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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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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Spatial Ontology Resource Report Resource Website |
Spatial Ontology (RRID:SCR_007860) | BSPO | ontology, data or information resource, controlled vocabulary | A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth. | obo | is listed by: BioPortal | SCR_007860 | 2026-08-04 09:41:58 | 0 | ||||||||||
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Human Dermatological Disease Ontology Resource Report Resource Website 1+ mentions |
Human Dermatological Disease Ontology (RRID:SCR_007648) | DERMO | ontology, data or information resource, controlled vocabulary | Ontology of human dermatologic disease | obo | is listed by: BioPortal | Dermatologic disease | nlx_157428 | SCR_007648 | 2026-08-04 09:41:54 | 1 | ||||||||
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Host Pathogen Interactions Ontology Resource Report Resource Website |
Host Pathogen Interactions Ontology (RRID:SCR_007647) | HPIO | ontology, data or information resource, controlled vocabulary | Ontology for host pathogen interactions in farmed animals | owl | is listed by: BioPortal | nlx_157427 | SCR_007647 | 2026-08-04 09:41:54 | 0 | |||||||||
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eagle-i research resource ontology Resource Report Resource Website 1+ mentions |
eagle-i research resource ontology (RRID:SCR_008784) | ERO | source code, storage service resource, software resource, controlled vocabulary, software application, data repository, service resource, ontology, database, data or information resource | Ontology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee. | research, resource, biomedical, owl |
is listed by: BioPortal is related to: Ontobee is related to: CTSA ShareCenter has parent organization: Eagle I has parent organization: Google Code |
ARRA ; NCRR U24RR029825 |
New BSD License | nlx_144312 | SCR_008784 | 2026-08-04 09:42:13 | 1 | |||||||
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Adult Mouse Anatomy Ontology Resource Report Resource Website 1+ mentions |
Adult Mouse Anatomy Ontology (RRID:SCR_006568) | MA | ontology, data or information resource, controlled vocabulary |
Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display. |
functionally, adult mouse, anatomical, anatomy, phenotype, postnatal, structure, theiler stage 28, obo, gene expression |
is listed by: BioPortal is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: Gene Expression Database |
NIH ; NICHD HD33745; NICHD F32 HD08435-01; NHGRI F32 HG00215-01 |
Acknowledgement requested | nif-0000-10300 | http://purl.bioontology.org/ontology/MA | SCR_006568 | Adult Mouse Anatomy Browser, MGI Adult Mouse Anatomical Dictionary Browser, Adult Mouse Anatomical Dictionary Browser, Mouse Adult Gross Anatomy Ontology, Anatomical Dictionary for the Adult Mouse | 2026-08-04 09:41:37 | 3 | |||||
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Breast Cancer Grading Ontology Resource Report Resource Website |
Breast Cancer Grading Ontology (RRID:SCR_006658) | BCGO | ontology, data or information resource, controlled vocabulary | Ontology that assigns a grade to a tumor starting from the 3 criteria of the NGS | owl | is listed by: BioPortal | Breast Cancer | nlx_157343 | SCR_006658 | 2026-08-04 09:41:38 | 0 | ||||||||
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Sleep Domain Ontology Resource Report Resource Website |
Sleep Domain Ontology (RRID:SCR_006808) | SDO | ontology, data or information resource, controlled vocabulary | An application ontology for the domain of Sleep Medicine. | owl | is listed by: BioPortal | nlx_157590 | SCR_006808 | 2026-08-04 09:41:40 | 0 | |||||||||
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Cell Behavior Ontology Resource Report Resource Website 1+ mentions |
Cell Behavior Ontology (RRID:SCR_007055) | CBO | ontology, data or information resource, controlled vocabulary | Ontology that describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors. | owl | is listed by: BioPortal | nlx_157353 | http://cbo.biocomplexity.indiana.edu/cbo/ | SCR_007055 | 2026-08-04 09:41:44 | 1 | ||||||||
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Cerebrotendinous Xanthomatosis Ontology Resource Report Resource Website |
Cerebrotendinous Xanthomatosis Ontology (RRID:SCR_007067) | CTX | ontology, data or information resource, controlled vocabulary | Ontology that represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was built reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value. | owl | is listed by: BioPortal | nlx_157360 | SCR_007067 | 2026-08-04 09:41:45 | 0 | |||||||||
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Cancer Chemoprevention Ontology Resource Report Resource Website |
Cancer Chemoprevention Ontology (RRID:SCR_006966) | CANCO | ontology, data or information resource, controlled vocabulary | A vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain. | owl | is listed by: BioPortal | Cancer | nlx_157350 | SCR_006966 | 2026-08-04 09:41:44 | 0 | ||||||||
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Clusters of Orthologous Groups Analysis Ontology Resource Report Resource Website 1+ mentions |
Clusters of Orthologous Groups Analysis Ontology (RRID:SCR_007232) | CAO | ontology, data or information resource, controlled vocabulary | Ontology designed for supporting the COG enrichment study by using Fisher''s exact test | owl |
is listed by: BioPortal has parent organization: COG |
nlx_157366 | http://cao.sourceforge.net/ | SCR_007232 | COG Analysis Ontology, Clusters of Orthologous Groups (COG) Analysis Ontology | 2026-08-04 09:41:48 | 2 | |||||||
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Alzheimer's disease ontology Resource Report Resource Website 1+ mentions |
Alzheimer's disease ontology (RRID:SCR_010289) | ADO | ontology, data or information resource, controlled vocabulary | An open, public ontology representing relevant knowledge on Alzheimer's disease. | owl, ontology, alzheimer | is listed by: BioPortal | Alzheimer's disease | Public, Open unspecified license | nlx_157314 | SCR_010289 | Alzheimers disease ontology | 2026-08-04 09:42:38 | 1 | ||||||
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Fungal Gross Anatomy Ontology Resource Report Resource Website |
Fungal Gross Anatomy Ontology (RRID:SCR_010322) | FAO | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary for the anatomy of fungi. | obo | is listed by: BioPortal | nlx_157409 | http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/ | SCR_010322 | 2026-08-04 09:42:42 | 0 | ||||||||
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Human Developmental Anatomy Ontology abstract version 1 Resource Report Resource Website |
Human Developmental Anatomy Ontology abstract version 1 (RRID:SCR_010323) | EHDAA | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just ''heart'' really means ''heart (CS 9-20)''. Timing details will be added to the abstract version of the ontology in a future release. | obo | is listed by: BioPortal | nlx_157429 | SCR_010323 | 2026-08-04 09:42:38 | 0 |
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