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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PhenX Phenotypic Terms Resource Report Resource Website |
PhenX Phenotypic Terms (RRID:SCR_004518) | PHENX | ontology, data or information resource, controlled vocabulary | Ontology for standard measures related to complex diseases, phenotypic traits and environmental exposures | owl |
is listed by: BioPortal has parent organization: Consensus Measures for Phenotype and Exposure is organization facet of: Phenotypes and eXposures Toolkit |
nlx_157548 | SCR_004518 | 2026-08-04 09:41:10 | 0 | |||||||||
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MeSH Resource Report Resource Website 10000+ mentions |
MeSH (RRID:SCR_004750) | MeSH | data or information resource, controlled vocabulary | A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic. | umls, database, health, thesaurus, medical, gold standard |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is related to: MEDLINE is related to: Public Health Image Library is related to: MEDLINE is related to: DermAtlas. is related to: Coremine Medical is related to: Unified Medical Language System is related to: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France is related to: Robert Hoehndorf Version of MeSH is related to: PharmGKB Ontology is related to: Linked Neuron Data is related to: PubMed has parent organization: National Library of Medicine |
Free | nlx_75424 | http://purl.bioontology.org/ontology/MESH | SCR_004750 | MeSH (Medical Subject Headings), Medical Subject Headings | 2026-08-04 09:41:12 | 31414 | ||||||
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PATO Resource Report Resource Website 10+ mentions |
PATO (RRID:SCR_004782) | PATO | ontology, data or information resource, controlled vocabulary | Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model). | plant trait, mammalian, phenotype, obo, quality, phenotypic quality |
is used by: Morpholino Database is listed by: BioPortal has parent organization: OBO |
nlx_77534 | http://obofoundry.org/wiki/index.php/PATO:Main_Page | SCR_004782 | PATO - Phenotypic Quality Ontology, Phenotype and Trait Ontology, Phenotypic Quality Ontology | 2026-08-04 09:41:13 | 29 | |||||||
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BFO Resource Report Resource Website 1+ mentions |
BFO (RRID:SCR_004818) | BFO | ontology, data or information resource, controlled vocabulary | A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences. | owl, gold standard |
is used by: Beta Cell Genomics Ontology is listed by: BioPortal has parent organization: IFOMIS |
Volkswagen Foundation | nlx_80606 | http://bioportal.bioontology.org/ontologies/BFO | SCR_004818 | Basic Formal Ontology | 2026-08-04 09:41:14 | 4 | ||||||
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Pharmacovigilance Ontology Resource Report Resource Website |
Pharmacovigilance Ontology (RRID:SCR_004499) | PVONTO | ontology, data or information resource, controlled vocabulary | A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms. | owl | is listed by: BioPortal | nlx_157547 | SCR_004499 | 2026-08-04 09:41:09 | 0 | |||||||||
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Bioinformatics Web Service Ontology Resource Report Resource Website |
Bioinformatics Web Service Ontology (RRID:SCR_004529) | OBIWS | ontology, data or information resource, controlled vocabulary | Ontology that extends the Ontology for Biomedical Investigations (OBI) to support consistent annotation of Bioinformatics Web services. | owl | is listed by: BioPortal | nlx_157332 | http://code.google.com/p/obi-webservice/ | SCR_004529 | 2026-08-04 09:41:10 | 0 | ||||||||
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PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | ontology, data or information resource, controlled vocabulary | A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases. | owl | is listed by: BioPortal | nlx_157549 | SCR_005139 | 2026-08-04 09:41:18 | 1 | |||||||||
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NIFSTD Resource Report Resource Website 10+ mentions |
NIFSTD (RRID:SCR_005414) | NIFSTD | ontology, data or information resource, controlled vocabulary | The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. | behavioral activity, behavioral paradigm, brain region, cell, neuron, disease, molecule, nervous system function, subcellular part, resource type, quality, brain, neuroscience, biological process, cellular anatomy, anatomy, subcellular, subcellular anatomy, organism, neurological disorder, neurologic disease, dysfunction, owl |
is listed by: BioPortal is listed by: FORCE11 is related to: NeuroLex is related to: OntoQuest is related to: InterLex has parent organization: Neuroscience Information Framework is parent organization of: NIF Cell Ontology provides: Neuron Phenotype Ontology |
PMID:18975148 PMID:22737162 |
nlx_144512 | http://bioportal.bioontology.org/ontologies/NIFSTD | https://confluence.crbs.ucsd.edu/display/NIF/Ontologies+and+Vocabularies | SCR_005414 | Neuroscience Information Framework Standard Ontology, NIF Ontology, NIF Standard, NIF-Ontology, Neuroscience Information Framework (NIF) Standard Ontology, NIF Standard Ontology, NIFSTD Ontology, NIF Ontologies | 2026-08-04 09:41:22 | 15 | |||||
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VIVO Resource Report Resource Website 50+ mentions |
VIVO (RRID:SCR_005246) | VIVO | portal, software resource, controlled vocabulary, software application, community building portal, service resource, ontology, data or information resource | Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work. | data sharing, network, semantic web, linked data, rdf, owl, database, people resource |
is listed by: BioPortal is related to: Clinical and Translational Science Awards Consortium is related to: DataStaR is related to: CTSAconnect is related to: CTSA ShareCenter has parent organization: University of Florida; Florida; USA |
NCRR U24 RR029822 | Open unspecified license | nlx_144266 | SCR_005246 | VIVO - enabling national networking of scientists | 2026-08-04 09:41:19 | 50 | ||||||
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Computer Retrieval of Information on Scientific Projects Thesaurus Resource Report Resource Website 10+ mentions |
Computer Retrieval of Information on Scientific Projects Thesaurus (RRID:SCR_005301) | CRISP | ontology, data or information resource, controlled vocabulary | Ontology of Computer retrieval of Information on Scientific Projects (CRISP). | umls | is listed by: BioPortal | nlx_157374 | SCR_005301 | 2026-08-04 09:41:20 | 41 | |||||||||
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FORCE11 Resource Report Resource Website 10+ mentions |
FORCE11 (RRID:SCR_005334) | FORCE11 | portal, blog, knowledge environment, community building portal, narrative resource, data or information resource | A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community. | scholarly communication, scholarship, dissemination, data sharing, knowledge, information technology, semantics, digital publishing, information gathering, research communication, e-scholarship, digital object, scientific communication |
lists: Scholarly Ontologies Project lists: Academia.edu lists: StratML lists: Evernote lists: NPG publishing format lists: Fiduswriter lists: Altmetric Bookmarklet lists: Altmetric Explorer lists: Epistemio lists: Hypothes.is lists: Bio-Formats lists: iSpyBio.com lists: BioLexicon lists: Craig Mod lists: KLEIO lists: aTag Generator lists: Knowledge Engineering from Experimental Design lists: Utopia Docs lists: Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure lists: Semantic Measures Library lists: Open Education Database lists: Brainspell lists: IPython lists: Adobe FormsCentral lists: Altmetric API lists: myExperiment lists: ISA Infrastructure for Managing Experimental Metadata lists: Minimum Information for Biological and Biomedical Investigations lists: A modular structure for scientific articles in an electronic environment lists: Liquid Publications: Scientific Publications meet the Web lists: AQnowledge Bookmarklet lists: Authorea lists: Bamboo DiRT lists: Altmetric Badges lists: ESIP Data Management Short Course for Scientists lists: Etherpad lists: Commons In A Box lists: CKAN lists: DMPTool lists: eScholarship lists: Git2PROV lists: OMERO lists: GitHub lists: GROTOAP lists: ImpactStory lists: JCB DataViewer lists: Memento lists: OME-TIFF Format lists: OpenDOAR lists: Open Journal Systems lists: Paper Rejection Repository lists: PLoS Impact Explorer lists: RDFaCE lists: Scholarly Open Access lists: ShareLaTeX lists: Mendeley lists: W3C Provenance Incubator Group Wiki lists: A.nnotate lists: Annotation Ontology lists: Support-of-PDF-annotations lists: Neuroscience Information Framework lists: AlzSWAN Knowledge Base lists: ResearchCompendia lists: resExomeDB lists: SobekCM lists: W3C Open Annotation Community Group lists: Webmaker lists: Wikispaces lists: Mobile Assay lists: WorkingWiki lists: Overleaf lists: Xournal lists: Citation Style Language lists: EnablingOpenScholarship lists: JournalGuide lists: Mindtouch DekiWiki lists: Knowledge Blog lists: DataCite lists: FAIRsharing lists: FigShare lists: CiTO - the Citation Typing Ontology lists: DOAJ - Directory of Open Access Journals lists: Code4Lib Journal WordPress Customizations lists: U-Compare lists: SciCrunch Registry lists: Google Docs lists: CSIBS lists: Europe PubMed Central lists: ORNL DAAC Data Product Citation Policy lists: Pensoft lists: OpenCalais lists: Universal Numerical Fingerprint lists: FAIRSharing Catalogue of Standards lists: Nanopub.org lists: JISC Open Citations lists: W3C Provenance Working Group lists: Workflow4Ever lists: Scholarly Electronic Publishing Bibliography lists: ROARMAP: Registry of Open Access Repositories Mandatory Archiving Policies lists: ROAR lists: total impact.org lists: Publish or perish lists: Scalar lists: PDFX lists: lapdftext lists: Cohere lists: Data Citation Awareness lists: DataCite Ontology lists: Semantic MediaWiki lists: Rubriq lists: VisTrails lists: RSC Prospect lists: HyBrow (Hypothesis Browser) lists: Biotea lists: crowdLabs lists: Argumentative Zoning: Information Extraction from Scientific Articles lists: Synapse lists: BioCreative lists: EZID lists: ResearchGate lists: F1000: Faculty of 1000 Post-Publication Peer Review lists: Acumen Consortium lists: DOI lists: GREC Corpus lists: National Centre for Text Mining lists: SPAR - Semantic Publishing and Referencing Ontologies lists: re3data.org lists: DataUp lists: Open Archives Initiative - Object Reuse and Exchange Initiative lists: Sapienta lists: OBO lists: GENIA Project: Mining literature for knowledge in molecular biology lists: ORCID - Open Researcher and Contributor ID lists: Wikibooks lists: CERMINE lists: CiteAb lists: iAnnotate lists: Eagle I lists: AcroMine lists: FACTA+. lists: Open Provenance Model lists: RightField lists: SEEK lists: BioPortal lists: Reflect lists: Ontology Development and Information Extraction lists: PubMed lists: Open PHACTS lists: NIFSTD lists: Open Provenance Model Vocabulary lists: MEDIE lists: Ontology for Biomedical Investigations lists: Antibody Registry lists: Semantic Web Applications in Neuromedicine (SWAN) Ontology is related to: ShareLaTeX is related to: ResearchCompendia is related to: Overleaf has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | Free, Public, The community can contribute to this resource, Acknowledgement requested | nlx_149434 | SCR_005334 | FORCE11 - the Future of Research Communications and e-Scholarship, Force 11 | 2026-08-04 09:41:20 | 13 | ||||||
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Epoch Clinical Trial Ontology Resource Report Resource Website |
Epoch Clinical Trial Ontology (RRID:SCR_000366) | CTONT | ontology, data or information resource, controlled vocabulary | Ontology of clinical trial terminology. | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157400 | SCR_000366 | 2026-08-04 09:40:07 | 0 | ||||||||
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MeGO Resource Report Resource Website |
MeGO (RRID:SCR_000110) | MeGO | ontology, data or information resource, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up. | phage, plasmid, protein family, mobile genetic element, obo |
is listed by: BioPortal is related to: OBO is related to: AmiGO is related to: Gene Ontology has parent organization: A Classification of Mobile genetic Elements |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156939 | SCR_000110 | Mobile Genetic Element Ontology | 2026-08-04 09:40:03 | 0 | |||||||
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Vertebrate Skeletal Anatomy Ontology Resource Report Resource Website |
Vertebrate Skeletal Anatomy Ontology (RRID:SCR_000313) | VSAO | ontology, data or information resource, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An anatomy ontology covering the vertebrate skeletal system that integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. | obo |
is used by: Teleost Anatomy Ontology is listed by: BioPortal |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157624 | SCR_000313 | 2026-08-04 09:40:06 | 0 | ||||||||
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Research Network and Patient Registry Inventory Ontology Resource Report Resource Website |
Research Network and Patient Registry Inventory Ontology (RRID:SCR_000308) | RNPRIO | ontology, data or information resource, controlled vocabulary | Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries | owl | is listed by: BioPortal | nlx_157575 | SCR_000308 | 2026-08-04 09:40:06 | 0 | |||||||||
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EnvO Resource Report Resource Website 10+ mentions |
EnvO (RRID:SCR_000182) | EnvO | ontology, data or information resource, controlled vocabulary | Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material. | biome, environmental feature, environmental material, environment, habitat |
is listed by: BioPortal is related to: Gramene |
The community can contribute to this resource | nlx_153832 | SCR_000182 | Environment Ontology | 2026-08-04 09:40:04 | 20 | |||||||
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Information Artifact Ontology Resource Report Resource Website 1+ mentions |
Information Artifact Ontology (RRID:SCR_000477) | IAO | ontology, data or information resource, controlled vocabulary | An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies. | owl, information, ontology |
uses: Ontology for Biomedical Investigations is used by: TRANSFoRm Clinical Data Integration Model is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Porifera Ontology is related to: Mental Functioning Ontology is related to: Beta Cell Genomics Ontology is related to: Biological Collections Ontology is related to: Chemical Methods Ontology is related to: Influenza Ontology is related to: Ontology for Genetic Interval is related to: Ontology for Parasite LifeCycle is related to: Ontology of Adverse Events is related to: Ontology of Medically Related Social Entities is related to: Population and Community Ontology is related to: Software Ontology is related to: Adverse Event Reporting Ontology is related to: Ontology for Biomedical Investigations |
Free, Available for download, Freely available | nlx_157441 | https://code.google.com/p/information-artifact-ontology/, http://purl.bioontology.org/ontology/IAO, http://purl.obolibrary.org/obo/iao.owl | http://purl.obolibrary.org/obo/iao | SCR_000477 | 2026-08-04 09:40:08 | 2 | ||||||
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Nursing Interventions Classification Resource Report Resource Website |
Nursing Interventions Classification (RRID:SCR_000911) | NIC | ontology, data or information resource, controlled vocabulary | Ontology of nursing interventions classification. | umls | is listed by: BioPortal | nlx_157512 | SCR_000911 | 2026-08-04 09:40:16 | 0 | |||||||||
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International Classification of Primary Care - 2 PLUS Resource Report Resource Website |
International Classification of Primary Care - 2 PLUS (RRID:SCR_000909) | ICPC2P | ontology, data or information resource, controlled vocabulary | Ontology of the international classification of primary care -2 PLUS | umls | is listed by: BioPortal | nlx_157454 | SCR_000909 | 2026-08-04 09:40:16 | 0 | |||||||||
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Synthetic Biology Open Language Visual Ontology Resource Report Resource Website |
Synthetic Biology Open Language Visual Ontology (RRID:SCR_001261) | SBOL | ontology, data or information resource, controlled vocabulary | Ontology to represent standardized graphical notation for synthetic biology. | obo | is listed by: BioPortal | Free, Available for download, Freely available | nlx_157601 | SCR_001261 | 2026-08-04 09:40:21 | 0 |
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