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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Clinical Measurement Ontology Resource Report Resource Website |
Clinical Measurement Ontology (RRID:SCR_003291) | CMO | data or information resource, ontology, controlled vocabulary | An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. | obo, phenotype, clinical, measurement, morphology, physiology |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO has parent organization: Medical College of Wisconsin; Wisconsin; USA |
PMID:22654893 | Free, Freely available | nlx_157364 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo |
SCR_003291 | 2026-02-14 02:00:45 | 0 | ||||||
|
Chemical Methods Ontology Resource Report Resource Website 1+ mentions |
Chemical Methods Ontology (RRID:SCR_003286) | CHMO, RSC CMO | data or information resource, ontology, controlled vocabulary | An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). | obo, chemistry, analytical chemistry, physical chemistry, material chemistry, method, health, mass spectrometry, electron microscopy, chemical experiment, sample ionization, chromatography, electrophoresis, instrument |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is listed by: Ontobee is related to: Information Artifact Ontology is related to: Ontology for Biomedical Investigations has parent organization: Royal Society of Chemistry |
Free, Available for download, Freely available | nlx_157363 | http://purl.bioontology.org/ontology/CHMO http://purl.obolibrary.org/obo/chmo.owl http://www.ontobee.org/browser/index.php?o=CHMO |
https://code.google.com/p/rsc-cmo/ | SCR_003286 | RSC Chemical Methods Ontology | 2026-02-14 02:00:44 | 1 | |||||
|
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 | 2026-02-14 02:00:25 | 0 | |||||||
|
Fission Yeast Phenotype Ontology Resource Report Resource Website |
Fission Yeast Phenotype Ontology (RRID:SCR_003315) | FYPO | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-14 02:00:45 | 0 | ||||||
|
Population and Community Ontology Resource Report Resource Website |
Population and Community Ontology (RRID:SCR_003462) | PCO | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-14 02:00:49 | 0 | |||||||
|
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 | 2026-02-14 02:00:49 | 0 | ||||||||
|
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 | 2026-02-14 02:00:34 | 0 | |||||||
|
Bioassay Ontology Resource Report Resource Website 1+ mentions |
Bioassay Ontology (RRID:SCR_002638) | BAO | data or information resource, ontology, controlled vocabulary | Ontology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation. | chemical biology, drug screening, assay, perturbation, high-throughput screening, owl |
is used by: LINCS Information Framework is listed by: BioPortal is parent organization of: G Protein-Coupled Receptor BioAssays Ontology |
Free, Freely available | nlx_156065 | SCR_002638 | 2026-02-14 02:00:28 | 7 | ||||||||
|
Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-14 02:00:49 | 0 | ||||||||
|
NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | web service, production service resource, service resource, data access protocol, software 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 | 2026-02-14 02:00:54 | 6 | |||||
|
Computer Assisted Brain Injury Rehabilitation Ontology Resource Report Resource Website |
Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) | CABRO | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-14 02:00:52 | 0 | ||||||||
|
Stanford Center for Biomedical Informatics Research Resource Report Resource Website |
Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) | BMIR | laboratory portal, data or information resource, organization portal, portal | 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 | 2026-02-14 02:01:09 | 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 | 2026-02-14 02:00:48 | 2 | ||||||
|
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 | 2026-02-14 02:00:49 | 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 | 2026-02-14 02:00:49 | 1 | ||||||
|
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 | 2026-02-14 02:00:49 | 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 | 2026-02-14 02:00:30 | 2 | |||||||||
|
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 | 2026-02-14 02:00:29 | 16 | ||||||
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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, 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 | 2026-02-14 02:00:50 | 1 | |||||||
|
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 | 2026-02-14 02:00:51 | 0 |
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