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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Suggested Ontology for Pharmacogenomics Resource Report Resource Website |
Suggested Ontology for Pharmacogenomics (RRID:SCR_003497) | SOPHARM, SO-Pharm | data or information resource, ontology, controlled vocabulary | A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains. | owl, pharmacogenomics, health, pathological, molecular, cellular, organismal, multi-organismal, drug, genomic variation, phenotype, trait, hypothesis, case study, investigation |
is listed by: BioPortal is listed by: OBO has parent organization: University of Lorraine; Lorraine; France |
nlx_157597 | http://purl.bioontology.org/ontology/SOPHARM SO-Pharm http://purl.oclc.org/NET/loria/sopharm/owl/sopharm |
SCR_003497 | 2026-02-14 02:00:50 | 0 | ||||||||
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Physico-Chemical Process Resource Report Resource Website |
Physico-Chemical Process (RRID:SCR_003530) | REX | data or information resource, ontology, controlled vocabulary | An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. | obo, physico-chemical process, physico-chemical, microscopic process, molecular entity, subatomic particle, macroscopic process, biochemical process |
is listed by: BioPortal is listed by: OBO is related to: Gene Ontology has parent organization: CHEBI |
nlx_157639 | http://purl.bioontology.org/ontology/MO ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/rex.obo http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=REX |
http://www.ebi.ac.uk/~kirill/REX/ | SCR_003530 | Physico-Chemical Process (REX) | 2026-02-14 02:00:51 | 0 | ||||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | data or information resource, ontology, controlled vocabulary | An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to). | owl, software, provenance, version, ontology |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge is related to: Information Artifact Ontology has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
JISC | The community can contribute to this resource | nlx_157591 | http://www.ebi.ac.uk/efo/swo http://purl.bioontology.org/ontology/SWO http://theswo.svn.sourceforge.net/viewvc/theswo/trunk/src/release/swoinowl/swo_merged/swo_merged.owl |
SCR_003493 | 2026-02-14 02:00:50 | 2 | ||||||
|
Subcellular Anatomy Ontology Resource Report Resource Website 1+ mentions |
Subcellular Anatomy Ontology (RRID:SCR_003486) | SAO, NIF Subcellular | data or information resource, ontology, controlled vocabulary | Ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. | electron microscopy, cellular structure, glial cell, light microscopy, macromolecule, nervous system, neuroanatomy, neuronal cell, neuropil, subcellular anatomy, subcellular structure, supracellular structure, synapse, owl, anatomy, sub-cellular, cellular component, cell, mesoscale |
is listed by: BioPortal is listed by: OBO is related to: Jinx has parent organization: Cell Centered Database |
NIH | PMID:18974798 | Free, Available for download, Freely available | nif-0000-00206 | https://bioportal.bioontology.org/ontologies/SAO | SCR_003486 | 2026-02-14 02:00:28 | 1 | |||||
|
Vertebrate Taxonomy Ontology Resource Report Resource Website |
Vertebrate Taxonomy Ontology (RRID:SCR_003518) | VTO | data or information resource, ontology, controlled vocabulary | An ontology that includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, they also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups. | owl, biology, evolution, obo-taxonomy, fossil, vertebrate, taxonmy, ontology |
uses: Teleost Taxonomy Ontology uses: AmphibiaWeb uses: Paleobiology Database uses: NCBI Taxonomy is listed by: BioPortal is listed by: OBO is listed by: Google Code has parent organization: Phenoscape |
PMID:24267744 | Open unspecified license | nlx_157625 | http://purl.obolibrary.org/obo/vto.owl http://code.google.com/p/vertebrate-taxonomy-ontology/ |
SCR_003518 | 2026-02-14 02:00:51 | 0 | ||||||
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International Classification for Patient Safety Resource Report Resource Website |
International Classification for Patient Safety (RRID:SCR_003553) | ICPS | data or information resource, ontology, controlled vocabulary | Ontology network about Patient Safety Incident. This work has been carried out by the Ontological Engineering Group, using sources from the University of Saint Etienne and the Australian Patient Safety Foundation. | owl | is listed by: BioPortal | World Health Organization ; International Classification for Patient Safety programme |
nlx_157446 | SCR_003553 | 2026-02-14 02:00:34 | 0 | ||||||||
|
Cognitive Paradigm Ontology Resource Report Resource Website 1+ mentions |
Cognitive Paradigm Ontology (RRID:SCR_002235) | CogPO | data or information resource, ontology, controlled vocabulary | Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. | functional neuroimaging, owl, cognition, behavior |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: BioPortal is related to: Human Imaging Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA has parent organization: Mind Research Network |
NIMH 1R01MH084812-01A1 | Free, Freely available | nlx_155537 | http://www.nitrc.org/projects/cogpo | SCR_002235 | 2026-02-14 02:00:23 | 9 | ||||||
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Nursing Interventions Classification Resource Report Resource Website |
Nursing Interventions Classification (RRID:SCR_000911) | NIC | data or information resource, ontology, controlled vocabulary | Ontology of nursing interventions classification. | umls | is listed by: BioPortal | nlx_157512 | SCR_000911 | 2026-02-14 01:59:55 | 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 | data or information resource, ontology, controlled vocabulary | Ontology of the international classification of primary care -2 PLUS | umls | is listed by: BioPortal | nlx_157454 | SCR_000909 | 2026-02-14 01:59:51 | 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 | data or information resource, ontology, 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 | 2026-02-14 01:59:59 | 0 | ||||||||
|
Teleost Taxonomy Ontology Resource Report Resource Website |
Teleost Taxonomy Ontology (RRID:SCR_001611) | TTO | data or information resource, ontology, controlled vocabulary | An ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish. It contains (as of August 2010) over 38,500 names, and over 44,000 taxonomic synonyms. A majority of the taxonomic names and synonyms were made available from the Catalog of Fishes. In July 2010 they added nearly 15,000 common names provided by Fishbase. Additional names and synonyms are added as a result of their curation activities. The ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for their project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant. | taxonomy, term, name, group, fish, phenotype, obo |
is used by: Vertebrate Taxonomy Ontology is listed by: BioPortal is related to: Catalog of Fishes is related to: FishBase has parent organization: Phenoscape Knowledgebase |
Free, Freely available | nlx_153877 | https://www.nescent.org/phenoscape/ | SCR_001611 | 2026-02-14 02:00:04 | 0 | |||||||
|
MGED Ontology Resource Report Resource Website 1+ mentions |
MGED Ontology (RRID:SCR_004484) | MO | data or information resource, ontology, controlled vocabulary | An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. | microarray, biomaterial, treatment, mage, owl |
is listed by: BioPortal is related to: MIAME is related to: MIAME is related to: RNA Abundance Database has parent organization: Functional Genomics Data Society has parent organization: SourceForge |
NIBIB ; NHGRI P41HG003619 |
PMID:16428806 | nlx_47223 | http://purl.bioontology.org/ontology/MO | SCR_004484 | Microarray and Gene Expression Data Ontology | 2026-02-14 02:00:59 | 1 | |||||
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PhenX Phenotypic Terms Resource Report Resource Website |
PhenX Phenotypic Terms (RRID:SCR_004518) | PHENX | data or information resource, ontology, 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 | 2026-02-14 02:00:44 | 0 | |||||||||
|
Ontology of Pneumology Resource Report Resource Website |
Ontology of Pneumology (RRID:SCR_004378) | ONTOPNEUMO | data or information resource, ontology, controlled vocabulary | Ontology of pneumology (french version) developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by Francois-Xavier Blanc in collaboration with Bruno Housset about medical expertise. | owl | is listed by: BioPortal | Creative Commons Attribution-NonCommercial-NoDerivs License, v2 UK | nlx_157537 | SCR_004378 | 2026-02-14 02:00:43 | 0 | ||||||||
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Pharmacovigilance Ontology Resource Report Resource Website |
Pharmacovigilance Ontology (RRID:SCR_004499) | PVONTO | data or information resource, ontology, 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 | 2026-02-14 02:00:44 | 0 | |||||||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | data or information resource, ontology, controlled vocabulary | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-02-14 02:00:58 | 44 | |||||
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Open Biological and Biomedical Ontologies Relationship Types Resource Report Resource Website 50+ mentions |
Open Biological and Biomedical Ontologies Relationship Types (RRID:SCR_004409) | OBOREL | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Ontology that defines core relations used in all OBO ontologies. Obsolete. Replaced with RO. | obo | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157539 | SCR_004409 | 2026-02-14 02:00:57 | 62 | ||||||||
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Bioinformatics Web Service Ontology Resource Report Resource Website |
Bioinformatics Web Service Ontology (RRID:SCR_004529) | OBIWS | data or information resource, ontology, 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 | 2026-02-14 02:00:45 | 0 | ||||||||
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MPO Resource Report Resource Website 10+ mentions |
MPO (RRID:SCR_004855) | MPO, MP | data or information resource, ontology, controlled vocabulary | Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome. | mus, phenotype, obo |
is used by: NIF Data Federation is listed by: BioPortal is related to: Rat Genome Database (RGD) is related to: MouseBook is related to: Neurocarta is related to: phenomeNET has parent organization: OBO has parent organization: Mouse Genome Informatics (MGI) |
PMID:17989687 | The community can contribute to this resource | nlx_83784 | http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype http://purl.bioontology.org/ontology/MP |
SCR_004855 | Mammalian Phenotype Ontology | 2026-02-14 02:00:48 | 19 | |||||
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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 | 2026-02-14 02:01:00 | 31414 |
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