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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Measurement Method Ontology Resource Report Resource Website |
Measurement Method Ontology (RRID:SCR_003373) | MMO | data or information resource, ontology, controlled vocabulary | An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. | obo, phenotype, clinical |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO |
PMID:22654893 | Free, Available for download, Freely available | nlx_157468 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo |
SCR_003373 | 2026-02-17 10:00:16 | 0 | ||||||
|
FMA Resource Report Resource Website 1+ mentions |
FMA (RRID:SCR_003379) | FMA | ontology, software application, data or information resource, data processing software, controlled vocabulary, data analysis software, database, software resource | A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model. | anatomy, informatics, model, neuroanatomy, protg, reference, standard, structural, taxonomy, owl, phenotype |
is listed by: BioPortal is related to: T3DB is related to: HIV Brain Sequence Database is related to: CELDA Ontology has parent organization: University of Washington; Seattle; USA |
RSNA-NIBIB ; University of Washington; Washington; USA ; Murdock Charitable Trust ; Microsoft ; Intel Corporation ; NLM LM006822; NLM LM06316; NLM contract LM03528; NHLBI HL08770 |
PMID:18688289 PMID:18360535 PMID:16779026 |
Free, Freely available | nif-0000-00066 | http://bioportal.bioontology.org/ontologies/FMA | SCR_003379 | Foundational Model of Anatomy Ontology, Foundational Model of Anatomy | 2026-02-17 10:00:16 | 8 | ||||
|
PharmGKB Ontology Resource Report Resource Website |
PharmGKB Ontology (RRID:SCR_003529) | pharmgkb-owl | data or information resource, ontology, controlled vocabulary | An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner. | owl, medical, drug |
is listed by: BioPortal is related to: Comparative Toxicogenomics Database (CTD) is related to: DrugBank is related to: MeSH is related to: Human Disease Ontology has parent organization: PharmGKB |
PMID:11928517 | New BSD License | nlx_157636 | SCR_003529 | 2026-02-17 10:00:21 | 0 | |||||||
|
Malaria Ontology Resource Report Resource Website |
Malaria Ontology (RRID:SCR_003369) | IDOMAL | data or information resource, ontology, controlled vocabulary | An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO). | obo, health, pathological, clinical, epidemiological, biological, intervention |
is listed by: BioPortal is listed by: OBO has parent organization: AnoBase: An Anopheles database |
Malaria | Free, Available for download, Freely available | nlx_157464 | http://purl.obolibrary.org/obo/idomal.obo http://anobase.vectorbase.org/idomal/IDOMAL.obo |
SCR_003369 | 2026-02-17 10:00:16 | 0 | ||||||
|
Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | data or information resource, ontology, controlled vocabulary | Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles. | adverse event, health, pathological, molecular, cellular, organismal, multi-organismal |
is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Ontology of Vaccine Adverse Events has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:25093068 | Free, Freely available | nlx_157522 | http://purl.bioontology.org/ontology/OAE http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl |
SCR_003428 | 2026-02-17 10:00:10 | 2 | ||||||
|
Minimal Anatomical Terminology Resource Report Resource Website |
Minimal Anatomical Terminology (RRID:SCR_003385) | MAT | data or information resource, ontology, controlled vocabulary | An ontology of minimal set of terms for anatomy. | obo, anatomy, organismal, ontology |
is listed by: BioPortal is listed by: OBO has parent organization: eMouseAtlas |
Free, Available for download, Freely available | nlx_157480 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo | SCR_003385 | 2026-02-17 10:00:10 | 0 | |||||||
|
Experimental Factor Ontology Resource Report Resource Website 10+ mentions |
Experimental Factor Ontology (RRID:SCR_003574) | EFO | data or information resource, ontology, controlled vocabulary | An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome. | gene expression, owl, experimental factor, disease, cell line, cell type, anatomy, gold standard |
is listed by: BioPortal is related to: ArrayExpress is related to: ArrayExpress is related to: Gene Expression Atlas has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory ; European Union FELICS contract 021902; European Union EMERALD LSHG-CT-2006-037686; European Union Gen2Phen contract 200754 |
PMID:20200009 | The community can contribute to this resource | nlx_11363 | SCR_003574 | 2026-02-17 10:00:13 | 16 | ||||||
|
Adverse Event Reporting Ontology Resource Report Resource Website 1+ mentions |
Adverse Event Reporting Ontology (RRID:SCR_003571) | AERO | data or information resource, ontology, controlled vocabulary | An ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. | owl, rdf, aero, bfo, ogms, iao, adverse event, clinician, health |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
New BSD License (code), Creative Commons Attribution License (content) | nlx_11209 | http://bioportal.bioontology.org/ontologies/1580 http://www.obofoundry.org/cgi-bin/detail.cgi?id=AERO http://purl.obolibrary.org/obo/aero.owl http://purl.obolibrary.org/obo/aero |
SCR_003571 | 2026-02-17 10:00:22 | 1 | |||||||
|
Rat Strain Ontology Resource Report Resource Website 1+ mentions |
Rat Strain Ontology (RRID:SCR_003449) | data or information resource, ontology, controlled vocabulary | Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. | rat strain, obo, gene, pathway, biological process, metabolic, regulatory, signaling, drug, disease, metabolic pathway, regulatory pathway, signaling pathway, drug pathway, disease pathway, gene |
is listed by: BioPortal is listed by: OBO has parent organization: Rat Genome Database (RGD) |
Free, Freely available | nlx_157569, nlx_157544, SCR_003473 | http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001 http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457 http://purl.bioontology.org/ontology/RS ftp://rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo |
SCR_003449 | 2026-02-17 10:00:19 | 1 | ||||||||
|
Ontology of Vaccine Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Vaccine Adverse Events (RRID:SCR_003442) | OVAE | data or information resource, ontology, controlled vocabulary | A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO). | owl, vaccine adverse event, vaccine, adverse event |
uses: Vaccine Ontology is listed by: BioPortal is listed by: OBO is related to: Ontology of Adverse Events has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:24279920 | Free, Freely available | nlx_157538 | http://purl.bioontology.org/ontology/OVAE http://ovae.googlecode.com/svn/trunk/src/ontology/ovae.owl |
SCR_003442 | 2026-02-17 10:00:00 | 1 | ||||||
|
NCI Thesaurus Resource Report Resource Website 1+ mentions |
NCI Thesaurus (RRID:SCR_003563) | NCIt | data or information resource, ontology, controlled vocabulary | A reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP). | thesaurus, clinical, treatment, prevention, biomedical, owl, health, drug, chemotherapy |
is listed by: OBO is listed by: BioPortal is related to: NCI Metathesaurus is related to: OnEx - Ontology Evolution Explorer has parent organization: National Cancer Institute |
Cancer | See license, http://evs.nci.nih.gov/ftp1/NCI_Thesaurus/NCI_THESAURUS_license.txt | nlx_157698 | ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ https://cabig.nci.nih.gov/concepts/EVS/ https://wiki.nci.nih.gov/display/EVS/NCI+Thesaurus+%28NCIt%29 http://nciterms.nci.nih.gov http://purl.bioontology.org/ontology/NCIT |
http://ncicb.nci.nih.gov/core/EVS | SCR_003563 | ncithesaurus | 2026-02-17 10:00:02 | 9 | ||||
|
Ontology of Medically Related Social Entities Resource Report Resource Website |
Ontology of Medically Related Social Entities (RRID:SCR_003439) | OMRSE | data or information resource, ontology, controlled vocabulary | An ontology covering the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital, etc.) | owl, medicine, health care, demographic |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157534 | http://purl.bioontology.org/ontology/OMRSE http://purl.obolibrary.org/obo/omrse.owl |
SCR_003439 | 2026-02-17 10:00:19 | 0 | |||||||
|
Medical Dictionary for Regulatory Activities Resource Report Resource Website 1+ mentions |
Medical Dictionary for Regulatory Activities (RRID:SCR_003751) | MEDDRA | data or information resource, ontology, controlled vocabulary | Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA) | umls | is listed by: BioPortal | nlx_157471 | SCR_003751 | 2026-02-17 10:00:06 | 2 | |||||||||
|
Mosquito Insecticide Resistance Ontology Resource Report Resource Website |
Mosquito Insecticide Resistance Ontology (RRID:SCR_003864) | MIRO | data or information resource, ontology, controlled vocabulary | Application ontology for entities related to insecticide resistance in mosquitos | obo | is listed by: BioPortal | nlx_157486 | SCR_003864 | 2026-02-17 10:00:07 | 0 | |||||||||
|
Minimal Standard Terminology of Digestive Endoscopy - French Resource Report Resource Website |
Minimal Standard Terminology of Digestive Endoscopy - French (RRID:SCR_003830) | MSTDE-FRE | data or information resource, ontology, controlled vocabulary | Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001 | umls | is listed by: BioPortal | nlx_157484 | SCR_003830 | Minimal Standard Terminology of Digestive Endoscopy French | 2026-02-17 10:00:29 | 0 | ||||||||
|
Medical Diagnostic Categories - Diagnosis Related Groups Resource Report Resource Website |
Medical Diagnostic Categories - Diagnosis Related Groups (RRID:SCR_003725) | MDCDRG | data or information resource, ontology, controlled vocabulary | Ontology of Medical Diagnostic Categories-Diagnosis Related Groups | owl | is listed by: BioPortal | nlx_157470 | SCR_003725 | 2026-02-17 10:00:27 | 0 | |||||||||
|
Mouse Gross Anatomy and Development Ontology Resource Report Resource Website |
Mouse Gross Anatomy and Development Ontology (RRID:SCR_003891) | EMAP | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). | obo | is listed by: BioPortal | nlx_157488 | SCR_003891 | 2026-02-17 10:00:20 | 0 | |||||||||
|
Systematized Nomenclature of Medicine - Clinical Terms Resource Report Resource Website 1+ mentions |
Systematized Nomenclature of Medicine - Clinical Terms (RRID:SCR_003915) | SNOMEDCT | data or information resource, ontology, controlled vocabulary | Ontology of SNOMED (Systematized Nomenclature of Medicine) clinical terms. | umls | is listed by: BioPortal | nlx_157603 | SCR_003915 | 2026-02-17 10:00:31 | 2 | |||||||||
|
Mouse Pathology Ontology Resource Report Resource Website |
Mouse Pathology Ontology (RRID:SCR_003950) | MPATH | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes | obo |
is listed by: BioPortal has parent organization: Pathbase |
nlx_157489 | SCR_003950 | 2026-02-17 10:00:29 | 0 | |||||||||
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NHS Quality Indicators Resource Report Resource Website 1+ mentions |
NHS Quality Indicators (RRID:SCR_004005) | NHSQI2009 | data or information resource, ontology, controlled vocabulary | Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable. | protege | is listed by: BioPortal | nlx_157491 | SCR_004005 | 2026-02-17 10:00:22 | 1 |
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