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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FlyBase Controlled Vocabulary Resource Report Resource Website |
FlyBase Controlled Vocabulary (RRID:SCR_003318) | FB-CV, FBcv | controlled vocabulary, data or information resource | A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them. | obo |
is listed by: BioPortal is listed by: OBO has parent organization: FlyBase |
Free, Available for download, Freely available | nlx_157408 | http://sourceforge.net/p/fbcv/code-0/HEAD/tree/releases/latest/fbcv-simple.obo?format=raw | SCR_003318 | 2026-08-29 11:21:29 | 0 | |||||||
|
Fission Yeast Phenotype Ontology Resource Report Resource Website |
Fission Yeast Phenotype Ontology (RRID:SCR_003315) | FYPO | controlled vocabulary, data or information resource, ontology | A formal ontology of phenotypes observed in fission yeast that is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions. | obo, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: PomBase |
Free, Available for download, Freely available | nlx_157405 | https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/releases/latest/fypo.obo?format=raw | https://sourceforge.net/apps/trac/pombase/wiki/FissionYeastPhenotypeOntology | SCR_003315 | 2026-08-29 11:21:29 | 0 | ||||||
|
Population and Community Ontology Resource Report Resource Website |
Population and Community Ontology (RRID:SCR_003462) | PCO | controlled vocabulary, data or information resource, ontology | An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO). | owl, community, population, biomedical, evolution, ecology |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
New BSD License, (Code) | nlx_157557 | http://purl.bioontology.org/ontology/PCO, http://purl.obolibrary.org/obo/pco.owl | SCR_003462 | 2026-08-29 11:21:34 | 0 | |||||||
|
Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | controlled vocabulary, data or information resource | A structured controlled vocabulary for the representation of plant environmental conditions. | obo, environment, gene expression, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157554 | http://purl.bioontology.org/ontology/PECO, http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo, http://www.gramene.org/plant_ontology/index.html#eo | SCR_003460 | 2026-08-29 11:21:57 | 0 | ||||||||
|
PharmGKB Ontology Resource Report Resource Website |
PharmGKB Ontology (RRID:SCR_003529) | pharmgkb-owl | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:34 | 0 | |||||||
|
Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:33 | 2 | ||||||
|
Rat Strain Ontology Resource Report Resource Website 1+ mentions |
Rat Strain Ontology (RRID:SCR_003449) | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:32 | 1 | ||||||||
|
Ontology of Vaccine Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Vaccine Adverse Events (RRID:SCR_003442) | OVAE | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:32 | 1 | ||||||
|
Ontology of Medically Related Social Entities Resource Report Resource Website |
Ontology of Medically Related Social Entities (RRID:SCR_003439) | OMRSE | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:33 | 0 | |||||||
|
Medical Dictionary for Regulatory Activities Resource Report Resource Website 1+ mentions |
Medical Dictionary for Regulatory Activities (RRID:SCR_003751) | MEDDRA | controlled vocabulary, data or information resource, ontology | Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA) | umls | is listed by: BioPortal | nlx_157471 | SCR_003751 | 2026-08-29 11:21:59 | 4 | |||||||||
|
Experimental Factor Ontology Resource Report Resource Website 10+ mentions |
Experimental Factor Ontology (RRID:SCR_003574) | EFO | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:37 | 19 | ||||||
|
Adverse Event Reporting Ontology Resource Report Resource Website 1+ mentions |
Adverse Event Reporting Ontology (RRID:SCR_003571) | AERO | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:37 | 1 | |||||||
|
Medical Diagnostic Categories - Diagnosis Related Groups Resource Report Resource Website |
Medical Diagnostic Categories - Diagnosis Related Groups (RRID:SCR_003725) | MDCDRG | controlled vocabulary, data or information resource, ontology | Ontology of Medical Diagnostic Categories-Diagnosis Related Groups | owl | is listed by: BioPortal | nlx_157470 | SCR_003725 | 2026-08-29 11:21:37 | 0 | |||||||||
|
NCI Thesaurus Resource Report Resource Website 10+ mentions |
NCI Thesaurus (RRID:SCR_003563) | NCIt | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:58 | 10 | ||||
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Mosquito Insecticide Resistance Ontology Resource Report Resource Website |
Mosquito Insecticide Resistance Ontology (RRID:SCR_003864) | MIRO | controlled vocabulary, data or information resource, ontology | Application ontology for entities related to insecticide resistance in mosquitos | obo | is listed by: BioPortal | nlx_157486 | SCR_003864 | 2026-08-29 11:21:46 | 0 | |||||||||
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Mouse Gross Anatomy and Development Ontology Resource Report Resource Website |
Mouse Gross Anatomy and Development Ontology (RRID:SCR_003891) | EMAP | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). | obo | is listed by: BioPortal | nlx_157488 | SCR_003891 | 2026-08-29 11:21:41 | 0 | |||||||||
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Minimal Standard Terminology of Digestive Endoscopy - French Resource Report Resource Website |
Minimal Standard Terminology of Digestive Endoscopy - French (RRID:SCR_003830) | MSTDE-FRE | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-29 11:21:44 | 0 | ||||||||
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BIRNLex Resource Report Resource Website |
BIRNLex (RRID:SCR_007326) | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Lexicon that provides entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. These sources may include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer''s disease or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN scientists in the context of their research, including common terms for neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance required for large-scale data integration across disparate experimental studies.The BIRNLex offers well defined terms from several domains of importance to neuroimaging across scales. | controlled vocabulary, owl |
is listed by: BioPortal has parent organization: Drexel University College of Medicine; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00199 | http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/ | SCR_007326 | BIRNLex | 2026-08-29 11:22:55 | 0 | |||||||
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Computational Neuroscience Ontology Resource Report Resource Website |
Computational Neuroscience Ontology (RRID:SCR_007289) | CNO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. | owl | is listed by: BioPortal | Creative Commons Attribution License, v3 Unported | nlx_157372 | SCR_007289 | 2026-08-29 11:23:07 | 0 | ||||||||
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Solanaceae Phenotype Ontology Resource Report Resource Website |
Solanaceae Phenotype Ontology (RRID:SCR_007832) | SPTO | controlled vocabulary, data or information resource, ontology | Ontology for Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance. | obo | is listed by: BioPortal | nlx_157592 | SCR_007832 | 2026-08-29 11:23:03 | 0 |
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