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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Minimal Anatomical Terminology Resource Report Resource Website |
Minimal Anatomical Terminology (RRID:SCR_003385) | MAT | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:44 | 0 | |||||||
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Experimental Factor Ontology Resource Report Resource Website 10+ mentions |
Experimental Factor Ontology (RRID:SCR_003574) | EFO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:45 | 16 | ||||||
|
Adverse Event Reporting Ontology Resource Report Resource Website 1+ mentions |
Adverse Event Reporting Ontology (RRID:SCR_003571) | AERO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:46 | 1 | |||||||
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Rat Strain Ontology Resource Report Resource Website 1+ mentions |
Rat Strain Ontology (RRID:SCR_003449) | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 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 | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:44 | 1 | ||||||
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NCI Thesaurus Resource Report Resource Website 1+ mentions |
NCI Thesaurus (RRID:SCR_003563) | NCIt | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:45 | 9 | ||||
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Ontology of Medically Related Social Entities Resource Report Resource Website |
Ontology of Medically Related Social Entities (RRID:SCR_003439) | OMRSE | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | |||||||
|
PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | ontology, controlled vocabulary, data or information resource | An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563). | database, obo, protein |
is listed by: BioPortal has parent organization: Protein Information Resource has parent organization: Georgetown University; Washington D.C.; USA |
NIH ; NIGMS GM080646-01 |
nlx_92849 | SCR_004964 | PRO, Protein Ontology | 2026-02-11 10:57:07 | 0 | |||||||
|
Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | ontology, controlled vocabulary, data or information resource | A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157358 | http://www.gramene.org/plant_ontology/ | SCR_005095 | 2026-02-11 10:57:03 | 0 | ||||||||
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NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | production service resource, software resource, web service, data access protocol, service resource | A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | ontology, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: STOP has parent organization: BioPortal has parent organization: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California |
NHGRI U54 HG004028 | PMID:19483092 | biotools:bioportal, nlx_144389, OMICS_01172 | https://bio.tools/bioportal | SCR_005329 | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-02-11 10:57:07 | 6 | |||||
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Computer Assisted Brain Injury Rehabilitation Ontology Resource Report Resource Website |
Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) | CABRO | ontology, controlled vocabulary, data or information resource | A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living. | owl | is listed by: BioPortal | Brain trauma | nlx_157373 | SCR_005288 | 2026-02-11 10:57:03 | 0 | ||||||||
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Stanford Center for Biomedical Informatics Research Resource Report Resource Website |
Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) | BMIR | organization portal, portal, laboratory portal, data or information resource | Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences. | biomedicine, informatics |
has parent organization: Stanford University; Stanford; California is parent organization of: CLENCH is parent organization of: BioPortal is parent organization of: Center for Expanded Data Annotation and Retrieval is parent organization of: Protege is parent organization of: WebProtege |
nlx_149147 | SCR_005698 | Stanford Medical Informatics | 2026-02-11 10:57:12 | 0 | ||||||||
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Cell Line Ontology Resource Report Resource Website 1+ mentions |
Cell Line Ontology (RRID:SCR_005840) | CLO | ontology, controlled vocabulary, data or information resource | A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan. | cell line, owl, ontology, standardization, information integration |
is listed by: BioPortal is listed by: OBO is related to: Cell Line Knowledge Base has parent organization: University of Michigan Medical School; Michigan; USA |
The community can contribute to this resource | nlx_149363 | http://bioportal.bioontology.org/ontologies/1245 http://purl.obolibrary.org/obo/clo.owl |
SCR_005840 | 2026-02-11 10:57:15 | 2 | |||||||
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Read Codes Clinical Terms Version 3 Resource Report Resource Website 1+ mentions |
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) | RCD | ontology, controlled vocabulary, data or information resource | Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre | umls | is listed by: BioPortal | nlx_157570 | SCR_006055 | Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) | 2026-02-11 10:57:19 | 1 | ||||||||
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Randomized Controlled Trials Ontology Resource Report Resource Website |
Randomized Controlled Trials Ontology (RRID:SCR_005992) | RCTONT | ontology, controlled vocabulary, data or information resource | Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis. | owl | is listed by: BioPortal | nlx_157568 | SCR_005992 | 2026-02-11 10:57:18 | 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 | ontology, controlled vocabulary, data or information resource | Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA) | umls | is listed by: BioPortal | nlx_157471 | SCR_003751 | 2026-02-11 10:56:47 | 2 | |||||||||
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Mosquito Insecticide Resistance Ontology Resource Report Resource Website |
Mosquito Insecticide Resistance Ontology (RRID:SCR_003864) | MIRO | ontology, controlled vocabulary, data or information resource | Application ontology for entities related to insecticide resistance in mosquitos | obo | is listed by: BioPortal | nlx_157486 | SCR_003864 | 2026-02-11 10:56:47 | 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 | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:48 | 0 | ||||||||
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Medical Diagnostic Categories - Diagnosis Related Groups Resource Report Resource Website |
Medical Diagnostic Categories - Diagnosis Related Groups (RRID:SCR_003725) | MDCDRG | ontology, controlled vocabulary, data or information resource | Ontology of Medical Diagnostic Categories-Diagnosis Related Groups | owl | is listed by: BioPortal | nlx_157470 | SCR_003725 | 2026-02-11 10:56:47 | 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 | ontology, controlled vocabulary, data or information resource | A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). | obo | is listed by: BioPortal | nlx_157488 | SCR_003891 | 2026-02-11 10:56:46 | 0 |
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