any process that modulates the frequency, rate or extent of protein localization to chromatin." - "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme." "NCIT:C13301 CALOHA:TS-0620 UMLS:C0162415 VHOG:0000170 EHDAA2:0003145 EV:0100007 ZFA:0000393 AAO:0010427 http://en.wikipedia.org/wiki/Mesenchyme AEO:0000145 BTO:0001393 XAO:0003046 http://linkedlifedata.com/resource/umls/id/C0162415 TAO:0000393" + "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme." "NCIT:C13301 CALOHA:TS-0620 UMLS:C0162415 VHOG:0000170 EHDAA2:0003145 EV:0100007 ZFA:0000393 AAO:0010427 http://en.wikipedia.org/wiki/Mesenchyme AEO:0000145 BTO:0001393 XAO:0003046 TAO:0000393 http://linkedlifedata.com/resource/umls/id/C0162415" "The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts." @@ -2651,7 +2652,7 @@ "A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra." "XAO:0003077 EMAPA:37722 MA:0002869" "The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]." "UMLS:C0225604 http://linkedlifedata.com/resource/umls/id/C0225604 FMA:62649 EMAPA:35192 NCIT:C49209 http://www.snomedbrowser.com/Codes/Details/278980009 MA:0001835" "Study of the efficacy, outcomes and adverse consequences of exposure to therapeutic use of ionizing and nonionizing radiation including RADIONUCLIDE THERAPY, therapeutic radiation with visible, laser, or ultraviolet light. Includes technical development of protocols and equipment." - "The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein." "UMLS:C0227518 http://linkedlifedata.com/resource/umls/id/C0227518 NCIT:C32732 http://www.snomedbrowser.com/Codes/Details/362194004 MA:0002494 EMAPA:35499 FMA:14471 http://en.wikipedia.org/wiki/Lobules_of_liver" + "The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein." "UMLS:C0227518 http://linkedlifedata.com/resource/umls/id/C0227518 NCIT:C32732 MA:0002494 http://www.snomedbrowser.com/Codes/Details/362194004 EMAPA:35499 FMA:14471 http://en.wikipedia.org/wiki/Lobules_of_liver" "A completely man-made radioactive actinide with atomic symbol Am, and atomic number 95. Its valence can range from +3 to +6. Because of its nonmagnetic ground state, it is an excellent superconductor. It is also used in bone mineral analysis and as a radiation source for radiotherapy" "An aircraft which flies at altitudes greater than commercial aircraft altitudes for research purposes." "Any process in which a macromolecule is transported to, or maintained in, a specific location." @@ -2866,7 +2867,6 @@ "Any apoptotic process in a fat cell." "Multi-tissue structure that arises from the heart rudiment and will become the heart tube." "EHDAA2:0001512 FMA:321916 ZFA:0000149 EHDAA:424 http://www.snomedbrowser.com/Codes/Details/361522004 EMAPA:16215 TAO:0000149 EHDAA:436 http://en.wikipedia.org/wiki/Primitive_heart_tube" "A major stable isotope of strontium with relative atomic mass 87.90561 and 82.58 atom percent natural abundance." "PMID:27829691 PMID:6337617 PMID:11893161 PMID:32350478 PMID:33328666 CAS:14119-10-9 PMID:33834832" - "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure." "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." "SNOMEDCT:67271001 NCIt:C16612" "A microtubule-based process that results in the transport of proteins." "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." @@ -2931,7 +2931,7 @@ "The disaggregation of a protein-containing macromolecular complex into its constituent components." "Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact." "Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens)." - "A tube extending from the mouth to the anus." "BILA:0000083 VHOG:0000309 BTO:0000545 EMAPA:16247 ZFA:0000112 NCIT:C34082 FBbt:00003125 http://linkedlifedata.com/resource/umls/id/C0017189 UMLS:C0017189 AAO:0010023 BTO:0000511 TAO:0000112 EHDAA:518 galen:AlimentaryTract WBbt:0005743 EHDAA2:0000726 TGMA:0001819 MA:0000917 FMA:45615" + "A tube extending from the mouth to the anus." "FMA:45615 BILA:0000083 VHOG:0000309 BTO:0000545 EMAPA:16247 ZFA:0000112 NCIT:C34082 FBbt:00003125 http://linkedlifedata.com/resource/umls/id/C0017189 UMLS:C0017189 AAO:0010023 BTO:0000511 TAO:0000112 EHDAA:518 galen:AlimentaryTract WBbt:0005743 EHDAA2:0000726 TGMA:0001819 MA:0000917" "Any process that modulates the frequency, rate or extent of translational termination." "A biological tissue mass, most commonly a mass of nerve cell bodies." "MIAA:0000343 ZFA:0000190 FMA:5884 EHDAA:5621 AEO:0000135 EFO:0000899 EHDAA:918 EHDAA:2897 TGMA:0001016 MESH:D005724 http://linkedlifedata.com/resource/umls/id/C0017067 MAT:0000207 WBbt:0005189 http://en.wikipedia.org/wiki/Ganglion VHOG:0000156 EHDAA2:0003135 NCIT:C12719 EMAPA:32846 BTO:0000497 MIAA:0000207 UMLS:C0017067 NLXANAT:100302 XAO:0000209 BAMS:G EHDAA:4662 CALOHA:TS-0397 TAO:0000190 MA:0002406 AAO:0010426 MAT:0000343 EV:0100372" "A smooth muscle cell that is located in the anorectum." @@ -3225,7 +3225,7 @@ "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems." "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems."@en "A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations."@en - "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." "VHOG:0000107 AAO:0011017 EFO:0003647 TAO:0001204 XAO:0000205 ZFA:0001204 http://en.wikipedia.org/wiki/Chordamesoderm" + "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." "AAO:0011017 EFO:0003647 TAO:0001204 XAO:0000205 ZFA:0001204 http://en.wikipedia.org/wiki/Chordamesoderm VHOG:0000107" "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." "BILA:0000066 FMA:9639 EMAPA:32738 BTO:0000416 UMLS:C0014609 HAO:0000066 XAO:0003045 CALOHA:TS-0288 TAO:0001486 FBbt:00007005 VHOG:0000387 MESH:D004848 CARO:0000066 http://en.wikipedia.org/wiki/Epithelium NCIT:C12710 GAID:402 http://www.snomedbrowser.com/Codes/Details/31610004 AEO:0000066 AAO:0000144 EHDAA2:0003066 ZFA:0001486 AAO:0010055 MA:0003060 http://linkedlifedata.com/resource/umls/id/C0014609" "The cytoplasm of an ovum." "Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis." @@ -3418,7 +3418,7 @@ "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." "FMA:86667" "Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process." "Epithelium lining the exocrine pancreas." "CALOHA:TS-2108" - "An artery that supplies an ovary." "http://www.snomedbrowser.com/Codes/Details/244280002 UMLS:C0226411 http://linkedlifedata.com/resource/umls/id/C0226411 EMAPA:18620 NCIT:C33242 FMA:14761 MA:0002012 http://en.wikipedia.org/wiki/Ovarian_artery" + "An artery that supplies an ovary." "UMLS:C0226411 http://www.snomedbrowser.com/Codes/Details/244280002 http://linkedlifedata.com/resource/umls/id/C0226411 EMAPA:18620 NCIT:C33242 FMA:14761 MA:0002012 http://en.wikipedia.org/wiki/Ovarian_artery" "A passive radon dosimeter in which a small plastic film or polycarbonate chip is exposed to radon gas. When radon decays, it emits alpha particles that leave microscopic tracks on the film. After exposure, the film is chemically etched to reveal the tracks, which are counted under a microscope to determine radon levels." "Any process that decreases the frequency, rate, or extent of lipid transporter activity." "Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." @@ -3979,7 +3979,6 @@ "Any small, fluid-filled, spherical organelle enclosed by membrane." "Wikipedia:Vesicle_(biology) NIF_Subcellular:sao221389602" "Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton." "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs." "EMAPA:35931 GAID:87 CALOHA:TS-2227 http://linkedlifedata.com/resource/umls/id/C0030797 galen:Pelvis UMLS:C0030797 EFO:0002805 NCIT:C12767 EV:0100012 FMA:9578 http://en.wikipedia.org/wiki/Pelvis http://www.snomedbrowser.com/Codes/Details/229765004 MESH:D010388 BTO:0001006 MA:0000030" - "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids." "The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster." @@ -4169,6 +4168,7 @@ "A part of a multicellular organism that is a collection of cell components that are not all contained in one cell."@en "A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel." "A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis." "http://www.snomedbrowser.com/Codes/Details/86915006 UMLS:C0225358 http://en.wikipedia.org/wiki/Muscular_layer BTO:0004838 http://linkedlifedata.com/resource/umls/id/C0225358" + "Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure." "The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues." "MetaCyc:GLYCOGENSYNTH-PWY" "GC_ID:1" "The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure." "Wikipedia:Histogenesis" @@ -4284,8 +4284,7 @@ "SWEETRealm:Canopy LTER:82 EcoLexicon:canopy" "Luminal space of the left ventricle of the heart." "EMAPA:26038 FMA:9466" - "One of the skeletal muscles of the head and neck, spine, and ribs." "MA:0003153 RETIRED_EHDAA2:0000160 TAO:0001954 EMAPA:18167 EHDAA:5982" - "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " + "One of the skeletal muscles of the head and neck, spine, and ribs." "MA:0003153 RETIRED_EHDAA2:0000160 EMAPA:18167 TAO:0001954 EHDAA:5982" "In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals')." "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus." "One of the two nuclear divisions that occur as part of the meiotic cell cycle." @@ -4309,7 +4308,7 @@ "GC_ID:1" "A smooth muscle cell of the subclavian artery." "Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation." - "An epithelium that is part of a rectum [Automatically generated definition]." "FMA:17510 VHOG:0001037 MA:0003219 EHDAA2:0001594 EMAPA:17898 CALOHA:TS-2066" + "An epithelium that is part of a rectum [Automatically generated definition]." "FMA:17510 VHOG:0001037 MA:0003219 EHDAA2:0001594 CALOHA:TS-2066 EMAPA:17898" "The process in which the anatomical structures of cardiac muscle tissue are generated and organized." "A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival." "CAS:14392-02-0" "A process in which an ion is transported across a membrane." @@ -4497,7 +4496,7 @@ "A directive information entity that describes an action the bearer will take."@en "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme." "EHDAA2:0004078" "GC_ID:1" - "A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system." "HBA:9177 VHOG:0001381 UMLS:C0175427 neuronames:569 EV:0100263 MBA:398 http://linkedlifedata.com/resource/umls/id/C0175427 MA:0001026 DHBA:12462 BAMS:SOC EMAPA:35840 MESH:D065832 FMA:72247 BIRNLEX:1307 http://en.wikipedia.org/wiki/Superior_olivary_complex" + "A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system." "HBA:9177 VHOG:0001381 UMLS:C0175427 neuronames:569 EV:0100263 MBA:398 http://linkedlifedata.com/resource/umls/id/C0175427 MA:0001026 DHBA:12462 EMAPA:35840 BAMS:SOC MESH:D065832 FMA:72247 BIRNLEX:1307 http://en.wikipedia.org/wiki/Superior_olivary_complex" "The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose." "EMAPA:37430 MA:0001917 FMA:49570 http://www.snomedbrowser.com/Codes/Details/145137009 http://en.wikipedia.org/wiki/Superior_labial_artery" "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle growth." @@ -4606,7 +4605,7 @@ "RETIRED_EHDAA2:0002089 EHDAA:924 EMAPA:16663" "A planned process during which an environmental system is modified to mitigate or nullify the impacts of flooding." - "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract." "EMAPA:25038 VHOG:0000139 TAO:0000066 http://en.wikipedia.org/wiki/Proctodeum FBbt:00000123 AAO:0011087 EHDAA2:0000121 XAO:0001019 http://linkedlifedata.com/resource/umls/id/C0231054 ZFA:0000066 UMLS:C0231054 NCIT:C34278" + "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract." "VHOG:0000139 EMAPA:25038 TAO:0000066 http://en.wikipedia.org/wiki/Proctodeum FBbt:00000123 AAO:0011087 EHDAA2:0000121 XAO:0001019 http://linkedlifedata.com/resource/umls/id/C0231054 ZFA:0000066 UMLS:C0231054 NCIT:C34278" "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052)." "FBbt:00000137" "An objective specification to transformation input data into output data"@en "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex." @@ -4686,7 +4685,7 @@ "Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation." - "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." "ZFA:0000279 TAO:0000279 VHOG:0000559 XAO:0000057 EMAPA:16752 AAO:0011086 EMAPA:16189 EFO:0001982" + "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." "ZFA:0000279 TAO:0000279 VHOG:0000559 XAO:0000057 AAO:0011086 EMAPA:16752 EMAPA:16189 EFO:0001982" "The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)." "A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material."@en "An atomic nucleus with 73 protons and 108 neutrons " @@ -4904,7 +4903,7 @@ "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." "BSA:0000039 CALOHA:TS-0229 FMA:69068 GAID:963 BILA:0000056 EHDAA2_RETIRED:0003236 OGEM:000001 AAO:0011035 VHOG:0001766 http://linkedlifedata.com/resource/umls/id/C0013935 ZFA:0000103 MIAA:0000019 MESH:D004622 EMAPA:16039 UMLS:C0013935 http://en.wikipedia.org/wiki/Embryo BTO:0000379 http://www.snomedbrowser.com/Codes/Details/57991002 FBbt:00000052 EHDAA2:0000002 AEO:0000169 NCIT:C28147 MAT:0000226 EHDAA:38 XAO:0000113 http://neurolex.org/wiki/Category:Embryonic_organism EFO:0001367" "A mesentery that is part of a colon [Automatically generated definition]." "http://www.snomedbrowser.com/Codes/Details/245457004 FMA:14645 EMAPA:18942" "The increased risk from induced cancer due to exposure when the effects over an entire lifetime are accounted for. Individuals who would have died of cancer anyway but die early because of exposure are not included" - "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]." "http://en.wikipedia.org/wiki/Large_intestine_(anatomy) EFO:0000840 EV:0100077 BTO:0000706 NCIT:C12379 EMAPA:19252 galen:LargeIntestine VHOG:0000054 AAO:0010396 http://linkedlifedata.com/resource/umls/id/C0021851 GAID:306 FMA:7201 MA:0000333 http://www.snomedbrowser.com/Codes/Details/181254001 XAO:0000131 CALOHA:TS-1306 UMLS:C0021851 MESH:D007420 MIAA:0000046" + "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]." "http://en.wikipedia.org/wiki/Large_intestine_(anatomy) EV:0100077 EFO:0000840 BTO:0000706 NCIT:C12379 EMAPA:19252 galen:LargeIntestine VHOG:0000054 AAO:0010396 http://linkedlifedata.com/resource/umls/id/C0021851 GAID:306 FMA:7201 MA:0000333 http://www.snomedbrowser.com/Codes/Details/181254001 XAO:0000131 CALOHA:TS-1306 UMLS:C0021851 MESH:D007420 MIAA:0000046" "The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins." "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei." "Wikipedia:Karyogamy" "The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." @@ -4936,6 +4935,7 @@ "An endothelium that is part of a sclera." "A stage at which the organism is a single cell produced by means of sexual reproduction." "VHOG:0000745 ZFS:0000001 XAO:1000001 FBdv:00005288 EHDAA:27 PdumDv:0000100 http://en.wikipedia.org/wiki/Zygote NCIT:C12601 BILS:0000106 BilaDO:0000005 EFO:0001322" "PMID:22982760 GC_ID:1" + "The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium.\" Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity." "Any collagen timer that is part of a basement membrane." "A blood vessel of the placenta." "http://www.snomedbrowser.com/Codes/Details/280716005" "A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans." "MA:0000721 EMAPA:37710 FMA:16012" @@ -5157,7 +5157,7 @@ "The process in which the anatomical structures of the ascending aorta are generated and organized. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once." "Any vesicle-mediated transport that occurs in a synapse." "The process in which the anatomical structures of ganglion are generated and organized." - "A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis." "http://en.wikipedia.org/wiki/Broad_ligament_of_the_uterus MESH:D001956 FMA:16516 http://www.snomedbrowser.com/Codes/Details/362723009 NCIT:C12318 UMLS:C0006205 http://linkedlifedata.com/resource/umls/id/C0006205" + "A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis." "MESH:D001956 http://en.wikipedia.org/wiki/Broad_ligament_of_the_uterus FMA:16516 http://www.snomedbrowser.com/Codes/Details/362723009 NCIT:C12318 UMLS:C0006205 http://linkedlifedata.com/resource/umls/id/C0006205" "A part of an astronomical body which is primarily composed of solid material."@en "EcoLexicon:landforms FTT:96 TGN:21401 SWEETRealm:Landform EcoLexicon:landform TGN:21400 FTT:754" @@ -5205,7 +5205,7 @@ "The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs." "A radiation environment outside a commonly defined boundary marking the beginning of space (frequently the Karman line)." "A portion of acidic water is a portion of water with a pH less than 7." - "A tubular structure that transports secreted or excreted substances." "NCIT:C12948 http://en.wikipedia.org/wiki/Duct_(anatomy) ZFA:0005171 FBbt:00100314 XAO:0004000 AAO:0011123 galen:Duct http://linkedlifedata.com/resource/umls/id/C0687028 http://www.snomedbrowser.com/Codes/Details/91726008 TAO:0005171 UMLS:C0687028 FMA:30320" + "A tubular structure that transports secreted or excreted substances." "http://en.wikipedia.org/wiki/Duct_(anatomy) ZFA:0005171 FBbt:00100314 XAO:0004000 AAO:0011123 galen:Duct http://linkedlifedata.com/resource/umls/id/C0687028 http://www.snomedbrowser.com/Codes/Details/91726008 TAO:0005171 UMLS:C0687028 NCIT:C12948 FMA:30320" "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide." "A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules." @@ -5232,7 +5232,7 @@ "The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components." "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum." "FMA:77169 EHDAA2:0002013 http://en.wikipedia.org/wiki/Thoracic_skeleton" - "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." "TAO:0000094 http://en.wikipedia.org/wiki/Blood_island_of_umbilical_vesicle TE:E5.11.2.0.0.0.4 VHOG:0000085 EFO:0003489 AAO:0011006 XAO:0000067 EHDAA:207 NCIT:C34113 ZFA:0000094 http://linkedlifedata.com/resource/umls/id/C1511224 UMLS:C1511224" + "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." "TAO:0000094 http://en.wikipedia.org/wiki/Blood_island_of_umbilical_vesicle TE:E5.11.2.0.0.0.4 VHOG:0000085 AAO:0011006 EFO:0003489 XAO:0000067 EHDAA:207 NCIT:C34113 ZFA:0000094 http://linkedlifedata.com/resource/umls/id/C1511224 UMLS:C1511224" "GC_ID:1" "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." "CAS:7440-31-5 UM-BBD_compID:c0585 WebElements:Sn" @@ -5408,6 +5408,7 @@ "A radiographic study used to evaluate a specific anatomic location for a specific purpose. This may include the assessment of imaging modalities and the development of new techniques. Includes PET, MRI, CT and related techniques." "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments." "The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products." "A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products." "An ectoderm that is part of a medial nasal prominence [Automatically generated definition]." "EHDAA2:0001078 FMA:312675 EMAPA:16809 VHOG:0000803" "An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem." @@ -5466,7 +5467,7 @@ "A venule located in the colon." "Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." "The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." - "Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition." "EMAPA:16046 BTO:0001840 VHOG:0000979 EHDAA2:0002091 EHDAA:56" + "Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition." "EMAPA:16046 BTO:0001840 VHOG:0000979 EHDAA:56 EHDAA2:0002091" "PMID:32761142 PMID:30365038 GC_ID:1" "A cyclic compound having as ring members atoms of carbon and at least of one other element." "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]." "FMA:45662 VHOG:0000382 MA:0000435 http://en.wikipedia.org/wiki/Lower_respiratory_tract EMAPA:16738 EHDAA2:0001036 http://www.snomedbrowser.com/Codes/Details/281488008" @@ -5725,7 +5726,6 @@ "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development." "The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity." "MESH:D012809 http://linkedlifedata.com/resource/umls/id/C0227391 NCIT:C33550 EFO:0000846 NCIT:C12384 MIAA:0000314 http://linkedlifedata.com/resource/umls/id/C0682612 MAT:0000314 CALOHA:TS-2044 EMAPA:36391 http://www.snomedbrowser.com/Codes/Details/362166007 galen:SigmoidColon BTO:0000645 UMLS:C0682612 http://en.wikipedia.org/wiki/Sigmoid_colon UMLS:C0227391 FMA:14548" "An arteriole that is located in the anorectum." - "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field." "Subdivision of skeleton which includes upper and lower jaw skeletons." "galen:Jaw UMLS:C0022359 BTO:0001749 NCIT:C48821 AAO:0000988 http://linkedlifedata.com/resource/umls/id/C0022359 GAID:214 MESH:D007568 FMA:54396 EMAPA:35455 http://en.wikipedia.org/wiki/Jaw MA:0001905 TAO:0001227 http://www.snomedbrowser.com/Codes/Details/181811001 ZFA:0001227" "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region." "EMAPA:37062 MA:0000529" @@ -5761,7 +5761,7 @@ "A brain disease that is characterized by damage to brain substance located_in cerebellum; has_symptom ataxia, has_symptom dysarthria, and has_symptom cerebellar cognitive affective syndrome." "MESH:D002526 SNOMEDCT_US_2021_09_01:267691001 UMLS_CUI:C0007760" "Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." "The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." - "The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]." "http://en.wikipedia.org/wiki/Chondrocranium UMLS:C1516496 FMA:76621 NCIT:C34121 AAO:0010153 XAO:0003059 http://linkedlifedata.com/resource/umls/id/C1516496 AAO:0000094 http://www.snomedbrowser.com/Codes/Details/155540009 EHDAA:6031" + "The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]." "http://en.wikipedia.org/wiki/Chondrocranium FMA:76621 UMLS:C1516496 NCIT:C34121 AAO:0010153 XAO:0003059 http://linkedlifedata.com/resource/umls/id/C1516496 AAO:0000094 http://www.snomedbrowser.com/Codes/Details/155540009 EHDAA:6031" "GC_ID:1" "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en @@ -6105,7 +6105,7 @@ "A surface layer which is part of an ocean or sea."@en "Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix." "A mucosa that is part of a left uterine tube [Automatically generated definition]." "FMA:18453" - "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." "ZFA:0001206 UMLS:C1284010 XAO:0000085 AAO:0010575 http://linkedlifedata.com/resource/umls/id/C1284010 http://en.wikipedia.org/wiki/Intermediate_mesoderm TAO:0001206 EMAPA:16178 http://www.snomedbrowser.com/Codes/Details/361476001 VHOG:0000087 FMA:293147 NCIT:C34193 EMAPA:16056" + "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." "ZFA:0001206 UMLS:C1284010 XAO:0000085 AAO:0010575 http://linkedlifedata.com/resource/umls/id/C1284010 http://en.wikipedia.org/wiki/Intermediate_mesoderm EMAPA:16178 TAO:0001206 http://www.snomedbrowser.com/Codes/Details/361476001 VHOG:0000087 FMA:293147 NCIT:C34193 EMAPA:16056" "Permafrost which contains inclusions of water-based ice." "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]." "ZFA:0005004 EFO:0003695 TAO:0005004 http://en.wikipedia.org/wiki/Aortic_arches EMAPA:16684 NCIT:C32123 EHDAA:7327 AAO:0010414 UMLS:C0003489 XAO:0000341 http://linkedlifedata.com/resource/umls/id/C0003489 VHOG:0000122 EHDAA2:0000186 EHDAA:398" "Any anatomical space that is part of a vertebral column." "AAO:0000700" @@ -6118,7 +6118,7 @@ "An epithelium that is part of a anterior chamber of eyeball." "EHDAA2:0000130" "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery."@en "A region of the stomach that is lined with glandular epithelium." "EMAPA:17623 UMLS:C0227197 NCIT:C77661 MA:0001613 http://www.snomedbrowser.com/Codes/Details/27633001 http://linkedlifedata.com/resource/umls/id/C0227197" - "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." "EFO:0000966 ZFA:0001115 MA:0000004 http://www.snomedbrowser.com/Codes/Details/262225004 galen:Trunk BTO:0001493 http://linkedlifedata.com/resource/umls/id/C0460005 BILA:0000116 NCIT:C33816 CALOHA:TS-1071 XAO:0000054 AAO:0010339 MIAA:0000296 XAO:0003025 FMA:7181 EMAPA:31857 TAO:0001115 UMLS:C0460005 MAT:0000296 http://en.wikipedia.org/wiki/Torso" + "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." "EFO:0000966 ZFA:0001115 MA:0000004 http://www.snomedbrowser.com/Codes/Details/262225004 galen:Trunk BTO:0001493 http://linkedlifedata.com/resource/umls/id/C0460005 BILA:0000116 NCIT:C33816 CALOHA:TS-1071 XAO:0000054 AAO:0010339 MIAA:0000296 XAO:0003025 EMAPA:31857 FMA:7181 TAO:0001115 UMLS:C0460005 MAT:0000296 http://en.wikipedia.org/wiki/Torso" "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA." "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." @@ -6268,7 +6268,7 @@ "A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]." "http://www.snomedbrowser.com/Codes/Details/189936008 EMAPA:17320 EHDAA2:0004154 FMA:7285 VHOG:0001225" "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." "BTO:0001338 CALOHA:TS-0998 FMA:66762" "A muscular coat that is part of a colon." "FMA:14986 EMAPA:27383 http://www.snomedbrowser.com/Codes/Details/362158003 MA:0003198" - "A head mesenchyme that develops_from a mesoderm." "AAO:0011051 VHOG:0000185 EHDAA2:0001118 EFO:0003337 EMAPA_RETIRED:16270 TAO:0000998 FMA:293859 XAO:0000053 EFO:0003603 ZFA:0000998 EHDAA:655 EMAPA:16099" + "A head mesenchyme that develops_from a mesoderm." "AAO:0011051 VHOG:0000185 EHDAA2:0001118 EFO:0003337 EMAPA_RETIRED:16270 TAO:0000998 FMA:293859 XAO:0000053 ZFA:0000998 EFO:0003603 EMAPA:16099 EHDAA:655" "Activity carried out by crewed or robotic vehicles outside the Earth's atmosphere but inside the Earth's inner radiation belt." "An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3." "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." @@ -6600,7 +6600,7 @@ "A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." "MESH:D004194 NCI:C2991 UMLS_CUI:C0012634 SNOMEDCT_US_2021_09_01:64572001" "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups." "Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus." - "The fluid-filled cavity that lies between the visceral and parietal pleurae." "VHOG:0000581 http://linkedlifedata.com/resource/umls/id/C0178802 EMAPA:16773 MA:0000055 EMAPA:16774 EHDAA2:0001475 http://www.snomedbrowser.com/Codes/Details/361999006 BTO:0004422 GAID:95 MESH:D035422 UMLS:C0178802 FMA:9740 http://en.wikipedia.org/wiki/Pleural_cavity NCIT:C12840" + "The fluid-filled cavity that lies between the visceral and parietal pleurae." "VHOG:0000581 http://linkedlifedata.com/resource/umls/id/C0178802 EMAPA:16773 MA:0000055 EMAPA:16774 http://www.snomedbrowser.com/Codes/Details/361999006 BTO:0004422 EHDAA2:0001475 GAID:95 MESH:D035422 UMLS:C0178802 FMA:9740 http://en.wikipedia.org/wiki/Pleural_cavity NCIT:C12840" "A stromal cell that is part_of a bone marrow." "The chemical reactions and pathways resulting in the formation of organic cyclic compound." "Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin." "EMAPA:37864 FMA:71297" @@ -6788,7 +6788,7 @@ "Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell." "CAS:7440-72-4 WebElements:Fm" - "The caudalmost subdivision of a digestive tract." "FMA:45618 XAO:0000104 MA:0001527 http://linkedlifedata.com/resource/umls/id/C0231053 VHOG:0000459 BILA:0000087 http://en.wikipedia.org/wiki/Hindgut TGMA:0001020 EHDAA:975 http://www.snomedbrowser.com/Codes/Details/362856002 BTO:0000510 UMLS:C0231053 AAO:0011052 FBbt:00005384 NCIT:C34188 EMAPA:16715 EHDAA2:0000779" + "The caudalmost subdivision of a digestive tract." "XAO:0000104 MA:0001527 http://linkedlifedata.com/resource/umls/id/C0231053 VHOG:0000459 BILA:0000087 http://en.wikipedia.org/wiki/Hindgut TGMA:0001020 EHDAA:975 http://www.snomedbrowser.com/Codes/Details/362856002 BTO:0000510 UMLS:C0231053 AAO:0011052 FBbt:00005384 NCIT:C34188 EMAPA:16715 EHDAA2:0000779 FMA:45618" "An active radon dosimeter that uses various sensors (e.g., scintillation detectors, ion chambers, or solid-state silicon detectors) to measure radon decay in real-time. They typically record radon levels at hourly intervals." "Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells." "A bone element that is part of a jaw region." "http://www.snomedbrowser.com/Codes/Details/369003004 EMAPA:35453 MA:0003130" @@ -6878,7 +6878,7 @@ "The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]." "UMLS:C0228590 EMAPA:18575 BAMS:VH http://linkedlifedata.com/resource/umls/id/C0228590 FMA:256541 BTO:0005151 MA:0001134 UMLS:C0228569 EMAPA:35794 NCIT:C33859 TAO:0000702 BIRNLEX:2668 http://linkedlifedata.com/resource/umls/id/C0228569 http://en.wikipedia.org/wiki/Anterior_horn_of_spinal_cord neuronames:1751 VHOG:0001288 http://www.snomedbrowser.com/Codes/Details/279443000 ZFA:0000702" "GC_ID:1" "Any process that modulates the frequency, rate or extent of myoblast proliferation." - "The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta." "http://www.snomedbrowser.com/Codes/Details/244668003 EHDAA2:0000597 http://en.wikipedia.org/wiki/Crus_of_diaphragm EMAPA:17703 VHOG:0001546" + "The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta." "EHDAA2:0000597 http://www.snomedbrowser.com/Codes/Details/244668003 http://en.wikipedia.org/wiki/Crus_of_diaphragm EMAPA:17703 VHOG:0001546" "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus." "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter." "A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction." @@ -7031,7 +7031,7 @@ "Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm)." "A mucosa that is part of a lower lip [Automatically generated definition]." "NCIT:C12225 http://www.snomedbrowser.com/Codes/Details/362089001 http://linkedlifedata.com/resource/umls/id/C0226939 UMLS:C0226939 FMA:59833" "Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction." - "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." "TAO:0000113 FMA:76622 EHDAA2:0000732 EMAPA_RETIRED:16269 ZFA:0000113 EHDAA:179 EMAPA:16098 EFO:0003492 VHOG:0000332" + "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." "FMA:76622 EHDAA2:0000732 EMAPA_RETIRED:16269 ZFA:0000113 EHDAA:179 EMAPA:16098 EFO:0003492 VHOG:0000332 TAO:0000113" "An integrin alpha-M that is encoded in the genome of human." "UniProtKB:P11215" "A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]." "FMA:72025 MA:0001573 EMAPA:35323" "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle fiber development." @@ -7187,7 +7187,7 @@ "The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars." "Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation." "Study on the modality, efficacy and responses to communication of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context." - "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." "FMA:34836 http://www.snomedbrowser.com/Codes/Details/182238002 EMAPA:37621 galen:JointCapsule MESH:D017746 http://linkedlifedata.com/resource/umls/id/C0206207 UMLS:C0206207 http://en.wikipedia.org/wiki/Articular_capsule NCIT:C84388 NCIT:C32259 MA:0001519 GAID:263" + "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." "FMA:34836 http://www.snomedbrowser.com/Codes/Details/182238002 EMAPA:37621 galen:JointCapsule MESH:D017746 http://linkedlifedata.com/resource/umls/id/C0206207 UMLS:C0206207 NCIT:C84388 http://en.wikipedia.org/wiki/Articular_capsule NCIT:C32259 MA:0001519 GAID:263" "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes." "Wikipedia:Gene_expression" "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length." "Study concerning the development, use, calibration or standardisation of technologies for the qualitative or quantitative measurement of radiation and radionuclides." @@ -7195,6 +7195,7 @@ "GC_ID:1" "The specification and formation of anisotropic intracellular organization of an epithelial cell." "Any process that modulates the frequency, rate or extent of cilium assembly." + "A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society." "GC_ID:1" "http://linkedlifedata.com/resource/umls/id/C0017133 http://en.wikipedia.org/wiki/Gastric_juice galen:GastricJuice UMLS:C0017133 MESH:D005750 MA:0002519 NCIT:C32661 FMA:62972 BTO:0000501 GAID:1160" "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." "EHDAA2:0003114 AEO:0000114 FBbt:00007474" @@ -7204,6 +7205,7 @@ "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)." "FMA:64781 XAO:0004030 http://www.snomedbrowser.com/Codes/Details/22560007 http://linkedlifedata.com/resource/umls/id/C0225333 http://en.wikipedia.org/wiki/Dense_regular_connective_tissue VSAO:0000050 UMLS:C0225333 NCIT:C33453" "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale."@en "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale." + "A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. " "Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth." "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." "Wikipedia:Organogenesis" "http://www.snomedbrowser.com/Codes/Details/362606005 FMA:12237 BIRNLEX:1019" @@ -7511,7 +7513,7 @@ "The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." - "Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree)." "http://www.snomedbrowser.com/Codes/Details/361354009 http://en.wikipedia.org/wiki/Biliary_system GAID:279 NCIT:C12678 FMA:79646 MESH:D001659 MA:0001273" + "Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree)." "http://www.snomedbrowser.com/Codes/Details/361354009 http://en.wikipedia.org/wiki/Biliary_system NCIT:C12678 GAID:279 FMA:79646 MESH:D001659 MA:0001273" "A developmental process, independent of morphogenetic (shape) change, that is required for the hindbrain to attain its fully functional state. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions." "A mesentery that is part of a uterus [Automatically generated definition]." "FMA:19816 EMAPA:35562 MA:0002931 http://www.snomedbrowser.com/Codes/Details/250172001 http://en.wikipedia.org/wiki/Mesometrium" "A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]." "BTO:0002501 FMA:85273 http://en.wikipedia.org/wiki/Trabecula" @@ -7520,6 +7522,7 @@ "Elucidation of the physical structure of a macromolecule, protein, carbohydrate, DNA or RNA, its analysis and manipulation based on structure/function considerations." "The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries." "http://www.snomedbrowser.com/Codes/Details/360401001 EHDAA:4340 EMAPA:17616 MA:0001985 EHDAA2:0000882 ZFA:0001061 XAO:0004165 TAO:0001061 VHOG:0000225" "GC_ID:1" + "A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle." "Any process that activates or increases the frequency, rate or extent of cell differentiation." "The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body." @@ -7530,7 +7533,7 @@ "A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point." "http://sweetontology.net/procStateChange/Freezing" "Chemical element (nickel group element atom) with atomic number 46." "Reaxys:4937491 Wikipedia:Palladium PMID:25097477 WebElements:Pd CAS:7440-05-3" "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." - "The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct." "EMAPA:16841 http://linkedlifedata.com/resource/umls/id/C0010672 http://en.wikipedia.org/wiki/Cystic_duct http://www.snomedbrowser.com/Codes/Details/245398005 UMLS:C0010672 MA:0000355 EHDAA2:0000333 TAO:0005166 NCIT:C32421 EHDAA:3045 MESH:D003549 GAID:290 VHOG:0000213 galen:CysticDuct ZFA:0005166 FMA:14539" + "The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct." "http://linkedlifedata.com/resource/umls/id/C0010672 http://en.wikipedia.org/wiki/Cystic_duct http://www.snomedbrowser.com/Codes/Details/245398005 MA:0000355 EHDAA2:0000333 UMLS:C0010672 TAO:0005166 NCIT:C32421 EHDAA:3045 MESH:D003549 GAID:290 VHOG:0000213 galen:CysticDuct ZFA:0005166 FMA:14539 EMAPA:16841" "The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery." "GAID:471 EHDAA2:0000132 http://en.wikipedia.org/wiki/Arch_of_aorta MA:0000475 http://www.snomedbrowser.com/Codes/Details/181300001 EFO:0002526 FMA:3768 EMAPA:17613 BTO:0000157 VHOG:0001196" "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA." @@ -7615,7 +7618,7 @@ "The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart." "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." "UMLS:C1516779 EHDAA2:0003235 http://en.wikipedia.org/wiki/Conceptus NCIT:C34131 AEO:0000194 http://linkedlifedata.com/resource/umls/id/C1516779 BTO:0003834 EMAPA:36040 EHDAA2:0000001" "Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation." - "Transudate contained in the pleural cavity." "BTO:0003080 MA:0002532 FMA:12273 MAT:0000500 http://en.wikipedia.org/wiki/Pleural_fluid ncithesaurus:Pleural_Fluid" + "Transudate contained in the pleural cavity." "BTO:0003080 MA:0002532 FMA:12273 http://en.wikipedia.org/wiki/Pleural_fluid MAT:0000500 ncithesaurus:Pleural_Fluid" "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." "galen:BodyFluid http://en.wikipedia.org/wiki/Body_fluid FMA:280556 EMAPA:37441 MESH:D001826 GAID:266 BIRNLEX:20" "The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." "An x-ray source operating at a voltage of 320 kV." @@ -7656,6 +7659,7 @@ "Any process that activates or increases the frequency, rate or extent of cell division." "A smooth muscle tissue that is part of a hypodermis." "FMA:77862" "Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a" + "The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle." "Binding to an anion, a charged atom or group of atoms with a net negative charge." "A bone that is part of the dorsal region of an animal." "EMAPA:37248 MA:0000494" "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]." "EHDAA2:0001730 http://en.wikipedia.org/wiki/Right_lung EMAPA:17661 NCIT:C33483 http://www.snomedbrowser.com/Codes/Details/361967000 http://linkedlifedata.com/resource/umls/id/C0225706 UMLS:C0225706 FMA:7309 EHDAA:4969 VHOG:0000301 MA:0000426" @@ -7843,7 +7847,7 @@ "Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor." "GC_ID:1" "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton." - "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." "EHDAA:350 EHDAA2:0001968 EHDAA:7860 EHDAA:4790 FMA:87656 EHDAA:1494 NCIT:C34309 EHDAA:4796 http://en.wikipedia.org/wiki/External_ectoderm EHDAA:4784 UMLS:C1515087 http://linkedlifedata.com/resource/umls/id/C1515087 EMAPA:16096" + "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." "EHDAA:350 EHDAA2:0001968 EHDAA:7860 EHDAA:4790 FMA:87656 EHDAA:1494 NCIT:C34309 EHDAA:4796 http://en.wikipedia.org/wiki/External_ectoderm EHDAA:4784 http://linkedlifedata.com/resource/umls/id/C1515087 UMLS:C1515087 EMAPA:16096" "An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions." "VSAO:0000305 galen:ShoulderGirdle http://www.snomedbrowser.com/Codes/Details/229759004 FMA:23217 EMAPA:37856" "A rigid covering that envelops an object." "A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye." "NCI:C3224 EFO:0000756 MESH:D008545 ICDO:8720/3 UMLS_CUI:C0025202 KEGG:05218 SNOMEDCT_US_2021_09_01:2092003" @@ -8192,7 +8196,7 @@ "Any portion of gas located in a part of the respiratory system." "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." "ENVO:02000022 EHDAA2_RETIRED:0003184 BTO:0000491 galen:Excretion FMA:9674 AEO:0000184" "The temperature of some soil." - "An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]." "EHDAA2:0000743 http://linkedlifedata.com/resource/umls/id/C1708552 MA:0002662 UMLS:C1708552 EHDAA:3053 NCIT:C43617" + "An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]." "NCIT:C43617 EHDAA2:0000743 http://linkedlifedata.com/resource/umls/id/C1708552 MA:0002662 UMLS:C1708552 EHDAA:3053" "An atomic nucleus with 36 protons and 48 neutrons " "Any process that activates or increases the frequency, rate or extent of cardiac ventricle development." "GC_ID:1" @@ -8288,7 +8292,7 @@ "A length unit which is equal to one millionth of a meter or 10^[-6] m." "Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." "An epithelial cell that is part of an endometrial gland." "EFO:0010710" - "A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones." "XAO:0003087 VHOG:0000429 EHDAA:8041 EHDAA2:0002128 MA:0001908 FMA:54397 AAO:0000622 EMAPA:17927" + "A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones." "VHOG:0000429 EHDAA:8041 XAO:0003087 EHDAA2:0002128 MA:0001908 FMA:54397 AAO:0000622 EMAPA:17927" "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." "EHDAA:420 UMLS:C0018787 TAO:0000114 CALOHA:TS-0445 EV:0100018 XAO:0000064 http://en.wikipedia.org/wiki/Heart BILA:0000020 MAT:0000036 EMAPA:16105 GAID:174 ZFA:0000114 EHDAA2:0000738 MESH:D006321 EFO:0000815 AAO:0010210 MA:0000072 VHOG:0000276 MIAA:0000036 FMA:7088 http://www.snomedbrowser.com/Codes/Details/302509004 galen:Heart http://linkedlifedata.com/resource/umls/id/C0018787 NCIT:C12727 BTO:0000562" "Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process"@en "A part of an astronomical body which is primarily composed of gaseous material."@en @@ -8603,7 +8607,7 @@ "The developmental process pertaining to the initial formation of the conus arteriosus from unspecified parts. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk." "An apical ectodermal ridge that is part of a pelvic appendage bud." "VHOG:0001066 ZFA:0001385 EMAPA:16892 EHDAA2:0003194 EFO:0003681 TAO:0001385" "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." - "Major subdivision of an organism that protrudes from the body[DOS, CARO]." "EFO:0000799 BTO:0001492 VSAO:0000075 FBbt:00007000 EHDAA2:0003193 http://linkedlifedata.com/resource/umls/id/C0598782 UMLS:C0598782 EMAPA:37283 NCIT:C61460 MESH:D005121 XAO:0000218 EV:0100155 HAO:0000144 AEO:0000193 MIAA:0000023 BILA:0000018 MAT:0000023 CARO:0010003 http://en.wikipedia.org/wiki/Appendage" + "Major subdivision of an organism that protrudes from the body[DOS, CARO]." "EFO:0000799 BTO:0001492 VSAO:0000075 FBbt:00007000 EHDAA2:0003193 http://linkedlifedata.com/resource/umls/id/C0598782 EMAPA:37283 UMLS:C0598782 NCIT:C61460 MESH:D005121 XAO:0000218 EV:0100155 HAO:0000144 AEO:0000193 MIAA:0000023 BILA:0000018 MAT:0000023 CARO:0010003 http://en.wikipedia.org/wiki/Appendage" "Uncharged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." "A solid astronomical body part which is part of the landmass of that body." @@ -8731,7 +8735,7 @@ "https://en.wikipedia.org/wiki/Air_filter" "A unilaminar epithelium that develops_from a ectoderm and is part of a anal region." "EMAPA:25040 EHDAA2:0004019" "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord." "EHDAA2:0001278 EHDAA:264 UMLS:C1518429 NCIT:C34231 VHOG:0001212 EMAPA:16101 http://linkedlifedata.com/resource/umls/id/C1518429" - "An anatomical junctions that overlaps the mouth and foregut." "EMAPA:16258 RETIRED_EHDAA2:0001205 EHDAA:534 VHOG:0000592" + "An anatomical junctions that overlaps the mouth and foregut." "EMAPA:16258 EHDAA:534 RETIRED_EHDAA2:0001205 VHOG:0000592" "A subdivision of a the reproductive tract in a female organism that is the site of embryo development." "WBbt:0006760 TADS:0000421 FBbt:00004924" "A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way." "FMA:62798" @@ -8749,7 +8753,7 @@ "A mesothelial cell that is part of the anterior chamber of eyeball." "FMA:70615" "Anatomical system that consists of all blood and lymph vessels." "NCIT:C33854 UMLS:C0489903 BTO:0001085 MA:0002718 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 http://linkedlifedata.com/resource/umls/id/C0489903" "The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut." - "Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw)." "BAMS:Vn BIRNLEX:869 MFMO:0000093 BM:VN EMAPA:17576 BAMS:5n neuronames:549 FMA:50866 VHOG:0000704 MA:0001100 BAMS:nV http://en.wikipedia.org/wiki/Trigeminal_nerve HBA:9322 ZFA:0000697 http://www.snomedbrowser.com/Codes/Details/362459002 EFO:0001402 UMLS:C0040996 MESH:D014276 EHDAA:3738 AAO:0010470 MBA:901 NCIT:C12806 TAO:0000697 BTO:0001072 GAID:726 EHDAA2:0002084 XAO:0003092 http://linkedlifedata.com/resource/umls/id/C0040996" + "Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw)." "BAMS:Vn BIRNLEX:869 MFMO:0000093 BM:VN EMAPA:17576 BAMS:5n neuronames:549 FMA:50866 VHOG:0000704 MA:0001100 BAMS:nV http://en.wikipedia.org/wiki/Trigeminal_nerve HBA:9322 ZFA:0000697 http://www.snomedbrowser.com/Codes/Details/362459002 EFO:0001402 UMLS:C0040996 EHDAA:3738 MESH:D014276 AAO:0010470 MBA:901 NCIT:C12806 TAO:0000697 BTO:0001072 GAID:726 EHDAA2:0002084 XAO:0003092 http://linkedlifedata.com/resource/umls/id/C0040996" "PO_GIT:467" "A blood vessel that is part of a heart [Automatically generated definition]." "EMAPA:35397 MA:0002483" "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." "NIF_Subcellular:sao1846835077 Wikipedia:Microtubule" @@ -8827,7 +8831,7 @@ "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." "Wikipedia:Exocytosis" "The regulated release of somatostatin from secretory granules in the D cells of the pancreas." "A serous membrane that is part of a uterine tube infundibulum." "EMAPA:29903 FMA:18324" - "A systemic artery that supplies the lung with with oxygenated blood." "GAID:477 EMAPA:18608 FMA:68109 http://linkedlifedata.com/resource/umls/id/C0006257 http://www.snomedbrowser.com/Codes/Details/244247009 NCIT:C32230 MA:0001923 http://en.wikipedia.org/wiki/Bronchial_artery MESH:D001981 UMLS:C0006257" + "A systemic artery that supplies the lung with with oxygenated blood." "GAID:477 FMA:68109 EMAPA:18608 http://linkedlifedata.com/resource/umls/id/C0006257 http://www.snomedbrowser.com/Codes/Details/244247009 NCIT:C32230 MA:0001923 http://en.wikipedia.org/wiki/Bronchial_artery MESH:D001981 UMLS:C0006257" "Hydrides are chemical compounds of hydrogen with other chemical elements." "The process in which the anatomical structures of the eye are generated and organized during embryonic development." "Any process that modulates the frequency, rate or extent of phosphate transmembrane transport." @@ -8877,6 +8881,7 @@ "GC_ID:1" "The process in which the labyrinthine layer of the placenta is generated and organized." "The increase in size or mass of an endochondral bone that contributes to the shaping of the bone." + "The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field." "The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure." "The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates." @@ -8890,7 +8895,7 @@ "A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container." "Wikipedia:Packaging_gas" "The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract." "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." - "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." "MA:0002437 AAO:0000306 NCIT:C12435 http://linkedlifedata.com/resource/umls/id/C2328219 UMLS:C2328219 EHDAA2:0003122 AEO:0000122 FMA:9641 galen:MuscleTissue EMAPA:32715 CALOHA:TS-0642 MESH:D009132 http://en.wikipedia.org/wiki/Muscle_tissue http://www.snomedbrowser.com/Codes/Details/91727004" + "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." "MA:0002437 AAO:0000306 NCIT:C12435 http://linkedlifedata.com/resource/umls/id/C2328219 UMLS:C2328219 EHDAA2:0003122 AEO:0000122 FMA:9641 EMAPA:32715 galen:MuscleTissue MESH:D009132 CALOHA:TS-0642 http://en.wikipedia.org/wiki/Muscle_tissue http://www.snomedbrowser.com/Codes/Details/91727004" "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." "The part of the venous system that drains the general body tissues[Kardong]." "FMA:45626 http://en.wikipedia.org/wiki/Systemic_venous_system" "The wetness of some soil." @@ -8978,7 +8983,7 @@ - "A nucleus of brain that is part of a trigeminal nuclear complex." "GAID:604 MESH:D014278 NCIT:C12807 http://www.snomedbrowser.com/Codes/Details/280164007 BM:V BTO:0001074 UMLS:C0040999 CALOHA:TS-2077 EMAPA:35883 http://linkedlifedata.com/resource/umls/id/C0040999 http://uri.neuinfo.org/nif/nifstd/nifext_11 MA:0001028 EV:0100271 VHOG:0001353 FMA:71247" + "A nucleus of brain that is part of a trigeminal nuclear complex." "GAID:604 MESH:D014278 NCIT:C12807 http://www.snomedbrowser.com/Codes/Details/280164007 BM:V BTO:0001074 UMLS:C0040999 EMAPA:35883 CALOHA:TS-2077 http://linkedlifedata.com/resource/umls/id/C0040999 http://uri.neuinfo.org/nif/nifstd/nifext_11 MA:0001028 EV:0100271 VHOG:0001353 FMA:71247" "The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens." "MA:0000262 VHOG:0001431 EMAPA:18231 http://en.wikipedia.org/wiki/Anterior_chamber_of_eyeball EHDAA:9033 BTO:0002084 FMA:58078 MESH:D000867 EHDAA2:0000129 http://www.snomedbrowser.com/Codes/Details/181160009 NCIT:C12667 GAID:889 UMLS:C0003151 http://linkedlifedata.com/resource/umls/id/C0003151" "A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]." "MA:0001532 EMAPA:37394" "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en "BFO:0000020" @@ -9034,7 +9039,7 @@ "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." "A smooth muscle cell that is part of the rectum." "FMA:17522" - "Transparent part of camera-type eye that helps to refract light to be focused on the retina." "VHOG:0000169 MA:0000275 MIAA:0000141 XAO:0000008 AAO:0010348 EMAPA:17838 BTO:0000723 http://linkedlifedata.com/resource/umls/id/C0023317 MESH:D007908 RETIRED_EHDAA2:0000975 http://www.snomedbrowser.com/Codes/Details/181169005 http://en.wikipedia.org/wiki/Lens_(anatomy) ZFA:0000035 MAT:0000141 TAO:0000035 CALOHA:TS-0545 FMA:58241 NCIT:C12743 EV:0100343 UMLS:C0023317 EHDAA:9057" + "Transparent part of camera-type eye that helps to refract light to be focused on the retina." "VHOG:0000169 MIAA:0000141 MA:0000275 XAO:0000008 AAO:0010348 EMAPA:17838 BTO:0000723 http://linkedlifedata.com/resource/umls/id/C0023317 MESH:D007908 RETIRED_EHDAA2:0000975 http://www.snomedbrowser.com/Codes/Details/181169005 http://en.wikipedia.org/wiki/Lens_(anatomy) ZFA:0000035 MAT:0000141 TAO:0000035 CALOHA:TS-0545 FMA:58241 NCIT:C12743 EV:0100343 UMLS:C0023317 EHDAA:9057" "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA." "The mean absorbed radiation dose in a specified tissue or organ of the human body." @@ -9067,7 +9072,7 @@ "An epithelium surrounding an ovary." "BTO:0003661" "A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction." "PIRSF:PIRSF016630 IUPHARobj:2764" "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." - "The liquid component of blood, in which erythrocytes are suspended." "GAID:1178 http://linkedlifedata.com/resource/umls/id/C0032105 MIAA:0000052 MESH:D010949 EMAPA:35690 CALOHA:TS-0800 FMA:62970 MAT:0000052 http://en.wikipedia.org/wiki/Blood_plasma NCIT:C13356 UMLS:C0032105 EFO:0001905 BTO:0000131 MA:0002501" + "The liquid component of blood, in which erythrocytes are suspended." "GAID:1178 MIAA:0000052 http://linkedlifedata.com/resource/umls/id/C0032105 MESH:D010949 EMAPA:35690 CALOHA:TS-0800 FMA:62970 MAT:0000052 http://en.wikipedia.org/wiki/Blood_plasma NCIT:C13356 UMLS:C0032105 EFO:0001905 BTO:0000131 MA:0002501" "A stromal cell found in the lamina propria of the large intestine." "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." "A mouth disease that is characterized by inflammation of the mouth and lips." "NCI:C26887 UMLS_CUI:C0038362 SNOMEDCT_US_2021_09_01:95361005 ICD10CM:K12.1 MESH:D013280" @@ -9173,7 +9178,7 @@ "The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell." "A bone element or fused bone that is part of pelvic girdle." "UMLS:C0030786 http://www.snomedbrowser.com/Codes/Details/426214007 EMAPA:18028 MA:0000293 http://linkedlifedata.com/resource/umls/id/C0030786 NCIT:C33287" "Any process that activates or increases the frequency, rate or extent of cholangiocyte proliferation." - "TGN:21642 FTT:258 FTT:506 TGN:21645 SWEETRealm:Forest TGN:21641 FTT:715 FTT:717 LTER:2 EcoLexicon:forest https://en.wikipedia.org/wiki/Forest Geonames:V.FRST" + "TGN:21642 FTT:258 FTT:506 TGN:21645 SWEETRealm:Forest TGN:21641 FTT:715 LTER:2 FTT:717 EcoLexicon:forest https://en.wikipedia.org/wiki/Forest Geonames:V.FRST" "A bone that is part of a post-anal tail." "EMAPA:18042 MA:0000696" "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom." "UMLS:C1512940 http://en.wikipedia.org/wiki/Intraembryonic_coelom NCIT:C34195 VHOG:0000316 EMAPA:16088 EHDAA:251 http://linkedlifedata.com/resource/umls/id/C1512940" "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." "EC:2.7.-.-" diff --git a/src/ontology/reports/class-count-by-prefix.tsv b/src/ontology/reports/class-count-by-prefix.tsv index 252e1bb..a5c8352 100644 --- a/src/ontology/reports/class-count-by-prefix.tsv +++ b/src/ontology/reports/class-count-by-prefix.tsv @@ -2,7 +2,7 @@ "ENVO" 630 "OBIB" 6 "UO" 529 -"RBO" 426 +"RBO" 430 "SO" 2 "OBCS" 5 "APOLLO" 2 diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv index 8d3b788..42acdd1 100644 --- a/src/ontology/reports/edges.tsv +++ b/src/ontology/reports/edges.tsv @@ -1,11149 +1,11149 @@ ?x ?p ?y - - - - - - - - - - - + + + - - - - - + + - + + + + - - - + + - - - - - + + + + + - - - + + + + - + + + + + - - - - - - - - - + + + + + + + - + + - - - - - - + + + + - - + - - - - - - - - + + + + + + + - - - + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - + + + + - 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- _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid2203 + @@ -23691,9 +23690,9 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + - @@ -23757,6 +23756,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid3047 @@ -23780,6 +23780,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid2422 @@ -23790,7 +23791,6 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid3183 @@ -23890,12 +23890,12 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid3188 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid1247 @@ -23966,6 +23966,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid2216 @@ -23988,7 +23989,6 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid2422 @@ -23997,8 +23997,8 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - + @@ -24036,14 +24036,16 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid3188 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid2190 - + @@ -24073,6 +24075,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid1241 @@ -24102,12 +24105,11 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid2190 - + @@ -24132,8 +24134,8 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - + @@ -24157,9 +24159,9 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - + @@ -24182,8 +24184,8 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - + @@ -24216,7 +24218,6 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid1247 @@ -24262,8 +24263,8 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - + @@ -24271,7 +24272,6 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid1241 @@ -24304,6 +24304,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B36d88627X2De642X2D43e6X2D9041X2Dbcc8ae4093bbgenid3183 @@ -24374,7 +24375,6 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B045ad62fX2D7147X2D470fX2Db95eX2D5e17407837eegenid3193 @@ -24741,8 +24741,6 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 - _:B3a8895aeX2De969X2D4027X2Da7c1X2Dbb077dcb71a3genid227 - _:B3a8895aeX2De969X2D4027X2Da7c1X2Dbb077dcb71a3genid216 @@ -24750,18 +24748,20 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + _:B0061728bX2Dded0X2D4fddX2DbfacX2D6fd5547a8374genid222 + _:B0061728bX2Dded0X2D4fddX2DbfacX2D6fd5547a8374genid130 - _:B3a8895aeX2De969X2D4027X2Da7c1X2Dbb077dcb71a3genid222 - _:B3a8895aeX2De969X2D4027X2Da7c1X2Dbb077dcb71a3genid130 + _:B0061728bX2Dded0X2D4fddX2DbfacX2D6fd5547a8374genid216 + _:B0061728bX2Dded0X2D4fddX2DbfacX2D6fd5547a8374genid227 - _:B0a066f38X2Def9dX2D44ffX2Da609X2D34a3326f65a1genid7 + _:Bfde147e1X2D536eX2D415bX2Da355X2Db6f0af80a5bagenid7 @@ -24781,6 +24781,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + @@ -24801,6 +24802,7 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + @@ -24831,11 +24833,13 @@ _:B0a2f1b96X2D81edX2D4c9eX2D8df7X2D83a29af9a903genid52639 + + diff --git a/src/ontology/reports/rbo-edit.owl-obo-report.tsv b/src/ontology/reports/rbo-edit.owl-obo-report.tsv index b2a61cb..05fe581 100644 --- a/src/ontology/reports/rbo-edit.owl-obo-report.tsv +++ b/src/ontology/reports/rbo-edit.owl-obo-report.tsv @@ -148,7 +148,7 @@ WARN annotation_whitespace Faxitron CP160 IAO:0000119 doi: 10.2349/biij.2.1.e1 WARN annotation_whitespace X-Rad320 IAO:0000115 A specific instance of an X-Rad320 x-ray source. WARN annotation_whitespace earth surface radiation environment IAO:0000115 The radiation environment at the surface of the Earth, consisting of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements on the surface; and anthropogenic radiation. The composition and strength of the radiation at a given point on the Earth's surface depends on factors including altitude, the composition of the surface material, and the temporal variation in incident space radiation, e.g. with solar cycle. WARN annotation_whitespace external radiation exposure IAO:0000112 Mice exposed to external radiation from a Sr source. -WARN annotation_whitespace senolytic IAO:0000115 A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. +WARN annotation_whitespace senolytic IAO:0000115 A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. WARN duplicate_label_synonym charged particle IAO:0000118 charged particle WARN duplicate_scoped_synonym ionizing radiation IAO:0000118 ionising radiation WARN duplicate_scoped_synonym ionizing radiation oboInOwl:hasExactSynonym ionising radiation diff --git a/src/ontology/reports/rbo.owl-obo-report.tsv b/src/ontology/reports/rbo.owl-obo-report.tsv index 62fb62a..d785550 100644 --- a/src/ontology/reports/rbo.owl-obo-report.tsv +++ b/src/ontology/reports/rbo.owl-obo-report.tsv @@ -1,5 +1,5 @@ Level Rule Name Subject Property Value -ERROR deprecated_class_reference planned process rdfs:subClassOf 1b63178e-f86e-48f2-99e2-495b9608c99bgenid35673 +ERROR deprecated_class_reference planned process rdfs:subClassOf 7023dee3-1bab-4fd2-9a03-b7aab1921f88genid35673 ERROR deprecated_class_reference planned process rdfs:subClassOf process ERROR deprecated_class_reference planned process rdfs:subClassOf completely executed planned process ERROR deprecated_class_reference planned process rdfs:subClassOf material extraction process @@ -12,8 +12,8 @@ ERROR deprecated_class_reference planned process rdfs:subClassOf radiobiology st ERROR deprecated_class_reference planned process rdfs:subClassOf planned radiation exposure ERROR deprecated_class_reference planned process rdfs:subClassOf planned anthropogenic radiation exposure ERROR deprecated_class_reference planned process owl:disjointWith biological process -ERROR deprecated_class_reference planned process owl:equivalentClass 1b63178e-f86e-48f2-99e2-495b9608c99bgenid35671 -ERROR deprecated_class_reference obsolete device rdfs:subClassOf 1b63178e-f86e-48f2-99e2-495b9608c99bgenid35806 +ERROR deprecated_class_reference planned process owl:equivalentClass 7023dee3-1bab-4fd2-9a03-b7aab1921f88genid35671 +ERROR deprecated_class_reference obsolete device rdfs:subClassOf 7023dee3-1bab-4fd2-9a03-b7aab1921f88genid35806 ERROR deprecated_class_reference obsolete device rdfs:subClassOf sensor ERROR deprecated_class_reference obsolete device rdfs:subClassOf manufactured product ERROR deprecated_class_reference obsolete device rdfs:subClassOf processed material @@ -24,7 +24,7 @@ ERROR deprecated_class_reference obsolete organism rdfs:subClassOf organismal en ERROR deprecated_class_reference obsolete organism rdfs:subClassOf root ERROR deprecated_class_reference obsolete organism rdfs:subClassOf Viruses ERROR deprecated_class_reference obsolete organism rdfs:subClassOf population of organisms -ERROR deprecated_class_reference obsolete organism owl:equivalentClass 1b63178e-f86e-48f2-99e2-495b9608c99bgenid35897 +ERROR deprecated_class_reference obsolete organism owl:equivalentClass 7023dee3-1bab-4fd2-9a03-b7aab1921f88genid35897 ERROR deprecated_class_reference earth surface rdfs:subClassOf radiation environment ERROR deprecated_class_reference earth atmosphere rdfs:subClassOf radiation environment ERROR deprecated_class_reference environmental study rdfs:subClassOf radiobiology study type @@ -708,6 +708,8 @@ ERROR multiple_definitions protein textual definition An amino acid chain that i ERROR multiple_definitions protein textual definition An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. ERROR multiple_definitions amino acid chain textual definition A molecule that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. ERROR multiple_definitions amino acid chain textual definition An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. +ERROR multiple_definitions occupational role textual definition A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. +ERROR multiple_definitions occupational role textual definition A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. ERROR multiple_definitions mass number textual definition Radon dosimeters are radiation dosimeters used to measure the presence and concentration of radon gas (Rn-222), a radioactive noble gas that can accumulate in buildings and pose health risks. Different types of radon detectors use various detection methods, based on the radioactive decay products of radon. ERROR multiple_definitions mass number textual definition The atomic mass (ma or m) is the mass of an atom. The protons and neutrons of the nucleus account for nearly all of the total mass of atoms, with the electrons and nuclear binding energy making minor contributions. It is measured in Daltons (unit). ERROR multiple_definitions inheres in textual definition a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.@en @@ -748,8 +750,8 @@ ERROR multiple_definitions has output textual definition p has output c iff c is ERROR multiple_definitions has output textual definition p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. ERROR multiple_definitions results in developmental progression of textual definition p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). ERROR multiple_definitions results in developmental progression of textual definition p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). -ERROR multiple_definitions inheres in part of textual definition q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. -ERROR multiple_definitions inheres in part of textual definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. +ERROR multiple_definitions characteristic of part of textual definition q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. +ERROR multiple_definitions characteristic of part of textual definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. ERROR multiple_definitions causally related to textual definition This relation groups causal relations between material entities and causal relations between processes ERROR multiple_definitions causally related to textual definition relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. ERROR multiple_definitions causally upstream of textual definition p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain @@ -986,8 +988,8 @@ ERROR multiple_labels results in formation of anatomical entity label results in ERROR multiple_labels results in formation of anatomical entity label results in formation of anatomical entity@en ERROR multiple_labels has habitat label has habitat ERROR multiple_labels has habitat label has habitat@en -ERROR multiple_labels inheres in part of label characteristic of part of@en -ERROR multiple_labels inheres in part of label inheres in part of +ERROR multiple_labels characteristic of part of label characteristic of part of@en +ERROR multiple_labels characteristic of part of label inheres in part of ERROR multiple_labels member of label is member of ERROR multiple_labels member of label member of@en ERROR multiple_labels has member label has member @@ -1124,7 +1126,7 @@ WARN annotation_whitespace X-Rad320 textual definition A specific instance of an WARN annotation_whitespace earth surface radiation environment textual definition The radiation environment at the surface of the Earth, consisting of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements on the surface; and anthropogenic radiation. The composition and strength of the radiation at a given point on the Earth's surface depends on factors including altitude, the composition of the surface material, and the temporal variation in incident space radiation, e.g. with solar cycle. WARN annotation_whitespace external radiation exposure example of usage Mice exposed to external radiation from a Sr source. WARN annotation_whitespace internal experimental radiation exposure rdfs:comment Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure -WARN annotation_whitespace senolytic textual definition A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. +WARN annotation_whitespace senolytic textual definition A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. WARN annotation_whitespace contained in editor note "Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) @@ -1455,7 +1457,7 @@ WARN duplicate_label_synonym thorium has exact synonym thorium WARN duplicate_label_synonym uranium has exact synonym uranium WARN duplicate_label_synonym charged particle alternative term charged particle WARN duplicate_label_synonym overlaps alternative term overlaps -WARN duplicate_label_synonym inheres in part of alternative term inheres in part of +WARN duplicate_label_synonym characteristic of part of alternative term inheres in part of WARN duplicate_label_synonym member of alternative term is member of WARN duplicate_label_synonym sympathetic nervous system has exact synonym sympathetic nervous system WARN duplicate_label_synonym endocrine pancreas has exact synonym endocrine pancreas @@ -4126,8 +4128,8 @@ INFO lowercase_definition results in development of textual definition p 'result INFO lowercase_definition has habitat textual definition x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. INFO lowercase_definition causally upstream of, positive effect textual definition p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. INFO lowercase_definition causally upstream of, negative effect textual definition p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. -INFO lowercase_definition inheres in part of textual definition q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. -INFO lowercase_definition inheres in part of textual definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. +INFO lowercase_definition characteristic of part of textual definition q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. +INFO lowercase_definition characteristic of part of textual definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. INFO lowercase_definition enables textual definition c enables p iff c is capable of p and c acts to execute p. INFO lowercase_definition part of structure that is capable of textual definition this relation holds between c and p when c is part of some c', and c' is capable of p. INFO lowercase_definition involved in textual definition c involved_in p if and only if c enables some process p', and p' is part of p diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv index 5a92acc..ce6b164 100644 --- a/src/ontology/reports/synonyms.tsv +++ b/src/ontology/reports/synonyms.tsv @@ -376,9 +376,9 @@ "ribonucleoprotein complex assembly" "cellular component disassembly" "plasma membrane protein complex" - "small molecule metabolic process" "occurrent"@en "occurrent" + "small molecule metabolic process" "carboxylic acid metabolic process" "amide biosynthetic process" "life cycle stage" @@ -452,11 +452,11 @@ "cellular response to X-ray" "positive regulation of response to gamma radiation" "positive regulation of macromolecule metabolic process" - "regulation of cellular response to stress" "chromosome" + "regulation of cellular response to stress" "regulation of cellular response to X-ray" - "DNA metabolic process" "positive regulation of DNA metabolic process" + "DNA metabolic process" "regulation of macromolecule metabolic process" "negative regulation of metabolic process" "positive regulation of cellular senescence" @@ -464,9 +464,9 @@ "molecule"@en "biological macromolecule" "Mus musculus" + "C57BL/6JxCAST/EiJ" "NZO/HlLtJ" "PWK/PhJ" - "C57BL/6JxCAST/EiJ" "CBA/J" "derived unit" "prefix" @@ -557,10 +557,10 @@ "hardness" "mass of ice and snow"@en "Eutheria" + "decreased position" "Teleostomi" "aerosol formation process"@en "temperate marine upwelling biome"@en - "decreased position" "fossil fuel power plant" "Theria " "collective plant organ structure" @@ -585,9 +585,9 @@ "ecological succession"@en "village"@en "leaf" - "marine environment" "environmental system determined by an organism"@en "animal-associated environment"@en + "marine environment" "contaminated water" "acidity of soil" "temperate coniferous forest biome" @@ -611,14 +611,14 @@ "mass fluid flow"@en "enriched soil" "brick material" - "amount" "flattened elevation"@en + "amount" "hydrosphere"@en "water flow process"@en "temperate grassland"@en "agricultural land conversion process"@en - "platinum ore" "flat" + "platinum ore" "sea water" "tropical broadleaf forest"@en "mixed potential and kinetic energy" @@ -718,9 +718,9 @@ "afforestation" "greenhouse gas" "iron molecular entity" + "energy" "snow mass"@en "upland soil" - "energy" "formation of a solid aerosol from gaseous material in an atmosphere"@en "coniferous forest biome" "ecological community"@en @@ -742,8 +742,8 @@ "tsunami"@en "dinitrogen" "portion of meristem tissue" - "granular" "Primates" + "granular" "chlorine molecular entity" "cropland biome" "sodium molecular entity" @@ -797,25 +797,25 @@ "subtropical grassland"@en "acidic water" "building roof" + "increased combustibility" "material diffusion process"@en "research station" "old plant" "planetary crust"@en "astronomical body part"@en - "increased combustibility" "sloped" "marine mining"@en "ecosystem process"@en "concentration of slit in soil" - "temperature of environmental material" "potential energy" + "temperature of environmental material" "litter layer" "nickel group molecular entity" "embryo" "hydrological condensation process"@en "tropical grassland"@en - "dry soil" "arid" + "dry soil" "embryonic tissue" "cold environment" "erosion"@en @@ -830,8 +830,8 @@ "saline water" "construction"@en "mass" - "acidic" "forest biome" + "acidic" "liquid accumulation process"@en "elemental pnictogen" "soil organic matter"@en @@ -1111,8 +1111,8 @@ "non-saline aerosol environment"@en "single-species collection of organisms"@en "quality of a liquid" - "tailings pond"@en "stellar radiation"@en + "tailings pond"@en "halide salt" "amorphous" "waste material" @@ -1236,8 +1236,8 @@ "molecular_function" "gene product or complex activity"@en "research facility" - "humidity" "compacted soil"@en + "humidity" "planet"@en "structural collapse process"@en "multilaminar epithelium" @@ -1307,8 +1307,8 @@ "subtropical environment"@en "multi-tissue plant structure" "halogen molecular entity" - "peripheral zone" "organic material" + "peripheral zone" "respiratory system basement membrane" "carbon oxide" "frozen soil"@en @@ -1356,8 +1356,8 @@ "anthropogenic generation of energy" "viscous" "ecoregion" - "Catarrhini" "tectonic movement"@en + "Catarrhini" "woodland canopy"@en "cryosphere"@en "decreased temperature" @@ -1406,11 +1406,11 @@ "ecozone" "tectonic earthquake"@en "inorganic sodium salt" - "acidity of water" "understory" "air filter" "masonry cement" "fluid astronomical body part"@en + "acidity of water" "iron group molecular entity" "Glaucocystophyceae" "Cancroidea" @@ -1692,10 +1692,10 @@ "positive regulation of myoblast proliferation" "tail external integument structure" "cystic duct development" - "erythrocyte development" "T-cell surface glycoprotein CD3 epsilon chain (mouse)" "hematopoietic oligopotent progenitor cell" "nuclear microtubule" + "erythrocyte development" "1st arch maxillary mesenchyme" "regulation of endothelial tube morphogenesis" "negative regulation of blood vessel morphogenesis" @@ -1758,8 +1758,8 @@ "regulation of secretion by cell" "regulation of cell projection assembly" "nuclear complex of neuraxis" - "keratocyte" "proximal-distal subdivision of colon" + "keratocyte" "cranial ganglion morphogenesis" "regulation of gastro-intestinal system smooth muscle contraction" "pericardial fluid" @@ -1788,8 +1788,8 @@ "negative regulation of intracellular transport" "positive regulation of colon smooth muscle contraction" "presynapse organization" - "His-Purkinje system" "negative regulation of branching morphogenesis of a nerve" + "His-Purkinje system" "negative regulation of cell fate commitment" "pancreas morphogenesis" "pancreas mesenchyme" @@ -1811,8 +1811,8 @@ "coronary capillary" "myoblast maturation" "submucosal gland" - "lung epithelium development" "interstitial cell of Cajal differentiation" + "lung epithelium development" "B-lymphocyte antigen CD20 (human)" "erythroid progenitor cell" "ocular surface region" @@ -1861,8 +1861,8 @@ "regulation of collagen catabolic process" "Purkinje myocyte of atrioventricular node" "secretory cell" - "linear tetrapyrrole anion" "hepaticobiliary system development" + "linear tetrapyrrole anion" "regulation of tetrapyrrole biosynthetic process" "dermal bone morphogenesis" "pancreas ventral primordium" @@ -1906,8 +1906,8 @@ "insect embryonic/larval head sense organ" "cellular homeostasis" "trophectodermal cell" - "myeloid lineage restricted progenitor cell" "presynapse assembly" + "myeloid lineage restricted progenitor cell" "regionalization" "monosaccharide biosynthetic process" "positive regulation of ossification" @@ -2000,8 +2000,8 @@ "hepatobiliary system" "trophoblast cell" "cranial muscle" - "increased process quality" "5beta steroid" + "increased process quality" "lung microvascular endothelial cell" "establishment of organelle localization" "proctodeum" @@ -2129,8 +2129,8 @@ "skeletal muscle tissue development" "anal canal" "trunk bone" - "cellular localization" "deep vasculature" + "cellular localization" "replacement bone" "subcutaneous abdominal adipose tissue" "positive regulation of immune response" @@ -2265,8 +2265,8 @@ "regulation of nematode larval development" "Golgi to plasma membrane transport" "bile acid and bile salt transport" - "regulation of protein localization to plasma membrane" "pigment epithelium of eye" + "regulation of protein localization to plasma membrane" "endodermal cell" "oral lamina propria" "RNA localization" @@ -2499,8 +2499,8 @@ "organic hydroxy compound" "negative regulation of response to external stimulus" "lung primordium" - "interventricular septum membranous part" "regulation of morphogenesis of a branching structure" + "interventricular septum membranous part" "execution phase of apoptosis" "central nervous system vasculogenesis" "left lung terminal bronchiole" @@ -2514,8 +2514,8 @@ "transparent" "phosphorus molecular entity" "phosphorylation" - "head paraxial mesoderm" "1st arch mandibular component" + "head paraxial mesoderm" "polysaccharide catabolic process" "sulfate transmembrane transporter activity" "negative regulation of skeletal muscle fiber development" @@ -2559,8 +2559,8 @@ "positive regulation of nematode larval development" "mesenchyme development" "dorsal part of neck" - "positive regulation of fibroblast proliferation" "chewing" + "positive regulation of fibroblast proliferation" "paired limb/fin bud" "Tetraodontoidei" "indole-containing compound metabolic process" @@ -2790,8 +2790,8 @@ "negative regulation of insulin secretion" "positive regulation of response to external stimulus" "enzyme activator activity" - "mesoderm-derived structure" "sclerotome" + "mesoderm-derived structure" "liver parenchyma" "regulation of asymmetric cell division" "epicardium" @@ -2916,9 +2916,9 @@ "regulation of leukocyte proliferation" "negative regulation of fibroblast proliferation" "regulation of vascular endothelial cell proliferation" - "lumen of intestine" "regulation of glial cell proliferation" "inorganic acid" + "lumen of intestine" "plasma membrane bounded cell projection assembly" "regulation of hormone secretion" "polysaccharide localization" @@ -2931,8 +2931,8 @@ "negative regulation of synapse assembly" "positive regulation of trophectodermal cell proliferation" "bilirubin transport" - "regulation of respiratory system process" "retinal cell programmed cell death" + "regulation of respiratory system process" "mucosa of right hepatic duct" "sympathetic ganglion development" "secondary heart field" @@ -3107,8 +3107,8 @@ "hepatic sinusoid" "response to organic cyclic compound" "myocardium" - "pneumatic cavity of bone" "Drosophila melanogaster" + "pneumatic cavity of bone" "spinal cord segment" "ectoderm development" "angiogenesis" @@ -3182,12 +3182,12 @@ "alpha-adrenergic drug" "positive regulation of bleb assembly" "roof of mouth" - "subdivision of digestive tract" "photoreceptor cell differentiation" + "subdivision of digestive tract" "superelliptic" + "norepinephrine metabolic process" "descending aorta development" "pancreatic A cell development" - "norepinephrine metabolic process" "behavior process" "myocardial endocrine cell" "heterocycle metabolic process" @@ -3197,8 +3197,8 @@ "establishment of cell polarity" "placental vein" "negative regulation of nervous system process" - "carbohydrate transport" "thoracic vein" + "carbohydrate transport" "cervical spinal cord gray matter" "negative regulation of myotube differentiation" "intrahepatic bile duct" @@ -3389,8 +3389,8 @@ "catecholamine catabolic process" "cholangiocyte apoptotic process" "neural precursor cell proliferation" - "cranial blood vasculature" "His-Purkinje system cell differentiation" + "cranial blood vasculature" "wall of subclavian artery" "Columbiformes" "dermis adipose tissue" @@ -3406,8 +3406,8 @@ "endoskeleton" "nucleolus organization" "polysaccharide metabolic process" - "protein localization to vacuole" "localization of cell" + "protein localization to vacuole" "ommatidium" "sensory organ morphogenesis" "monocarboxylic acid anion" @@ -3469,16 +3469,16 @@ "hepatic duct smooth muscle" "positive regulation of secretory granule organization" "negative regulation of multicellular organismal process" - "hindgut contraction" "intestinal epithelial cell development" + "hindgut contraction" "right ventricular trabecular myocardium" "larval" "negative regulation of catalytic activity" "sulfur compound metabolic process" "intralobular duct" "negative regulation of motor neuron apoptotic process" - "dorsal pancreas" "blastocyst formation" + "dorsal pancreas" "atrioventricular node cell differentiation" "negative regulation of carbohydrate metabolic process" "nucleate erythrocyte development" @@ -3703,11 +3703,11 @@ "His-Purkinje system cell development" "right side of back" "subdivision of organism along main body axis" - "sphenoid endochondral element" "regulation of development, heterochronic" - "muscular coat" + "sphenoid endochondral element" "visceral serous pericardium" "reproductive behavior" + "muscular coat" "food additive" "negative regulation of hindgut contraction" "myocardial layer" @@ -3747,8 +3747,8 @@ "cardiac muscle tissue growth" "myoblast proliferation" "external anal region" - "regulation of leukocyte mediated immunity" "glycoprotein catabolic process" + "regulation of leukocyte mediated immunity" "regulation of organelle organization" "organic acid transmembrane transporter activity" "camera-type eye photoreceptor cell" @@ -3798,12 +3798,12 @@ "negative regulation of protein localization to nucleolus" "polysaccharide" "jaw epithelium" + "organ component layer" "protein transporter activity" "regulation of photoreceptor cell differentiation" - "organ component layer" "epithelial sheet" - "pancreatic D cell development" "regulation of postsynapse organization" + "pancreatic D cell development" "detection of electrical stimulus involved in sensory perception of pain" "endo-epithelial cell" "pancreas primordium" @@ -3922,8 +3922,8 @@ "regulation of smooth muscle cell proliferation" "negative regulation of protein-containing complex disassembly" "renal tubular secretion" - "left lung morphogenesis" "exocrine pancreas epithelium" + "left lung morphogenesis" "positive regulation of epithelial cell differentiation" "vein of upper lip" "positive regulation of lipid metabolic process" @@ -3960,8 +3960,8 @@ "positive regulation of fertilization" "glial cell" "negative regulation of nematode larval development" - "head morphogenesis" "regulation of mitotic nuclear envelope disassembly" + "head morphogenesis" "regulation of microtubule polymerization or depolymerization" "vasculature of liver" "positive regulation of multicellular organism growth" @@ -4065,8 +4065,8 @@ "Chimaeriformes" "glandular cell of the large intestine" "cell-cell junction assembly" - "trabecula carnea of atrium" "interatrial septum" + "trabecula carnea of atrium" "outflow part of right atrium" "reproductive structure" "pelvic appendage" @@ -4079,8 +4079,8 @@ "serous membrane" "positive regulation of cell population proliferation" "muscle layer of rectum" - "extracellular matrix secreting cell" "cellular biosynthetic process" + "extracellular matrix secreting cell" "positive regulation of angiogenesis" "regulation of aortic smooth muscle cell differentiation" "spinal cord mantle layer" @@ -4174,9 +4174,9 @@ "negative regulation of neuron death" "synaptic signaling" "regulation of extracellular matrix organization" + "small intestine" "tubulin binding" "post-juvenile adult stage" - "small intestine" "cardiac pacemaker cell development" "response to endogenous stimulus" "orthochromatic erythroblast" @@ -4201,8 +4201,8 @@ "gallbladder fibroblast" "respiratory system lamina propria" "negative regulation of morphogenesis of an epithelium" - "ciliated columnar oviduct epithelium" "bone tissue" + "ciliated columnar oviduct epithelium" "pleural fluid" "regulation of fertilization" "panarthropod head" @@ -4234,8 +4234,8 @@ "positive regulation of smooth muscle cell proliferation" "right lung morphogenesis" "vein of lower lip" - "negative regulation of meiotic nuclear division" "blood vessel endothelial cell" + "negative regulation of meiotic nuclear division" "microtubule-based movement" "tetrapyrrole biosynthetic process" "positive regulation of cardiac conduction" @@ -4249,8 +4249,8 @@ "positive regulation of fat cell differentiation" "lamina propria of large intestine" "leading edge membrane" - "epithelium of trachea" "left pulmonary artery" + "epithelium of trachea" "pre-chordal neural plate" "in utero embryonic development" "layer of muscle tissue" @@ -4348,8 +4348,8 @@ "positive regulation of embryonic development" "gallbladder" "phlegm" - "pectoral appendage blood vessel" "mesenchymal cell proliferation involved in lung development" + "pectoral appendage blood vessel" "carbohydrate binding" "apoptotic process involved in outflow tract morphogenesis" "anal canal epithelium" @@ -4428,8 +4428,8 @@ "negative regulation of cardiac muscle fiber development" "1st arch mandibular mesenchyme" "parietal pleura" - "striated muscle contraction" "axial mesoderm formation" + "striated muscle contraction" "regulation of sister chromatid segregation" "skin of thorax" "anatomical surface region" @@ -4564,8 +4564,8 @@ "negative regulation of angiogenesis" "future trigeminal ganglion" "negative regulation of extracellular matrix organization" - "microtubule depolymerization" "actomyosin" + "microtubule depolymerization" "hindgut morphogenesis" "megakaryocyte progenitor cell" "reproductive system development" @@ -4649,8 +4649,8 @@ "peritoneal cavity" "anatomical junction" "frontonasal process epithelium" - "esophagus secretion" "pharyngeal arch cartilage" + "esophagus secretion" "positive regulation of gonad development" "gravid organism" "regulation of retinal cell programmed cell death" @@ -4678,8 +4678,8 @@ "foregut epithelium" "differentiating neuroepithelium" "left dorsal aorta" - "lipid biosynthetic process" "protein localization to membrane" + "lipid biosynthetic process" "oligopotent" "pleura" "cardiac fibroblast cell development" @@ -4705,8 +4705,8 @@ "neural plate morphogenesis" "lung growth" "pectoral appendage apical ectodermal ridge" - "negative regulation of bile acid secretion" "nuclear lumen" + "negative regulation of bile acid secretion" "lung neuroendocrine cell" "apical ectodermal ridge formation" "phosphorus oxoacid" @@ -4727,9 +4727,9 @@ "polysaccharide binding" "response to salt" "arterial system smooth muscle" + "muscle of pectoral girdle" "myotube" "acinar cell differentiation" - "muscle of pectoral girdle" "buccopharyngeal membrane" "trigeminal nerve" "negative regulation of sister chromatid segregation" @@ -4806,8 +4806,8 @@ "regulation of basement membrane organization" "pancreatic ductal cell" "bronchial epithelial cell" - "negative regulation of megakaryocyte differentiation" "optic vesicle" + "negative regulation of megakaryocyte differentiation" "organic substance metabolic process" "lung epithelium" "regulation of meiotic cell cycle process involved in oocyte maturation" @@ -4878,8 +4878,8 @@ "iris blood vessel" "negative regulation of cardiac muscle cell differentiation" "neural crest cell differentiation" - "noradrenergic cell groups" "positive regulation of extracellular matrix organization" + "noradrenergic cell groups" "glial cell projection" "atrioventricular node cell development" "left hepatic vein" @@ -4951,8 +4951,8 @@ "enzyme activator complex" "regulation of stem cell division" "regulation of immune effector process" - "pelvic appendage bud mesenchyme" "mesoderm morphogenesis" + "pelvic appendage bud mesenchyme" "terminal bronchiole" "external soft tissue zone" "regulation of actomyosin structure organization" @@ -4960,8 +4960,8 @@ "negative regulation of apoptotic process involved in outflow tract morphogenesis" "pectoral girdle region" "negative regulation of vascular associated smooth muscle cell proliferation" - "ciliated epithelial cell of esophagus" "pectoral appendage vasculature" + "ciliated epithelial cell of esophagus" "positive regulation of AV node cell action potential" "liquid configuration" "neuron projection membrane" @@ -5057,8 +5057,8 @@ "steroid acid" "negative regulation of peptide hormone secretion" "AV node cell action potential" - "negative regulation of cell migration" "collagen trimer" + "negative regulation of cell migration" "female gonad morphogenesis" "glycan" "sulfur atom" @@ -5285,15 +5285,15 @@ "positive regulation of apoptotic process involved in outflow tract morphogenesis" "regulation of insulin secretion" "gland of foregut" - "regulation of microtubule depolymerization" "epithelium of gall bladder" + "regulation of microtubule depolymerization" "vacuolar membrane" "sulfur oxide" "lip" "solid configuration" "positive regulation of muscle hypertrophy" - "rhombomere boundary formation" "regulation of glial cell differentiation" + "rhombomere boundary formation" "compound eye morphogenesis" "compound eye development" "positive regulation of mesoderm development" @@ -5304,8 +5304,8 @@ "negative regulation of cardiac muscle cell proliferation" "chorionic mesenchyme" "negative regulation of transferase activity" - "positive regulation of cardiac muscle cell myoblast differentiation" "entire pharyngeal arch endoderm" + "positive regulation of cardiac muscle cell myoblast differentiation" "acid secretion" "smooth muscle cell apoptotic process" "anti-inflammatory agent" @@ -5328,8 +5328,8 @@ "pulmonary lobule" "neural crest derived fat cell" "flat bone" - "subcutaneous fat cell" "norepinephrine uptake" + "subcutaneous fat cell" "carbonate" "lens vesicle epithelium" "neural tube lateral wall" @@ -5426,9 +5426,9 @@ "synovial cell" "negative regulation of mitotic nuclear envelope disassembly" "tracheal mucosa" - "fibroblast of the aortic adventitia" "positive regulation of cardiac myofibril assembly" "peptide hormone secreting cell" + "fibroblast of the aortic adventitia" "integrin alpha-M" "pancreatic PP cell" "positive regulation of amino acid biosynthetic process" @@ -5469,9 +5469,9 @@ "signal release" "regulation of lipid catabolic process" "sex differentiation" + "subserosa of uterine tube" "adult skeletal muscle myoblast" "thoracic skeleton" - "subserosa of uterine tube" "apoptotic chromosome condensation" "cell communication involved in cardiac conduction" "positive regulation of protein localization to presynapse" @@ -5509,8 +5509,8 @@ "microtubule polymerization based protein transport" "layer of synovial tissue" "circulatory system process" - "meso-epithelium" "positive regulation of tetrapyrrole catabolic process" + "meso-epithelium" "endometrium epithelium" "multi-ciliated epithelial cell differentiation" "bile acid transmembrane transporter activity" @@ -5521,8 +5521,8 @@ "left cardiac atrium" "pigment granule organization" "pulmonary capillary" - "cardiovascular system endothelium" "regulation of establishment of protein localization to chromosome" + "cardiovascular system endothelium" "CD19 molecule" "megakaryocyte" "oxidising agent" @@ -5536,8 +5536,8 @@ "mesothelium of serous pericardium" "pharyngeal arch artery morphogenesis" "cellularity" - "female germ line stem cell" "rhombencephalon neural crest" + "female germ line stem cell" "regulation of gastric acid secretion" "neural crest derived neuroblast" "mitotic cell cycle process" @@ -5818,8 +5818,8 @@ "regulation of protein localization to microtubule" "cervical spinal cord ventral horn" "positive regulation of epithelial cell proliferation involved in lung morphogenesis" - "metal cation" "negative regulation of myeloid progenitor cell differentiation" + "metal cation" "coronary vasculature morphogenesis" "positive regulation of gastric acid secretion" "Chondrostei" @@ -6022,8 +6022,8 @@ "gonad" "transmission of nerve impulse" "regulation of Golgi organization" - "sulfuric acid" "peptide hormone" + "sulfuric acid" "negative regulation of blood circulation" "positive regulation of lipid catabolic process" "skeletal muscle hypertrophy" @@ -6035,8 +6035,8 @@ "organ or tissue specific immune response" "endothelial tube formation" "agrochemical" - "axo-dendritic protein transport" "positive regulation of muscle organ development" + "axo-dendritic protein transport" "amine transmembrane transporter activity" "multi-ciliated epithelial cell" "regulation of chondrocyte differentiation" @@ -6146,8 +6146,8 @@ "central nervous system neuron differentiation" "midbrain neural tube" "appendage morphogenesis" - "integument" "peritoneal fluid" + "integument" "aortic smooth muscle cell" "Pipoidea" "inorganic ion transmembrane transport" @@ -6204,8 +6204,8 @@ "aortico-pulmonary spiral septum" "heart primordium" "negative regulation of female gonad development" - "contractile cell" "duodenal gland" + "contractile cell" "response to hormone" "intercostal nerve" "positive regulation of vacuole organization" @@ -6232,8 +6232,8 @@ "digestive system process" "biladienes" "cervical region" - "translation at synapse" "embryonic morphogenesis" + "translation at synapse" "positive regulation of cytoskeleton organization" "negative regulation of cell cycle process" "positive regulation of oocyte maturation" @@ -6352,8 +6352,8 @@ "cellular metabolic process" "adipocyte of epicardial fat of left ventricle" "regulation of chromatin binding" - "positive regulation of type B pancreatic cell proliferation" "future superior salivatory nucleus" + "positive regulation of type B pancreatic cell proliferation" "negative regulation of sarcomere organization" "positive regulation of eye photoreceptor cell development" "phosphate(3-)" @@ -6363,8 +6363,8 @@ "cell-cell junction organization" "carbohydrate derivative biosynthetic process" "hindbrain venous system" - "lower jaw opening" "larval development" + "lower jaw opening" "outflow tract aortic component" "heart morphogenesis" "negative regulation of organelle assembly" @@ -6505,8 +6505,8 @@ "egg cell" "gonad mesenchyme" "submucosa of duodenum" - "digestive system" "response to monoamine" + "digestive system" "anterior segment of eyeball" "artery morphogenesis" "ventricular trabecula myocardium morphogenesis" @@ -6570,8 +6570,8 @@ "notochord morphogenesis" "response to chemical" "microvascular endothelial cell" - "intestinal mucosa" "neurectodermal cell" + "intestinal mucosa" "basal layer of endometrium" "organonitrogen compound catabolic process" "enzyme regulator activity" @@ -6662,8 +6662,8 @@ "Sphenodontia" "hydridodioxygen(1+)" "regulation of protein localization to cell leading edge" - "organic salt" "pectoral appendage skeleton" + "organic salt" "bronchus basement membrane" "future nervous system" "non-keratinized stratified squamous epithelium" @@ -6678,8 +6678,8 @@ "pontine raphe nucleus" "post-embryonic development" "corneal primordium" - "basement membrane assembly" "positive regulation of macromolecule biosynthetic process" + "basement membrane assembly" "cytoskeleton organization" "sphenoid bone pre-cartilage condensation" "endocardium" @@ -6736,8 +6736,8 @@ "regulation of kinase activity" "neural cell adhesion molecule 1 (human)" "stomach smooth muscle" - "hyaluronic acid" "negative regulation of vesicle fusion with Golgi apparatus" + "hyaluronic acid" "cardiac septum development" "positive regulation of protein transport" "bone of lower jaw" @@ -6929,9 +6929,9 @@ "coelom" "tracheobronchial serous cell"@en "neck nerve" - "closure" "nucleobase-containing compound catabolic process" "inorganic cation transmembrane transporter activity" + "closure" "intraembryonic coelom" "positive regulation of myoblast differentiation" "positive regulation of steroid biosynthetic process" @@ -6989,9 +6989,9 @@ "fundamental metabolite" "aminoglycan biosynthetic process" "positive regulation of developmental growth" - "respiratory system arteriole" "serous cell of epithelium of terminal bronchiole" "pericardium development" + "respiratory system arteriole" "endocardial cell" "regulation of formation of translation initiation ternary complex" "insulin secretion" @@ -7118,10 +7118,10 @@ "oral opening" "cartilage of bronchus" "endothelial cell of arteriole" - "liver subserosa" "regulation of gliogenesis" "wall of small intestine" "negative regulation of muscle contraction" + "liver subserosa" "regulation of Golgi inheritance" "intracellular organelle lumen" "respiratory system skeletal muscle" @@ -7181,9 +7181,9 @@ "lung vasculature development" "mandibular prominence" "striated muscle cell development" - "insect larval sense organ" "cardiac muscle cell myoblast differentiation" "circulating cell" + "insect larval sense organ" "endodermal part of digestive tract" "vacuolar localization" "positive regulation of axo-dendritic protein transport" @@ -7253,8 +7253,8 @@ "regulation of amide catabolic process" "regulation of amino acid transmembrane transport" "microvillus assembly" - "head external integument structure" "positive regulation of binding" + "head external integument structure" "establishment of epithelial cell polarity" "progenitor cell of endocrine pancreas" "positive regulation of transporter activity" @@ -7324,11 +7324,11 @@ "zygote stage" "T-cell surface glycoprotein CD5 (human)" "trunk ganglion" + "postcranial axial skeletal system" "protein localization to actin filament bundle" "secretion by cell" "heterobicyclic compound" "epithelial cell of esophagus" - "postcranial axial skeletal system" "venous blood vessel development" "gray matter" "hematopoietic multipotent progenitor cell" @@ -7355,8 +7355,8 @@ "extraembryonic membrane development" "negative regulation of steroid hormone secretion" "neuron of the ventral spinal cord" - "negative regulation of protein localization to ciliary membrane" "blastocyst growth" + "negative regulation of protein localization to ciliary membrane" "stem cell of epidermis" "heterogeneous tissue" "presynaptic actin cytoskeleton organization" @@ -7392,8 +7392,8 @@ "liver trabecula" "nematode larva" "heart blood vessel" - "cardiac muscle cell development" "regulation of catecholamine metabolic process" + "cardiac muscle cell development" "musculoskeletal system" "negative regulation of protein polymerization" "capsule of lens" @@ -7403,8 +7403,8 @@ "trigeminal ganglion formation" "regulation of protein localization to nucleus" "cell-cell signaling" - "heterochromatin" "positive regulation of mesenchymal cell apoptotic process" + "heterochromatin" "leukocyte" "epithelium of lower jaw" "posterior neural tube" @@ -7420,9 +7420,9 @@ "serous sac" "heart" "future lower lip" + "submucosa of bronchus" "oral cavity" "grooved" - "submucosa of bronchus" "muscle cell" "domed" "esophagus skeletal muscle" @@ -7451,9 +7451,9 @@ "blood vessel smooth muscle cell"@en "protein localization to ciliary membrane" "regulation of CD4 production" - "regulation of cell fate commitment" "presynapse" "outflow tract" + "regulation of cell fate commitment" "arterial blood" "cardiac mesenchyme" "CD3 epsilon" @@ -7484,9 +7484,9 @@ "cardiac myofibril assembly" "positive regulation of germ cell proliferation" "endothelial cell of artery" + "somite border" "muscle cell differentiation" "negative regulation of gliogenesis" - "somite border" "positive regulation of muscle contraction" "chondrocyte morphogenesis" "melanogaster group" @@ -7623,8 +7623,8 @@ "negative regulation of branching involved in lung morphogenesis" "presumptive blood" "negative regulation of acinar cell proliferation" - "camera-type eye" "appendage girdle complex" + "camera-type eye" "negative regulation of organ growth" "musculature of back" "lung parenchyma" @@ -7660,8 +7660,8 @@ "gastrointestinal system epithelium" "positive regulation of steroid hormone secretion" "3-D shape" - "endometrium" "programmed cell death" + "endometrium" "Amoebozoa" "vertebral element" "negative regulation of biosynthetic process" @@ -7714,8 +7714,8 @@ "epidermis gland" "respiration organ" "monoamine molecular messenger" - "negative regulation of protein localization to nucleus" "presynaptic signal transduction" + "negative regulation of protein localization to nucleus" "pharyngeal region of foregut" "paired limb/fin cartilage" "transferrin receptor protein 1 (mouse)" @@ -7958,8 +7958,8 @@ "DCMI Type Vocabulary"@en-us "transformed data item"@en "Reference System"@en - "radionuclide dispersal modelling study" "epidemiological study" + "radionuclide dispersal modelling study" "picovolt" "nanodosimetric measurement datum" "watt" @@ -7998,8 +7998,8 @@ "performance status value specification" "attitudinal study" "therapeutics study" - "histologic grade for ovarian tumor according to the World Health Organization" "radian per second based unit" + "histologic grade for ovarian tumor according to the World Health Organization" "lux" "microgray" "classified data set"@en @@ -8196,8 +8196,8 @@ "hectare" "mega" "Resource Relation Encoding Schemes"@en-us - "Resource Identifier Encoding Schemes"@en-us "interview study" + "Resource Identifier Encoding Schemes"@en-us "pH" "cancer study" "Measurement Unit of Momentum"@en @@ -8405,8 +8405,8 @@ "electrical conduction unit" "high-altitude balloon" "fraction" - "fractionated radiation exposure" "cross validation objective"@en + "fractionated radiation exposure" "processed material entity"@en "genetic study" "dose equivalent unit" @@ -8502,8 +8502,8 @@ "concentration unit" "atom" "atom"@en - "drawing a conclusion based on data"@en "beyond low earth orbit" + "drawing a conclusion based on data"@en "radiance unit" "support vector machine" "enzyme unit based unit" @@ -8611,8 +8611,8 @@ "kilodalton" "unit per liter based unit" "quarter" - "nuclear industry study" "dose equivalent" + "nuclear industry study" "cubic meter per mole" "meter per second per second based unit" "gray per minute based unit" @@ -9168,6 +9168,7 @@ "active radiation shielding" "radiation attenuation" "electret ion chamber radon dosimeter" + "ionization cluster size" "space station" "quality factor" "planet surface" @@ -9175,6 +9176,7 @@ "nuclear power reactor" "lineal energy measurement datum" "non-ionizing background radiation" + "ionization cluster size measurement datum" "natural non-ionizing background radiation" "organ dose" "interplanetary space" @@ -9232,9 +9234,11 @@ "high linear energy transfer" "multiple ion irradiation" "multi-purpose nuclear reactor" + "particle track core" "semiconductor radiation detector" "space radiation field" "military nuclear reactor" + "particle track penumbra" "Van Allen belts" "spacecraft module" "earth surface radiation environment" @@ -10577,9 +10581,9 @@ "trilaminar germ" "trilaminar disc" "trilaminar disk" - "trilaminar blastoderm" "trilaminar blastocyst" "tri-laminar disc" + "trilaminar blastoderm" "conifers" "positive regulation of nuclear genome maintenance" "positive regulation of maintenance of genome integrity" @@ -10826,13 +10830,13 @@ "oral ectoderm" "oral pit" "mouth pit" + "eye pigment epithelium" "regulation of protein localisation in plasma membrane" "regulation of protein targeting to plasma membrane" "regulation of establishment of protein localization in plasma membrane" "regulation of protein-plasma membrane targeting" "regulation of establishment of protein localisation in plasma membrane" "regulation of establishment of protein localization to plasma membrane" - "eye pigment epithelium" "AER" "crista ectodermalis apicalis" "articulatio atlantooccipitalis" @@ -10981,10 +10985,10 @@ "spiral septa" "regulation of collagen fibrillogenesis" "phosphorus molecular entities" - "somitomeric mesoderm" - "somitomere" "ventral mandibular arch" "ventral visceral arch 1" + "somitomeric mesoderm" + "somitomere" "sulfate permease activity" "cardiomyocyte generation" "flagellum" @@ -11192,10 +11196,10 @@ "vascular element" "vena" "cartilage" - "gut lumen" "mineral acids" "mineral acid" "inorganic acids" + "gut lumen" "ventricle cardiac muscle" "sphenoid complex" "os sphenoidale" @@ -11756,6 +11760,9 @@ "body segment" "main body segment" "developmental timing" + "pericardium visceral mesothelium" + "epicardium" + "single-organism reproductive behavior" "tunica muscularis" "muscularis externa" "muscular coat" @@ -11763,9 +11770,6 @@ "muscularis propria" "tunica externa" "transverse muscular fibers" - "pericardium visceral mesothelium" - "epicardium" - "single-organism reproductive behavior" "food additives" "regulation of muscle plasticity" "downregulation of secretory granule organization and biogenesis" @@ -11920,8 +11924,8 @@ "dermamyotome" "PA" "arteria subclavia" - "mesenchyma dermatomiale" "epimere mesoderm" + "mesenchyma dermatomiale" "neuroglia" "liver vascular element" "hepatic vascular element" @@ -12013,12 +12017,12 @@ "Itgam" "Gneticae" "Chlamydospermopsida" + "c. vertebralis" "spinal canal" "spinal cavity" "vertebral canal" "foramen vertebrale" "neural canal" - "c. vertebralis" "haemolymphoid system" "frontonasal process" "prominentia frontonasalis" @@ -12046,10 +12050,10 @@ "hagfishes" "Myxinoidea" "timing of cell differentiation" - "epithelium of uterine tube" - "uterine tube epithelium" "portion of bone tissue" "bone" + "epithelium of uterine tube" + "uterine tube epithelium" "muscle of pectoral girdle and limb" "positive regulation of protein complex disassembly" "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport" @@ -12153,9 +12157,9 @@ "negative regulation of vacuolar protein catabolism" "down-regulation of vacuolar protein degradation" "inhibition of vacuolar protein catabolism" + "inhibition of vacuolar protein breakdown" "downregulation of vacuolar protein degradation" "down regulation of vacuolar protein catabolism" - "inhibition of vacuolar protein breakdown" "downregulation of vacuolar protein catabolism" "inhibition of vacuolar protein catabolic process" "down-regulation of vacuolar protein breakdown" @@ -12386,8 +12390,8 @@ "positive regulation of vacuolar protein breakdown" "toxin resistance" "toxin susceptibility/resistance" - "eye anlage" "eye field" + "eye anlage" "optic field" "optic placodes" "skin of lips" @@ -12718,8 +12722,8 @@ "labia oris" "lips" "polycyclic compounds" - "positive regulation of cardiac myoblast differentiation" "pharyngeal arch endoderm" + "positive regulation of cardiac myoblast differentiation" "antiinflammatory agent" "anti-inflammatory agents" "antiinflammatory agents" @@ -12987,9 +12991,9 @@ "neural retinal epithelium" "single-organism carbohydrate catabolic process" "spinal neural crest" - "succus pancreaticus" "pancreatic fluid" "pancreatic secretion" + "succus pancreaticus" "labium inferius oris" "striated muscle plasticity" "medulla spinalis" @@ -13084,6 +13088,8 @@ "atrioventricular canal cushion" "gonads" "regulation of Golgi organization and biogenesis" + "peptide hormones" + "polypeptide hormone" "H2SO4" "Acide sulfurique" "[SO2(OH)2]" @@ -13092,8 +13098,6 @@ "Schwefelsaeureloesungen" "Acidum sulfuricum" "sulphuric acid" - "peptide hormones" - "polypeptide hormone" "inhibition of hemolymph circulation" "negative regulation of hemolymph circulation" "downregulation of hemolymph circulation" @@ -13393,8 +13397,8 @@ "embryonic circulatory system" "fetal circulatory system" "down regulation of morphogenetic apoptosis" - "downregulation of apoptosis involved in development" "negative regulation of morphogenetic apoptosis" + "downregulation of apoptosis involved in development" "down-regulation of apoptosis involved in development" "inhibition of morphogenetic apoptosis" "downregulation of morphogenetic apoptosis" @@ -13471,9 +13475,9 @@ "[HO2](+)" "HOO(+)" "HO2(+)" + "cheiropterygium" "organisches Salz" "organic salts" - "cheiropterygium" "induction of compound eye retinal cell programmed cell death" "raphe (mediana pontina)" "raphe pontis nucleus" @@ -13822,10 +13826,10 @@ "AIGF" "heparin-binding growth factor 8" "cardium" + "submucous layer of bronchi" "bucca" "creased" "channeled" - "submucous layer of bronchi" "nuclei trigemini" "aminoalkylindoles" "noradrenaline" @@ -13845,13 +13849,13 @@ "regulation of cellular component organization and biogenesis" "vascular system development" "heart myofibril assembly" - "myogenesis" "intersomitic boundary" "somite boundary" "inter-somited border" "intersomitic fissure" "segmental border" "intersomitic junction" + "myogenesis" "wall of ventricle" "atlantoaxial" "articulatio atlantoepistrophica" @@ -13910,8 +13914,8 @@ "Katalysator" "catalyseur" "colony forming unit hematopoietic" - "respiratory system secretion" "respiratory system fluid" + "respiratory system secretion" "posterior end of organism" "posterior" "ganglia development" @@ -13933,11 +13937,11 @@ "cranial somite" "regulation of signalling pathway" "regulation of signaling pathway" + "limb" "orbital part of face" "camera-type eye plus associated structures" "orbital region" "eyes" - "limb" "pulmonary parenchyma" "parenchyma of lung" "basal cell layer of skin" @@ -13951,11 +13955,11 @@ "expulsion of gland contents" "ducts" "epithelial cell of colon" - "uterine mucous membrane" - "uterine mucosa" "RCD" "PCD" "caspase-independent apoptosis" + "uterine mucous membrane" + "uterine mucosa" "Siluraninae" "left ventricle cardiac muscle" "positive regulation of serotonin release" @@ -15951,8 +15955,8 @@ "cranial conduit" "bone marrow tissue" "multicellular organismal polysaccharide metabolic process" - "glycan metabolic process" "glycan metabolism" + "glycan metabolic process" "main pathways of carbohydrate metabolic process" "main pathways of carbohydrate metabolism" "negative regulation of neurite development" @@ -16007,8 +16011,8 @@ "down-regulation of epitheliocyte apoptosis" "inhibition of epitheliocyte apoptotic process" "downregulation of epitheliocyte apoptosis" - "inhibition of epithelial cell apoptosis" "downregulation of epithelial cell apoptosis" + "inhibition of epithelial cell apoptosis" "negative regulation of epithelial cell apoptosis" "inhibition of epithelial cell apoptotic process" "activation of RNA binding" @@ -16032,8 +16036,8 @@ "cranial skeleton development" "os frontal" "frontal" - "frontal bone" "frontal bone" + "frontal bone" "activation of leukocyte proliferation" "stimulation of leukocyte proliferation" "inhibition of patterning of blood vessels" @@ -16168,9 +16172,9 @@ "encephalon" "activation of smooth muscle contraction" "stimulation of smooth muscle contraction" + "inhibition of eukaryotic chromosome condensation" "inhibition of chromosome condensation" "inhibition of nuclear chromosome condensation" - "inhibition of eukaryotic chromosome condensation" "inhibition of post-embryonic development" "mixed synapse" "inhibition of aorta morphogenesis" @@ -16839,9 +16843,9 @@ "inhibition of blood circulation" "activation of lipid catabolic process" "stimulation of lipid catabolic process" - "axonal protein transport" "stimulation of muscle development" "activation of muscle development" + "axonal protein transport" "inhibition of RNA synthesis" "inhibition of RNA biosynthetic process" "inhibition of RNA formation" @@ -17246,8 +17250,8 @@ "inhibition of protein localization in ciliary membrane" "striated muscle cell apoptosis" "inhibition of protein polymerization" - "nuclear heterochromatin" "positive regulation of mesenchymal cell apoptosis" + "nuclear heterochromatin" "branchial heart" "activation of execution phase of apoptosis" "activation of eukaryotic chromosome condensation" @@ -18184,8 +18188,8 @@ "ribonucleoprotein complex subunit organisation" "protein-RNA complex subunit organization" "ribonucleoprotein complex subunit organization" - "protein synthesis" "protein formation" + "protein synthesis" "protein translation" "protein biosynthesis" "protein anabolism" @@ -18299,12 +18303,12 @@ "regulation of physiological process" "cellular response to X-ray radiation stimulus" "regulation of cellular response to X-ray radiation stimulus" - "DNA metabolism" - "cellular DNA metabolism" "positive regulation of DNA metabolism" "up-regulation of DNA metabolic process" "up regulation of DNA metabolic process" "upregulation of DNA metabolic process" + "DNA metabolism" + "cellular DNA metabolism" "downregulation of metabolic process" "down regulation of metabolic process" "down-regulation of metabolic process" @@ -18680,10 +18684,10 @@ "squashed" "compressed" "soil salt concentration" - "water acidity" "understorey" "undergrowth" "under story" + "water acidity" "glaucocystophytes" "glaucocystophytes" "euphyllophytes" @@ -18974,11 +18978,11 @@ "down-regulation of respiratory gaseous exchange" "down regulation of respiratory gaseous exchange" "downregulation of respiratory gaseous exchange" - "RBC development" - "red blood cell development" "T-cell surface antigen T3/Leu-4 epsilon chain (mouse)" "mCD3E" "CD3e (mouse)" + "RBC development" + "red blood cell development" "mesenchyme of maxillary component" "thorax muscle organ" "muscle organ of thorax" @@ -19487,6 +19491,7 @@ "sympathetic nervous system ganglion" "ganglion sympatheticum" "down-regulation of protein localization in cell leading edge" + "negative regulation of protein localization in cell leading edge" "downregulation of protein localization in cell leading edge" "down regulation of protein localisation in cell leading edge" "down-regulation of protein localization to cell leading edge" @@ -19500,7 +19505,6 @@ "down regulation of protein localization to cell leading edge" "negative regulation of protein localisation to cell leading edge" "downregulation of protein localisation to cell leading edge" - "negative regulation of protein localization in cell leading edge" "upregulation of cellular metabolic process" "up regulation of cellular metabolic process" "up-regulation of cellular metabolic process" @@ -19643,8 +19647,8 @@ "grey substance of brain" "gray matter of brain" "brain grey matter" - "mucosa of organ of uterine tube" "mucosa of organ of fallopian tube" + "mucosa of organ of uterine tube" "organ mucosa of uterine tube" "mucous membrane of fallopian tube" "fallopian tube organ mucosa" @@ -19701,8 +19705,8 @@ "elastic tissue of bronchus" "bronchial trunk elastic connective tissue" "bronchi textus connectivus elasticus" - "bronchial trunk elastic tissue" "textus connectivus elasticus of bronchial trunk" + "bronchial trunk elastic tissue" "elastic connective tissue of bronchus" "bronchus textus connectivus elasticus" "bronchial trunk epithelium" @@ -19750,11 +19754,11 @@ "negative regulation of CD4 synthesis" "down regulation of CD4 biosynthetic process" "negative regulation of CD4 formation" - "panniculus adiposus telae subcutaneae" "panniculus adiposus (tela subcutanea)" "subcutaneous fat layer" "fatty layer of subcutaneous tissue" "hypodermis fat layer" + "panniculus adiposus telae subcutaneae" "visceral muscle contraction" "mucous membrane of pyloric antrum" "mucosa of organ of pyloric antrum" @@ -19837,11 +19841,11 @@ "bone organ of torso" "torso bone organ" "bone of trunk" + "deep part of circulatory system" "establishment and maintenance of localization in cell or cell membrane" "cellular localisation" "single organism cellular localization" "establishment and maintenance of cellular localization" - "deep part of circulatory system" "replacement bones" "abdominal subcutaneous adipose tissue" "subcutaneous fat of abdominal region" @@ -19870,8 +19874,8 @@ "up-regulation of intracellular transport" "upregulation of intracellular transport" "positive regulation of stomach mucosal blood circulation" - "upregulation of gastric mucosal blood circulation" "up-regulation of gastric mucosal blood circulation" + "upregulation of gastric mucosal blood circulation" "up regulation of stomach mucosal blood circulation" "up-regulation of stomach mucosal blood circulation" "upregulation of stomach mucosal blood circulation" @@ -19930,8 +19934,8 @@ "pelvic girdle plus posterior limb or fin" "pelvic girdle plus pelvic limb or fin" "pelvic appendage/girdle complex" - "nucleate RBC maturation" "nucleate red blood cell maturation" + "nucleate RBC maturation" "serosa of infundibulum of fallopian tube" "serosa of infundibulum of oviduct" "TfR1 (human)" @@ -20033,8 +20037,8 @@ "homeostasis of cell number" "cell population homeostasis" "cilium resorption" - "muscle system of body" "set of all muscles" + "muscle system of body" "muscle system" "vertebrate muscular system" "muscular system" @@ -20075,6 +20079,7 @@ "atlantooccipital joint" "craniovertebral joint" "positive regulation of protein localisation in cell leading edge" + "up regulation of protein localization in cell leading edge" "upregulation of protein localisation in cell leading edge" "upregulation of protein localization in cell leading edge" "up-regulation of protein localization to cell leading edge" @@ -20084,11 +20089,10 @@ "up regulation of protein localization to cell leading edge" "upregulation of protein localization to cell leading edge" "up regulation of protein localisation to cell leading edge" - "upregulation of protein localisation to cell leading edge" "up-regulation of protein localisation in cell leading edge" - "up-regulation of protein localisation to cell leading edge" + "upregulation of protein localisation to cell leading edge" "positive regulation of protein localisation to cell leading edge" - "up regulation of protein localization in cell leading edge" + "up-regulation of protein localisation to cell leading edge" "regulation of breakdown" "regulation of degradation" "regulation of catabolism" @@ -20599,12 +20603,12 @@ "regulation of collagen fibril organisation" "hyaline" "clear" + "ventral pharyngeal arch 1" "cranial paraxial mesoderm" "cranial paraxial mesenchyme" "cephalic paraxial mesoderm" "head paraxial mesenchyme" "cephalic paraxial mesenchyme" - "ventral pharyngeal arch 1" "polysaccharide catabolism" "polysaccharide degradation" "polysaccharide breakdown" @@ -20681,19 +20685,19 @@ "back of neck" "posterior part of neck" "nuchal region" - "up regulation of fibroblast proliferation" - "upregulation of fibroblast proliferation" - "up-regulation of fibroblast proliferation" "chew"@en "mastication" "gnaw"@en + "up regulation of fibroblast proliferation" + "upregulation of fibroblast proliferation" + "up-regulation of fibroblast proliferation" "limb - fin bud" "paired limb/fin bud" "paired appendage bud" "ketole metabolism" "indole and derivative metabolic process" - "indole and derivative metabolism" "ketole metabolic process" + "indole and derivative metabolism" "indole-containing compound metabolism" "tetrapyrrole" "tetrapyrroles" @@ -20828,8 +20832,8 @@ "skeletal system subdivision" "upregulation of exosomal secretion" "positive regulation of secretion of exosome" - "upregulation of extracellular vesicular exosome secretion" "positive regulation of exosomal secretory pathway" + "upregulation of extracellular vesicular exosome secretion" "positive regulation of extracellular vesicular exosome secretion" "upregulation of exosomal secretory pathway" "up-regulation of exosomal secretion" @@ -21153,8 +21157,8 @@ "up-regulation of response to external stimulus" "upregulation of response to external stimulus" "up regulation of response to external stimulus" - "mesodermal derivative" "sclerotomes" + "mesodermal derivative" "parenchyma of liver" "liver parenchyme" "hepatic parenchyma" @@ -21560,7 +21564,6 @@ "down regulation of programmed cell death by apoptosis involved in anatomical structure development" "negative regulation of programmed cell death by apoptosis involved in anatomical structure development" "down-regulation of apoptotic programmed cell death involved in development of an anatomical structure" - "portion of connective tissue of bronchial trunk" "portion of connective tissue of bronchus" "connective tissue of bronchus" "bronchi portion of connective tissue" @@ -21577,6 +21580,7 @@ "bronchial trunk portion of connective tissue" "textus connectivus of bronchus" "connective tissue of bronchial trunk" + "portion of connective tissue of bronchial trunk" "lipid metabolism" "up-regulation of vesicle fusion" "up regulation of vesicle fusion" @@ -21784,8 +21788,8 @@ "response to organic cyclic substance" "muscle of heart" "heart myocardium" - "air space of bone" "fruit fly" + "air space of bone" "segment of spinal cord" "axial part of spinal cord" "axial regional part of spinal cord" @@ -21898,12 +21902,12 @@ "roof of oral cavity" "roof of buccal cavity" "Lamé curve" - "pancreatic alpha cell development" "noradrenaline metabolic process" "levarterenol metabolic process" "norepinephrine metabolism" "levarterenol metabolism" "noradrenaline metabolism" + "pancreatic alpha cell development" "behaviour" "behavior" "heterocycle metabolism" @@ -22252,11 +22256,11 @@ "replacement skeleton" "nucleolus organisation" "polysaccharide metabolism" - "protein localisation to vacuole" "establishment and maintenance of cell localization" "cell localization" "localisation of cell" "establishment and maintenance of localization of cell" + "protein localisation to vacuole" "omatidium" "sense organ system" "epithelium of mucosa of mouth" @@ -22446,7 +22450,6 @@ "post-vent region skin" "skin of tail" "skin of post-vent region" - "female reproductive system gonada vein" "ovary vein" "female reproductive system gonad vein" "vein of gonada of female reproductive system" @@ -22456,10 +22459,11 @@ "vein of female reproductive system gonad" "vein of ovary" "vein of gonad of female reproductive system" + "female reproductive system gonada vein" "future digestive tract" "primitive gut" - "future digestive tube" "future gut" + "future digestive tube" "contractile fibre" "female external genitalia" "external female genital organ" @@ -22482,8 +22486,8 @@ "positive regulation of tetrapyrrole biosynthesis" "upregulation of tetrapyrrole anabolism" "up regulation of tetrapyrrole synthesis" - "up-regulation of tetrapyrrole biosynthesis" "activation of tetrapyrrole anabolism" + "up-regulation of tetrapyrrole biosynthesis" "positive regulation of tetrapyrrole anabolism" "up-regulation of tetrapyrrole anabolism" "activation of tetrapyrrole formation" @@ -22669,8 +22673,8 @@ "bowel non-striated muscle" "non-striated muscle of bowel" "bowel involuntary muscle" - "smooth muscle of bowel" "intestine non-striated muscle" + "smooth muscle of bowel" "involuntary muscle of intestine" "apparatus respiratorius vein" "vein of apparatus respiratorius" @@ -22749,12 +22753,9 @@ "hemopoietic or lymphoid organ development" "endochondral replacement element" "axial subdivision of organism" - "sphenoid element" "temporal regulation of development" "heterochronic regulation of development" - "tunica muscularis" - "muscular layer" - "muscularis layer" + "sphenoid element" "visceral lamina of serous pericardium" "visceral layer of serous pericardium" "serous visceral pericardium" @@ -22762,6 +22763,9 @@ "lamina visceralis pericardii serosi" "reproductive behaviour" "reproductive behavior in a multicellular organism" + "tunica muscularis" + "muscular layer" + "muscularis layer" "myocardium layer" "layer of myocardium" "regulation of protein polymer breakdown" @@ -22822,11 +22826,11 @@ "basement membrane organisation" "left lung mesenchyme" "heart muscle growth" - "regulation of leucocyte mediated immunity" - "regulation of immune cell mediated immunity" "glycoprotein degradation" "glycoprotein breakdown" "glycoprotein catabolism" + "regulation of leucocyte mediated immunity" + "regulation of immune cell mediated immunity" "regulation of organelle organisation" "camera type eye photoreceptor cell" "upregulation of actin filament-based movement" @@ -22901,9 +22905,9 @@ "polysaccharides" "Polysaccharide" "regulation of photoreceptor differentiation" - "pancreatic delta cell development" "regulation of postsynapse structure" "regulation of postsynapse organisation" + "pancreatic delta cell development" "perception of pain, sensory transduction of electrical stimulus" "perception of pain, detection of electrical stimulus" "perception of pain, sensory detection of electrical stimulus" @@ -22970,8 +22974,8 @@ "down-regulation of small intestine smooth muscle contraction" "downregulation of small intestine smooth muscle contraction" "down regulation of small intestine smooth muscle contraction" - "pancreas primordium dorsal bud" "pancreas dorsal primordium duct bud" + "pancreas primordium dorsal bud" "primary pancreatic bud" "negative regulation of extracellular matrix degradation" "down-regulation of extracellular matrix disassembly" @@ -23247,8 +23251,8 @@ "organic substance synthesis" "mucosa of organ of bronchi" "tunica mucosa bronchi" - "bronchus mucous membrane" "mucosa of bronchi" + "bronchus mucous membrane" "bronchi mucosa of organ" "organ mucosa of bronchial trunk" "bronchus organ mucosa" @@ -23402,8 +23406,8 @@ "down regulation of photoreceptor differentiation" "right ventricle lumen" "right ventricular cavity" - "pancreatic buds" "pancreatic bud" + "pancreatic buds" "regulation of chromosome organisation" "ventricular trabecular myocardium" "trabecular cardiac ventricle muscle" @@ -23634,11 +23638,11 @@ "vena labialis inferior" "inferior labial vein" "lower lip vein" + "cuboidal endothelial cell of vascular tree" "downregulation of meiosis" "down-regulation of meiosis" "negative regulation of meiosis" "down regulation of meiosis" - "cuboidal endothelial cell of vascular tree" "tetrapyrrole formation" "tetrapyrrole biosynthesis" "tetrapyrrole synthesis" @@ -23660,6 +23664,8 @@ "large intestinal lamina propria" "large intestine lamina propria" "lamina propria of mucosa of large intestine" + "left pulmonary arterial tree" + "left main pulmonary artery" "trachea epithelial tissue" "epithelial tissue of windpipe" "tracheal epithelium" @@ -23668,8 +23674,6 @@ "epithelial tissue of trachea" "epithelium of windpipe" "windpipe epithelium" - "left pulmonary arterial tree" - "left main pulmonary artery" "down regulation of muscle tissue development" "downregulation of muscle tissue development" "down-regulation of muscle tissue development" @@ -24161,8 +24165,8 @@ "camera-style eye morphogenesis" "vacuolar membrane transport" "vertebral cartilage condensation" - "upregulation of insulin secretion" "up-regulation of insulin secretion" + "upregulation of insulin secretion" "up regulation of insulin secretion" "regulation of cardiomyocyte differentiation" "transmembrane cation transporter activity" @@ -24177,10 +24181,10 @@ "downregulation of extracellular matrix organisation" "down regulation of extracellular matrix organisation" "down regulation of extracellular matrix organization" - "microtubule disassembly" - "microtubule shortening" "actomyosin structure" "actomyosin complex" + "microtubule disassembly" + "microtubule shortening" "CFU-Meg" "megacaryocyte progenitor cell" "colony-forming unit-megakaryocyte" @@ -24293,14 +24297,14 @@ "receptor cell" "SMC proliferation" "anatomical junction" + "splanchnocranium cartilage" + "pharyngeal arch cartilages" "gullet secretion" "esophageal secretion" "secretion of oesophagus" "secretion of gullet" "secretion of esophagus" "oesophagus secretion" - "splanchnocranium cartilage" - "pharyngeal arch cartilages" "upregulation of gonadogenesis" "positive regulation of gonadogenesis" "up-regulation of gonadogenesis" @@ -24387,13 +24391,13 @@ "adipose cell apoptotic process" "regulation of cellular amide metabolic process" "regulation of amide metabolism" + "protein localisation in membrane" + "protein localization in membrane" "lipid synthesis" "lipogenesis" "lipid biosynthesis" "lipid formation" "lipid anabolism" - "protein localisation in membrane" - "protein localization in membrane" "wall of pleural sac" "upregulation of myeloid cell differentiation" "up regulation of myeloid cell differentiation" @@ -24458,10 +24462,10 @@ "arterial smooth muscle" "smooth muscle of artery" "artery smooth muscle" - "single cell sarcomere" - "myotubule" "muscle of shoulder girdle" "pectoral girdle muscle" + "single cell sarcomere" + "myotubule" "nervus trigeminus" "trigeminal v nerve" "trigeminal nerve [V]" @@ -24810,9 +24814,9 @@ "brain box" "trunk mesenchyme from neural crest" "trunk neural crest derived mesenchyme" + "non-membrane-bounded organelle formation" "non-membrane-enclosed organelle formation" "non-membrane-enclosed organelle assembly" - "non-membrane-bounded organelle formation" "Ly-6G.1" "Ly6g" "Ly-6G" @@ -24840,6 +24844,7 @@ "down regulation of VSMC proliferation" "down regulation of vascular smooth muscle cell proliferation" "down-regulation of VSMC proliferation" + "up regulation of AV node cell action potential" "up-regulation of AV node cardiac muscle cell action potential" "up regulation of AV node cardiac muscle cell action potential" "positive regulation of atrioventricular node cardiac muscle cell action potential" @@ -24850,7 +24855,6 @@ "up regulation of atrioventricular node cardiac muscle cell action potential" "up-regulation of AV node cell action potential" "upregulation of AV node cell action potential" - "up regulation of AV node cell action potential" "liquid" "portion of blood" "vertebrate blood" @@ -24964,10 +24968,10 @@ "esophagus involuntary muscle" "involuntary muscle of oesophagus" "gullet smooth muscle" - "smooth muscle tissue of gullet" "non-striated muscle of gullet" "oesophagus non-striated muscle" "non-striated muscle of esophagus" + "smooth muscle tissue of gullet" "esophageal smooth muscle" "involuntary muscle of gullet" "cornea endothelium" @@ -25285,8 +25289,8 @@ "up-regulation of response to biotic stimulus" "up regulation of response to biotic stimulus" "response to amine stimulus" - "bronchiolar epithelium" "bronchiole epithelium" + "bronchiolar epithelium" "bronchiole epithelial tissue" "epithelial tissue of bronchiole" "organic sodium salt" @@ -25420,14 +25424,14 @@ "up regulation of apoptotic process involved in outflow tract morphogenesis" "up-regulation of apoptotic process involved in outflow tract morphogenesis" "foregut gland" - "regulation of microtubule disassembly" - "gallbladder epithelium" "epithelial tissue of gallbladder" + "gallbladder epithelium" "gall bladder epithelium" "epithelial tissue of gall bladder" "gall bladder epithelial tissue" "gallbladder epithelial tissue" "epithelium of gallbladder" + "regulation of microtubule disassembly" "solid" "regulation of glia cell differentiation" "regulation of neuroglia differentiation" @@ -25486,13 +25490,13 @@ "regulation of transmembrane ion transport" "regulation of ion membrane transport" "lobulus pulmonis" - "subcutaneous adipocyte" "noradrenaline uptake" "norepinephrine reuptake" "levarterenol uptake" "levarterenol reuptake" "norepinephrine import" "noradrenaline reuptake" + "subcutaneous adipocyte" "trioxidocarbonate(2-)" "carbonate" "lateral wall neural tube" @@ -25662,8 +25666,8 @@ "rhombencephalon development" "synoviocyte" "down regulation of mitotic nuclear envelope catabolism" - "downregulation of mitotic nuclear envelope breakdown" "negative regulation of mitotic nuclear envelope degradation" + "downregulation of mitotic nuclear envelope breakdown" "negative regulation of mitotic nuclear envelope catabolism" "downregulation of mitotic nuclear envelope disassembly" "down regulation of mitotic nuclear envelope disassembly" @@ -25786,11 +25790,11 @@ "regulation of lipid degradation" "regulation of lipid catabolism" "regulation of lipid breakdown" + "subserosa of fallopian tube" + "subserosa of oviduct" "thoracic skeleton" "skeleton of thorax" "thoracic part of axial skeleton" - "subserosa of fallopian tube" - "subserosa of oviduct" "pyknosis" "upregulation of protein localisation to presynapse" "positive regulation of protein localization in presynapse" @@ -25870,8 +25874,6 @@ "down regulation of amine transport" "midgut lumen" "synovium" - "mesoderm-derived epithelium" - "mesoepithelium" "up regulation of tetrapyrrole catabolic process" "upregulation of tetrapyrrole catabolic process" "activation of tetrapyrrole degradation" @@ -25890,6 +25892,8 @@ "activation of tetrapyrrole catabolism" "positive regulation of tetrapyrrole degradation" "up-regulation of tetrapyrrole catabolism" + "mesoderm-derived epithelium" + "mesoepithelium" "epithelium of tunica mucosa of endometrium" "epithelium of endometrium" "endometrium epithelial tissue" @@ -26179,8 +26183,8 @@ "non-striated muscle of outflow tract" "smooth muscle of outflow tract" "smooth muscle tissue of outflow tract" - "involuntary muscle of outflow tract" "outflow tract involuntary muscle" + "involuntary muscle of outflow tract" "outflow tract non-striated muscle" "outflow tract smooth muscle tissue" "large bowel" @@ -26723,9 +26727,9 @@ "up-regulation of lipid catabolic process" "upregulation of lipid catabolic process" "positive regulation of lipid degradation" - "aorta smooth muscle" "aorta non-striated muscle" "aortic smooth muscle" + "aorta smooth muscle" "regulation of retina development in camera-style eye" "vein system" "immune response in organ or tissue" @@ -26741,8 +26745,8 @@ "acinic cell" "acinous cell" "down regulation of RNA biosynthesis" - "down-regulation of RNA synthesis" "negative regulation of RNA synthesis" + "down-regulation of RNA synthesis" "downregulation of RNA biosynthetic process" "down-regulation of RNA anabolism" "downregulation of RNA biosynthesis" @@ -27667,10 +27671,11 @@ "Glycogen" "response to chemical stimulus" "response to chemical substance" + "neurectoderm cell" "mucous membrane of intestine" "organ mucosa of bowel" - "tunica mucosa intestini" "bowel mucous membrane" + "tunica mucosa intestini" "mucosa of organ of intestine" "bowel mucosa" "bowel mucosa of organ" @@ -27681,10 +27686,9 @@ "mucosa of bowel" "intestine organ mucosa" "bowel organ mucosa" - "mucous membrane of bowel" "intestine mucous membrane" + "mucous membrane of bowel" "intestine mucosa of organ" - "neurectoderm cell" "stratum basalis of endometrium" "pars basalis of endometrium" "organonitrogen compound breakdown" @@ -28202,9 +28206,9 @@ "vein of gonad" "gonad vein" "microtubule assembly" - "downregulation of skeletal muscle development" "down-regulation of skeletal muscle development" "down regulation of skeletal muscle development" + "downregulation of skeletal muscle development" "downregulation of compound eye retinal cell apoptotic process" "down regulation of compound eye retinal cell apoptotic process" "down-regulation of compound eye retinal cell apoptotic process" @@ -28221,18 +28225,18 @@ "neural tube segment" "neuromeres" "neural tube metameric segment" - "smooth muscle tissue of anal triangle" "non-striated muscle of anal part of perineum" "smooth muscle of anal triangle" "anal part of perineum smooth muscle" + "smooth muscle tissue of anal triangle" "involuntary muscle of anal region" "anal part of perineum smooth muscle tissue" "smooth muscle of anal region" "smooth muscle tissue of anal region" "smooth muscle of anal part of perineum" "anal triangle involuntary muscle" - "anal region smooth muscle tissue" "non-striated muscle of anal region" + "anal region smooth muscle tissue" "anal part of perineum non-striated muscle" "anal region non-striated muscle" "anal triangle smooth muscle" @@ -28502,8 +28506,8 @@ "endocardium of cardiac atrium" "cardiac atrium endocardium" "atrial endocardium" - "atrium endocardium" "endocardium of heart atrium" + "atrium endocardium" "up regulation of microtubule polymerization" "up-regulation of microtubule polymerization" "upregulation of microtubule polymerization" @@ -28648,11 +28652,6 @@ "cartilagines bronchiales" "cartilage of bronchi" "bronchial trunk cartilage" - "tela subserosa (hepar)" - "subserosal tissue of liver" - "hepatic subserosa" - "subserous layer of liver" - "tela subserosa hepatis" "small intestinal wall" "small bowel wall" "small bowel anatomical wall" @@ -28664,6 +28663,11 @@ "down regulation of muscle contraction" "downregulation of muscle contraction" "down-regulation of muscle contraction" + "tela subserosa (hepar)" + "subserosal tissue of liver" + "hepatic subserosa" + "subserous layer of liver" + "tela subserosa hepatis" "respiratory system skeletal muscle tissue" "skeletal muscle tissue of apparatus respiratorius" "skeletal muscle of respiratory system" @@ -28751,8 +28755,8 @@ "primary amino compound metabolism" "wall of organ" "pulmonary vasculature development" - "larval sense organ" "myocardial precursor cell differentiation" + "larval sense organ" "endodermal gut" "gut endoderm" "maintenance of vacuolar localization" @@ -28885,8 +28889,8 @@ "female reproductive system fluid/secretion" "regulation of amide breakdown" "regulation of amide degradation" - "regulation of amide catabolism" "regulation of cellular amide catabolic process" + "regulation of amide catabolism" "regulation of amino acid membrane transport" "up-regulation of binding" "upregulation of binding" @@ -28924,8 +28928,8 @@ "camera-type eye skin gland" "vertebrate eye skin gland" "vertebrate eye skin glands set" - "skin glands set of vertebrate eye" "skin gland of camera-type eye" + "skin glands set of vertebrate eye" "skin glands set of camera-type eye" "vascular network" "vertebra neural canal" @@ -28983,12 +28987,12 @@ "hCD5" "body ganglion" "trunk ganglia" + "post-cranial axial skeletal system" "protein localization in actin filament bundle" "protein localisation in actin filament bundle" "protein localisation to actin filament bundle" "cellular secretion" "heterobicyclic compounds" - "post-cranial axial skeletal system" "grey matter" "gray matter of neuraxis" "grey substance" @@ -29054,13 +29058,13 @@ "down-regulation of protein localisation to ciliary membrane" "epidermal stem cell" "portion of heterogeneous tissue" - "arterial endothelium of apparatus respiratorius" "respiratory system artery endothelium" + "arterial endothelium of apparatus respiratorius" "apparatus respiratorius arterial endothelium" "artery endothelium of apparatus respiratorius" "endothelium of artery of apparatus respiratorius" - "apparatus respiratorius endothelium of artery" "artery endothelium of respiratory system" + "apparatus respiratorius endothelium of artery" "apparatus respiratorius artery endothelium" "endothelium of artery of respiratory system" "arterial endothelium of respiratory system" @@ -29130,11 +29134,11 @@ "negative regulation of oxygen metabolism" "liver trabeculae" "blood vessel of heart" + "regulation of catecholamine metabolism" "cardiomyocyte cell development" "cardiac muscle fiber development" "heart muscle cell development" "cardiac muscle fibre development" - "regulation of catecholamine metabolism" "musculo-skeletal system" "down regulation of protein polymerization" "down-regulation of protein polymerization" @@ -29176,8 +29180,6 @@ "chambered heart" "vertebrate heart" "lower jaw future lip" - "buccal cavity" - "cavity of mouth" "bronchial trunk submucosa" "bronchi submucosa" "submucosa of bronchi" @@ -29185,6 +29187,8 @@ "bronchial submucosa" "submucosa of bronchial trunk" "tela submucosa bronchi" + "buccal cavity" + "cavity of mouth" "myocyte" "muscle fiber" "skeletal muscle of esophagus" @@ -29328,8 +29332,8 @@ "anatomical wall of heart ventricle" "cardiac ventricle anatomical wall" "wall of ventricle of heart" - "lower chamber of heart anatomical wall" "ventricle of heart wall" + "lower chamber of heart anatomical wall" "anatomical wall of ventricle of heart" "wall of heart ventricle" "anatomical wall of cardiac ventricle" @@ -29510,11 +29514,11 @@ "downregulation of acinic cell proliferation" "negative regulation of acinous cell proliferation" "down-regulation of acinous cell proliferation" - "regio orbitalis" "appendage-girdle complex" "appendage/girdle complex" "girdle plus limb or fin" "appendage complex" + "regio orbitalis" "muscles of back" "muscle group of back" "set of muscles of back" @@ -29698,7 +29702,7 @@ "organ of respiratory system" "respiratory system organ" "breathing organ" - "down regulation of protein localization in nucleus" + "presynaptic signaling pathway" "down-regulation of protein localization to nucleus" "downregulation of protein localization in nucleus" "downregulation of protein localization in cell nucleus" @@ -29713,7 +29717,7 @@ "downregulation of protein localisation to nucleus" "down-regulation of protein localisation to nucleus" "down-regulation of protein localization in nucleus" - "presynaptic signaling pathway" + "down regulation of protein localization in nucleus" "pharyngeal region" "CD71 (mouse)" "TfR (mouse)" diff --git a/src/ontology/reports/xrefs.tsv b/src/ontology/reports/xrefs.tsv index 22f8d43..2b2a489 100644 --- a/src/ontology/reports/xrefs.tsv +++ b/src/ontology/reports/xrefs.tsv @@ -765,8 +765,8 @@ "EHDAA:4796" "EHDAA:4784" - "UMLS:C1515087" + "UMLS:C1515087" "EMAPA:16096" "SWEETRealm:Aerosol" "EcoLexicon:aerosol" @@ -857,8 +857,8 @@ "SWEETRealm:Forest" "TGN:21641" "FTT:715" - "FTT:717" "LTER:2" + "FTT:717" "EcoLexicon:forest" "https://en.wikipedia.org/wiki/Forest" "Geonames:V.FRST" @@ -1697,6 +1697,7 @@ "UMLS:C1707055" "NCIT:C49213" "BTO:0004401" + "FMA:45615" "BILA:0000083" "VHOG:0000309" "BTO:0000545" @@ -1715,7 +1716,6 @@ "EHDAA2:0000726" "TGMA:0001819" "MA:0000917" - "FMA:45615" "Wikipedia:Neurotransmission" "VHOG:0001678" @@ -2059,8 +2059,8 @@ "MA:0001026" "DHBA:12462" - "BAMS:SOC" "EMAPA:35840" + "BAMS:SOC" "MESH:D065832" "FMA:72247" "BIRNLEX:1307" @@ -2221,8 +2221,8 @@ "EMAPA:37369" "UMLS:C0227900" - "EFO:0000840" "EV:0100077" + "EFO:0000840" "BTO:0000706" "NCIT:C12379" "EMAPA:19252" @@ -2363,8 +2363,8 @@ "FMA:9616" "EMAPA:18172" - "EMAPA:25038" "VHOG:0000139" + "EMAPA:25038" "TAO:0000066" "FBbt:00000123" @@ -2699,8 +2699,8 @@ "FMA:87177" "GC_ID:1" "FMA:16014" - "UMLS:C0226411" + "EMAPA:18620" "NCIT:C33242" @@ -3153,8 +3153,8 @@ "Wikipedia:Golgi_apparatus" - "GAID:279" "NCIT:C12678" + "GAID:279" "FMA:79646" "MESH:D001659" "MA:0001273" @@ -3463,13 +3463,13 @@ "EMAPA:31264" "FMA:18336" "Wikipedia:Phosphorylation" - "EMAPA:16171" - "EHDAA2:0000736" - "EHDAA:364" "EHDAA2:0000031" "EHDAA:583" "EMAPA:16382" "VHOG:0000510" + "EMAPA:16171" + "EHDAA2:0000736" + "EHDAA:364" "Reactome:R-HSA-8875871" "Reactome:R-HSA-3560789" "Reactome:R-HSA-427555" @@ -3565,8 +3565,8 @@ "FMA:295568" "AAO:0011102" "FMA:69065" - "MESH:D001956" + "FMA:16516" "NCIT:C12318" @@ -3585,8 +3585,8 @@ "EMAPA:35360" "Gmelin:533978" "GAID:1178" - "MIAA:0000052" + "MESH:D010949" "EMAPA:35690" "CALOHA:TS-0800" @@ -4216,11 +4216,11 @@ "GC_ID:1" "FMA:84782" "BTO:0000125" + "Wikipedia:Mineral_acid" "ZFA:0005807" "WBbt:0005791" "FMA:14586" "TADS:0000495" - "Wikipedia:Mineral_acid" "MA:0000082" "VHOG:0000604" "ZFA:0005061" @@ -4484,8 +4484,8 @@ "EMAPA:17201" "MESH:D003135" - "NCIT:C12698" "TAO:0005165" + "NCIT:C12698" "ZFA:0005165" "GAID:282" @@ -4670,8 +4670,8 @@ "GAID:173" "MAT:0000453" - "FMA:24028" "GC_ID:1" + "FMA:24028" "BIRNLEX:2665" "FMA:62420" "MA:0003080" @@ -4691,9 +4691,9 @@ "UMLS:C1518306" "BTO:0001766" "Wikipedia:Cellular_differentiation" - "XAO:0003087" "VHOG:0000429" "EHDAA:8041" + "XAO:0003087" "EHDAA2:0002128" "MA:0001908" "FMA:54397" @@ -4859,12 +4859,12 @@ "EHDAA2:0001161" "EMAPA:17567" "Reactome:R-HSA-2142859" + "NCIT:C43617" "EHDAA2:0000743" "MA:0002662" "UMLS:C1708552" "EHDAA:3053" - "NCIT:C43617" "MFMO:0000072" "EHDAA2:0000486" "EMAPA:17844" @@ -4912,8 +4912,8 @@ "Reactome:R-HSA-1299475" "Reactome:R-HSA-5244404" "Reactome:R-HSA-9636375" - "Reactome:R-HSA-5336420" "Reactome:R-HSA-5244428" + "Reactome:R-HSA-5336420" "Reactome:R-HSA-5250616" "Reactome:R-HSA-5246514" "Reactome:R-HSA-5205661" @@ -5080,8 +5080,8 @@ "MESH:D017746" "UMLS:C0206207" - "NCIT:C84388" + "NCIT:C32259" "MA:0001519" "GAID:263" @@ -5130,8 +5130,8 @@ "MA:0001161" "BTO:0001123" - "UMLS:C1516496" "FMA:76621" + "UMLS:C1516496" "NCIT:C34121" "AAO:0010153" "XAO:0003059" @@ -5145,8 +5145,8 @@ "FBbt:00007000" "EHDAA2:0003193" - "UMLS:C0598782" "EMAPA:37283" + "UMLS:C0598782" "NCIT:C61460" "MESH:D005121" "XAO:0000218" @@ -5448,8 +5448,8 @@ "AAO:0010575" - "TAO:0001206" "EMAPA:16178" + "TAO:0001206" "VHOG:0000087" "FMA:293147" @@ -5727,11 +5727,6 @@ "VSAO:0000139" "XAO:0004017" "ZFA:0005620" - - "UMLS:C0225358" - - "BTO:0004838" - "EMAPA:19032" "EMAPA:16589" @@ -5739,6 +5734,11 @@ "FMA:84882" "MA:0000484" + + "UMLS:C0225358" + + "BTO:0004838" + "Wikipedia:Food_additive" "EMAPA:37475" "MA:0000080" @@ -5881,10 +5881,10 @@ "TAO:0000998" "FMA:293859" "XAO:0000053" - "EFO:0003603" "ZFA:0000998" - "EHDAA:655" + "EFO:0003603" "EMAPA:16099" + "EHDAA:655" "KEGG:C01558" "Wikipedia:Bleb_(cell_biology)" "FMA:225251" @@ -5906,9 +5906,9 @@ "KEGG:C00420" "MA:0003220" "EMAPA:32904" + "FMA:82485" "Reactome:R-HSA-9662818" "Reactome:R-HSA-9662747" - "FMA:82485" "FMA:69075" "ZFA:0000254" "FMA:79792" @@ -6240,8 +6240,8 @@ "EHDAA:1719" "UMLS:C0180383" - "AAO:0011028" "EHDAA:1731" + "AAO:0011028" "EHDAA:1737" "EHDAA:1725" "NCIT:C61572" @@ -6451,8 +6451,8 @@ "UMLS:C0459556" "EMAPA:16258" - "RETIRED_EHDAA2:0001205" "EHDAA:534" + "RETIRED_EHDAA2:0001205" "VHOG:0000592" "EFO:0003498" "ZFA:0000133" @@ -6744,15 +6744,6 @@ "EHDAA2:0001962" "UMLS:C0042459" "galen:SuperiorVenaCava" - "OGES:000027" - "XAO:1000093" - "BILS:0000113" - "ZFS:0000044" - "OGES:000026" - "EV:0300064" - "MmusDv:0000110" - "EV:0300070" - "MIAA:0000403" "EV:0100072" "EFO:0000841" @@ -6775,6 +6766,15 @@ "FMA:7200" "XAO:0000130" + "OGES:000027" + "XAO:1000093" + "BILS:0000113" + "ZFS:0000044" + "OGES:000026" + "EV:0300064" + "MmusDv:0000110" + "EV:0300070" + "MIAA:0000403" "FMA:84646" "UniProtKB:P06729" "GC_ID:1" @@ -6795,8 +6795,6 @@ "EMAPA:16261" "EMAPA:37576" "MA:0001821" - "MA:0001719" - "FMA:62016" "ZFA:0005621" "EMAPA:35179" "MA:0002780" @@ -6810,11 +6808,13 @@ "FMA:224804" "galen:BoneTissue" "CALOHA:TS-2011" + "MA:0001719" + "FMA:62016" "BTO:0003080" "MA:0002532" "FMA:12273" - "MAT:0000500" + "MAT:0000500" "ncithesaurus:Pleural_Fluid" "FBbt:00000004" "AAO:0010687" @@ -6830,8 +6830,8 @@ "EFO:0000888" "MESH:D018482" "GAID:141" - "AAO:0011099" "MIAA:0000302" + "AAO:0011099" "EMAPA:35988" "CALOHA:TS-0933" "XAO:0000174" @@ -6927,6 +6927,15 @@ "UMLS:C1708644" "FMA:15654" + "NCIT:C32971" + "MA:0002032" + "FMA:50873" + + "galen:LeftPulmonaryArtery" + + "EMAPA:37097" + + "UMLS:C0923925" "VHOG:0001045" "CALOHA:TS-1061" "MA:0001862" @@ -6939,15 +6948,6 @@ "EHDAA:5007" "FMA:62015" "NCIT:C33797" - "NCIT:C32971" - "MA:0002032" - "FMA:50873" - - "galen:LeftPulmonaryArtery" - - "EMAPA:37097" - - "UMLS:C0923925" "AAO:0011084" "TAO:0007016" "ZFA:0007016" @@ -7804,14 +7804,14 @@ "FMA:5898" "EHDAA2:0004108" "EMAPA:32918" + "TAO:0001460" + "EFO:0003689" + "ZFA:0001460" "MA:0002514" "UMLS:C0227179" "NCIT:C52555" "FMA:79662" - "TAO:0001460" - "EFO:0003689" - "ZFA:0001460" "BTO:0004733" "MA:0002833" "FMA:84428" @@ -7912,9 +7912,9 @@ "BTO:0000087" "MA:0000704" "EMAPA:36503" - "FBbt:00005812" "EMAPA:17748" "FMA:37347" + "FBbt:00005812" "EHDAA2:0000189" @@ -7939,8 +7939,8 @@ "EFO:0001402" "UMLS:C0040996" - "MESH:D014276" "EHDAA:3738" + "MESH:D014276" "AAO:0010470" "MBA:901" "NCIT:C12806" @@ -7977,13 +7977,12 @@ "EFO:0004245" "GAID:917" "TAO:0001238" - "EMAPA:16841" - "UMLS:C0010672" "MA:0000355" "EHDAA2:0000333" + "UMLS:C0010672" "TAO:0005166" "NCIT:C32421" "EHDAA:3045" @@ -7993,6 +7992,7 @@ "galen:CysticDuct" "ZFA:0005166" "FMA:14539" + "EMAPA:16841" "EMAPA:18662" "MA:0003107" @@ -8059,8 +8059,8 @@ "VHOG:0001037" "MA:0003219" "EHDAA2:0001594" - "EMAPA:17898" "CALOHA:TS-2066" + "EMAPA:17898" "EMAPA:36299" "NCIT:C33818" @@ -8091,15 +8091,15 @@ "EMAPA:16046" "BTO:0001840" "VHOG:0000979" - "EHDAA2:0002091" "EHDAA:56" + "EHDAA2:0002091" "Wikipedia:Glycosaminoglycan" "KEGG:C02545" "EMAPA:16777" "EHDAA2:0002205" "NCIT:C33881" - "UMLS:C0225776" + "UMLS:C0225776" "VHOG:0001496" "FMA:9734" "MA:0002489" @@ -8228,13 +8228,13 @@ "TAO:0002233" "ZFA:0001724" "MetaCyc:PHENOLDEG-PWY" - "VHOG:0000107" "AAO:0011017" "EFO:0003647" "TAO:0001204" "XAO:0000205" "ZFA:0001204" + "VHOG:0000107" "EMAPA:37946" "FMA:12224" "Reactome:R-HSA-390347" @@ -8730,9 +8730,9 @@ "EMAPA:16773" "MA:0000055" "EMAPA:16774" - "EHDAA2:0001475" "BTO:0004422" + "EHDAA2:0001475" "GAID:95" "MESH:D035422" "UMLS:C0178802" @@ -8847,8 +8847,8 @@ "VHOG:0000328" "NCIT:C12868" "EMAPA:17321" - "galen:RightAtrium" + "XAO:0003192" "MA:0000075" "BTO:0001703" @@ -9008,8 +9008,8 @@ "TAO:0000279" "VHOG:0000559" "XAO:0000057" - "EMAPA:16752" "AAO:0011086" + "EMAPA:16752" "EMAPA:16189" "EFO:0001982" "ZFA:0005386" @@ -9195,8 +9195,8 @@ "AEO:0000145" "BTO:0001393" "XAO:0003046" - "TAO:0000393" + "EMAPA:18045" "Wikipedia:Micronutrient" "EHDAA:4442" @@ -9500,13 +9500,13 @@ "FMA:18149" "BTO:0003157" - "FBbt:00004873" "EMAPA:35747" "VHOG:0001210" "TAO:0007063" "ZFA:0007063" "EHDAA:362" "EHDAA2:0001628" + "FBbt:00004873" "FMA:62774" "MA:0000522" @@ -9921,8 +9921,8 @@ "UMLS:C0227518" "NCIT:C32732" - "MA:0002494" + "EMAPA:35499" "FMA:14471" @@ -10058,6 +10058,7 @@ "PIRSF:PIRSF028749" "FMA:268736" "GC_ID:1" + "UMLS:C1518263" "EMAPA:17171" "EHDAA:4763" "EHDAA2:0001253" @@ -10073,7 +10074,6 @@ "EMAPA:18590" "BTO:0000929" "ZFA:0000046" - "UMLS:C1518263" "VHOG:0001006" "EMAPA:16881" "EHDAA:696" @@ -10127,7 +10127,6 @@ "XAO:0000020" "BAMS:SP" - "FMA:45618" "XAO:0000104" "MA:0001527" @@ -10144,6 +10143,7 @@ "NCIT:C34188" "EMAPA:16715" "EHDAA2:0000779" + "FMA:45618" "galen:Cavity" "MA:0002447" "EMAPA:37442" @@ -10298,8 +10298,8 @@ "Wikipedia:Nucleolus" "NIF_Subcellular:sao1820400233" "CALOHA:TS-1277" - "MA:0000311" "XAO:0003076" + "MA:0000311" "MESH:D002574" "galen:CervicalVertebra" @@ -10679,6 +10679,12 @@ "AEO:0000119" "ZFA:0007039" "TAO:0007039" + "FMA:16515" + "ncithesaurus:Peritoneal_Fluid" + "BTO:0001031" + "EMAPA:35683" + + "MA:0002531" "FMA:74657" "BTO:0000634" "TAO:0000368" @@ -10688,12 +10694,6 @@ "EMAPA:37504" "galen:Integument" "AAO:0000239" - "FMA:16515" - "ncithesaurus:Peritoneal_Fluid" - "BTO:0001031" - "EMAPA:35683" - - "MA:0002531" "BTO:0004577" "GC_ID:1" "FMA:83410" @@ -11178,8 +11178,8 @@ "GC_ID:1" "MA:0002499" "NCIT:C33342" - "FMA:17523" + "FMA:17523" "UMLS:C0227514" @@ -12229,8 +12229,8 @@ "MA:0003153" "RETIRED_EHDAA2:0000160" - "TAO:0001954" "EMAPA:18167" + "TAO:0001954" "EHDAA:5982" "FMA:9690" "EHDAA2:0004737" @@ -12349,8 +12349,8 @@ "EHDAA2:0000598" "VHOG:0000169" - "MA:0000275" "MIAA:0000141" + "MA:0000275" "XAO:0000008" "AAO:0010348" "EMAPA:17838" @@ -12506,8 +12506,8 @@ "BM:V" "BTO:0001074" "UMLS:C0040999" - "CALOHA:TS-2077" "EMAPA:35883" + "CALOHA:TS-2077" "MA:0001028" @@ -12572,9 +12572,9 @@ "MA:0000029" "GAID:16" "CALOHA:TS-1249" + "FMA:263082" "MA:0001803" "EMAPA:37568" - "FMA:263082" "FMA:75621" "MA:0001854" "EMAPA:37552" @@ -12671,7 +12671,6 @@ "galen:AbdominalCavity" "EMAPA:36505" - "TAO:0000113" "FMA:76622" "EHDAA2:0000732" "EMAPA_RETIRED:16269" @@ -12680,6 +12679,7 @@ "EMAPA:16098" "EFO:0003492" "VHOG:0000332" + "TAO:0000113" "Reactome:R-HSA-2161500" "Reactome:R-HSA-549304" "Reactome:R-HSA-549279" @@ -12938,8 +12938,8 @@ "AAO:0010339" "MIAA:0000296" "XAO:0003025" - "FMA:7181" "EMAPA:31857" + "FMA:7181" "TAO:0001115" "UMLS:C0460005" "MAT:0000296" @@ -13089,9 +13089,9 @@ "MIAA:0000344" "EFO:0000901" "TAO:0001573" + "FMA:302077" "Wikipedia:Secretion" "FMA:63071" - "FMA:302077" "VHOG:0001768" "EHDAA2_RETIRED:0004658" @@ -13188,8 +13188,8 @@ "EFO:0002525" "MA:0002569" - "EHDAA2:0000597" + "EMAPA:17703" "VHOG:0001546" @@ -13257,10 +13257,10 @@ "FMA:62852" "MESH:D007962" "CALOHA:TS-0549" + "EHDAA2:0001019" "VHOG:0000802" "EHDAA:7999" "EMAPA:35516" - "EHDAA2:0001019" "TAO:0007037" "AAO:0011082" "XAO:0000250" @@ -13319,6 +13319,14 @@ "NCIT:C12727" "BTO:0000562" "EHDAA2:0001020" + "MA:0001837" + "UMLS:C0225601" + "NCIT:C49214" + + + "BTO:0002108" + "FMA:62653" + "EMAPA:37449" "TGMA:0000102" "NCIT:C12421" @@ -13341,14 +13349,6 @@ "EV:0100057" "FMA:20292" "EMAPA:17411" - "MA:0001837" - "UMLS:C0225601" - "NCIT:C49214" - - - "BTO:0002108" - "FMA:62653" - "EMAPA:37449" "BTO:0000902" "WBbt:0003675" "BTO:0000888" @@ -13538,8 +13538,8 @@ "TE:E5.11.2.0.0.0.4" "VHOG:0000085" - "EFO:0003489" "AAO:0011006" + "EFO:0003489" "XAO:0000067" "EHDAA:207" "NCIT:C34113" @@ -13633,10 +13633,10 @@ "EHDAA2:0003122" "AEO:0000122" "FMA:9641" - "galen:MuscleTissue" "EMAPA:32715" - "CALOHA:TS-0642" + "galen:MuscleTissue" "MESH:D009132" + "CALOHA:TS-0642" "VSAO:0000130" @@ -13694,6 +13694,9 @@ "TAO:0000568" "AAO:0000468" "ZFA:0000568" + "FMA:7182" + "VSAO:0000214" + "EMAPA:37858" "NCIT:C12401" "UMLS:C1280202" "EHDAA2:0000484" @@ -13712,9 +13715,6 @@ "XAO:0000179" - "FMA:7182" - "VSAO:0000214" - "EMAPA:37858" "FMA:71291" "FMA:27360" @@ -13768,7 +13768,6 @@ "EFO:0003497" "TAO:0000131" "ZFA:0000131" - "NCIT:C12948" "ZFA:0005171" "FBbt:00100314" @@ -13779,11 +13778,13 @@ "TAO:0005171" "UMLS:C0687028" + "NCIT:C12948" "FMA:30320" "BTO:0004297" "FMA:256157" "MA:0001520" "EMAPA:32683" + "Wikipedia:Programmed_cell_death" "EFO:0000980" "MESH:D004717" @@ -13801,7 +13802,6 @@ "NCIT:C12313" "BTO:0001422" - "Wikipedia:Programmed_cell_death" "PMID:30257078" "PMID:23020233" "GC_ID:1" @@ -13841,8 +13841,8 @@ "GAID:477" - "EMAPA:18608" "FMA:68109" + "EMAPA:18608" "NCIT:C32230" diff --git a/src/templates/RBO_classes.owl b/src/templates/RBO_classes.owl index 27e8152..91df59f 100644 --- a/src/templates/RBO_classes.owl +++ b/src/templates/RBO_classes.owl @@ -94,6 +94,12 @@ + + + + + + @@ -244,6 +250,12 @@ + + + + + + @@ -871,7 +883,7 @@ Radiation response modifiers that are peptides. - Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 + Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 peptide radiation response modifier @@ -892,7 +904,7 @@ A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. - Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 + Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 nuclear industry worker @@ -1244,7 +1256,7 @@ - A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. + A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. occupational role @@ -2816,15 +2828,7 @@ A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. - Heavy ion radiation has several notable characteristics and contexts: - -High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. - -Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. - -Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. - -In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. + Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -3304,7 +3308,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 + The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to radiation @@ -3683,7 +3687,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2�7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. + A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products. charcoal cannister radon dosimeter @@ -3705,7 +3709,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects� internal structure. + Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure. research reactor Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development research nuclear reactor @@ -3882,8 +3886,7 @@ In common use, the distinction between heavy ions and light ions is somewhat fle - A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation�typically more than 1 Gray (Gy)�over a short period (minutes to hours). -Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1�10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5�20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (?20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. + A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis. acute radiation sickness, ARS Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome acute radiation syndrome @@ -3989,7 +3992,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The radiation environment consisting of the water at the surface of the Earth, including all of Earth�s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. + The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle. earth hydrosphere radiation environment @@ -4005,6 +4008,51 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati + + + + + The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size + ionization cluster size + + + + + + + + + A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle. + In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter." + ionisation cluster size measurement datum + ionization cluster size measurement datum + + + + + + + + + The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium." Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity. + Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf + particle track penumbra + + + + + + + + + In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle. + particle track core + + + + @@ -4030,7 +4078,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers - See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale nanodosimetry assay @@ -4042,7 +4090,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers - See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. + See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale microdosimetry assay @@ -4527,7 +4575,7 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth�s magnetic field. + The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field. http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 https://www.swpc.noaa.gov/phenomena/earths-magnetosphere geomagnetosphere @@ -4615,10 +4663,10 @@ Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fati - A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells�cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. + A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction. Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies. http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 - See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients� treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 + See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4 senolytic