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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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OMIM Resource Report Resource Website 5000+ mentions |
OMIM (RRID:SCR_006437) | OMIM, MIM | database, data or information resource, catalog | Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources. | gene, genetics, phenotype, genotype, genetic loci, mutation, clinical, trait, disorder, umls, ontology, gold standard, FASEB list |
is used by: Human Phenotype Ontology is used by: NIF Data Federation is used by: MitoMiner is used by: Schizo-Pi is used by: GEMINI is used by: MARRVEL is used by: HmtPhenome is listed by: BioPortal is listed by: OMICtools is related to: HomoloGene is related to: TopoSNP is related to: phenomeNET is related to: Integrated Gene-Disease Interaction is related to: OMIA - Online Mendelian Inheritance in Animals is related to: Europhenome Mouse Phenotyping Resource is related to: Homophila is related to: Biomine is related to: MalaCards is related to: PhenoTips is related to: KOBAS is related to: Integrated Manually Extracted Annotation is related to: aGEM is related to: biomaRt has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: NCBI works with: Human Mouse Disease Connection works with: Database of genes related to Repeat Expansion Diseases |
Genetic disorder, Mendelian disorder, Developmental disorder | PMID:22477700 PMID:22470145 PMID:21472891 PMID:19728286 PMID:18842627 PMID:18428346 PMID:17642958 PMID:17357067 PMID:15608251 PMID:15360913 PMID:11752252 PMID:10845565 PMID:10612823 PMID:9805561 PMID:7937048 PMID:1867277 |
Restricted | nif-0000-03216, r3d100010416, OMICS_00278 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim, http://www.ncbi.nlm.nih.gov/Omim/, http://purl.bioontology.org/ontology/OMIM, https://doi.org/10.17616/R3188W | SCR_006437 | Online Mendelian Inheritance in Man, OMIM - Online Mendelian Inheritance in Man, MIM, The Online Mendelian Inheritance in Man Morbid Map | 2026-08-08 11:58:58 | 7365 | ||||
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LexGrid Resource Report Resource Website 1+ mentions |
LexGrid (RRID:SCR_006627) | LexGrid | software resource | LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, parse, ontology |
is listed by: BioPortal is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: European Bioinformatics Institute has parent organization: National Cancer Institute |
NIH ; Cancer Biomedical Informatics Grid ; NLM LM07319 |
PMID:19261933 | Free for academic use | nlx_149194 | http://www.lexgrid.org/ | SCR_006627 | Lexical Grid | 2026-08-08 11:58:47 | 1 | ||||
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Dictyostelium Discoideum Anatomy Ontology Resource Report Resource Website |
Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) | DDANAT | data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. | obo, anatomy, organismal, cellular |
is listed by: BioPortal is listed by: OBO has parent organization: Dictyostelium discoideum genome database |
Free, Available for download, Freely available | nlx_157387 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo | SCR_003309 | Dictyostelium discoideum anatomy | 2026-08-08 11:57:57 | 0 | ||||||
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FlyBase Controlled Vocabulary Resource Report Resource Website |
FlyBase Controlled Vocabulary (RRID:SCR_003318) | FB-CV, FBcv | data or information resource, controlled vocabulary | 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 | 2026-08-08 11:57:57 | 0 | |||||||
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Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | data or information resource, controlled vocabulary | 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 | 2026-08-08 11:58:05 | 0 | ||||||||
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Population and Community Ontology Resource Report Resource Website |
Population and Community Ontology (RRID:SCR_003462) | PCO | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:44 | 0 | |||||||
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PharmGKB Ontology Resource Report Resource Website |
PharmGKB Ontology (RRID:SCR_003529) | pharmgkb-owl | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:45 | 0 | |||||||
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Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:47 | 2 | ||||||
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Experimental Factor Ontology Resource Report Resource Website 10+ mentions |
Experimental Factor Ontology (RRID:SCR_003574) | EFO | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:45 | 19 | ||||||
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Adverse Event Reporting Ontology Resource Report Resource Website 1+ mentions |
Adverse Event Reporting Ontology (RRID:SCR_003571) | AERO | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:46 | 1 | |||||||
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Medical Diagnostic Categories - Diagnosis Related Groups Resource Report Resource Website |
Medical Diagnostic Categories - Diagnosis Related Groups (RRID:SCR_003725) | MDCDRG | data or information resource, controlled vocabulary, ontology | Ontology of Medical Diagnostic Categories-Diagnosis Related Groups | owl | is listed by: BioPortal | nlx_157470 | SCR_003725 | 2026-08-09 09:03:47 | 0 | |||||||||
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Rat Strain Ontology Resource Report Resource Website 1+ mentions |
Rat Strain Ontology (RRID:SCR_003449) | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:44 | 1 | ||||||||
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Ontology of Vaccine Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Vaccine Adverse Events (RRID:SCR_003442) | OVAE | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:44 | 1 | ||||||
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NCI Thesaurus Resource Report Resource Website 10+ mentions |
NCI Thesaurus (RRID:SCR_003563) | NCIt | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:46 | 10 | ||||
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Ontology of Medically Related Social Entities Resource Report Resource Website |
Ontology of Medically Related Social Entities (RRID:SCR_003439) | OMRSE | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:44 | 0 | |||||||
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Medical Dictionary for Regulatory Activities Resource Report Resource Website 1+ mentions |
Medical Dictionary for Regulatory Activities (RRID:SCR_003751) | MEDDRA | data or information resource, controlled vocabulary, ontology | Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA) | umls | is listed by: BioPortal | nlx_157471 | SCR_003751 | 2026-08-09 09:03:54 | 4 | |||||||||
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Mosquito Insecticide Resistance Ontology Resource Report Resource Website |
Mosquito Insecticide Resistance Ontology (RRID:SCR_003864) | MIRO | data or information resource, controlled vocabulary, ontology | Application ontology for entities related to insecticide resistance in mosquitos | obo | is listed by: BioPortal | nlx_157486 | SCR_003864 | 2026-08-09 09:03:48 | 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 | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). | obo | is listed by: BioPortal | nlx_157488 | SCR_003891 | 2026-08-09 09:03:58 | 0 | |||||||||
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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, controlled vocabulary, ontology | Ontology of SNOMED (Systematized Nomenclature of Medicine) clinical terms. | umls | is listed by: BioPortal | nlx_157603 | SCR_003915 | 2026-08-09 09:03:58 | 2 | |||||||||
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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 | data or information resource, controlled vocabulary, 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 | 2026-08-09 09:03:56 | 0 |
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