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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PATO Resource Report Resource Website 10+ mentions |
PATO (RRID:SCR_004782) | PATO | data or information resource, ontology, 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 | 2026-02-14 02:00:47 | 29 | |||||||
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BFO Resource Report Resource Website 1+ mentions |
BFO (RRID:SCR_004818) | BFO | data or information resource, ontology, 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 | 2026-02-14 02:00:45 | 4 | ||||||
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Zebrafish Anatomical Ontology Resource Report Resource Website 1+ mentions |
Zebrafish Anatomical Ontology (RRID:SCR_005887) | ZFA | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability. | anatomy, structure, anatomical structure, obo |
is used by: Teleost Anatomy Ontology is recommended by: Zebrafish Brain Atlas is listed by: BioPortal is related to: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: Zebrafish Information Network (ZFIN) |
nlx_149454 | SCR_005887 | Zebrafish Anatomy and Development Ontology, ZFIN - Zebrafish Anatomical Ontology | 2026-02-14 02:01:01 | 4 | ||||||||
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Physical Medicine and Rehabilitation Resource Report Resource Website |
Physical Medicine and Rehabilitation (RRID:SCR_005948) | PMR | data or information resource, ontology, controlled vocabulary | Ontology for knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT. | owl | is listed by: BioPortal | nlx_157551 | SCR_005948 | 2026-02-14 02:01:13 | 0 | |||||||||
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Human Phenotype Ontology Resource Report Resource Website 50+ mentions |
Human Phenotype Ontology (RRID:SCR_006016) | HPO, HP | data or information resource, ontology, controlled vocabulary | Provides standardized vocabulary of phenotypic abnormalities encountered in human disease. Structured and controlled vocabulary for phenotypic features encountered in human hereditary and other disease. HPO is being developed in collaboration with members of OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including FMA, GO, ChEBI, and MPATH. | phenotype, genetics, disease, phenomizer, obo, clinical, phenome, pathological, organismal, FASEB list |
uses: OMIM uses: Phenexplorer is used by: DisGeNET is used by: HmtPhenome is used by: MONARCH Initiative is used by: NIF Data Federation is listed by: BioPortal is listed by: OBO is related to: Phenexplorer is related to: Phenomizer is related to: PhenoTips is related to: Neurocarta is related to: GWASdb is related to: Phenomizer has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany works with: Human Mouse Disease Connection |
Monogenic disease, Hereditary disease | PMID:20412080 | Free, Freely available | SCR_006219, nlx_151406, nlx_151835 | http://purl.bioontology.org/ontology/HP http://compbio.charite.de/svn/hpo/trunk/src/ontology/human-phenotype-ontology.obo |
SCR_006016 | Human Phenotype Ontology (HPO), Human Phenotype Ontology | 2026-02-14 02:01:03 | 73 | ||||
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Reference Sequence Annotation Resource Report Resource Website 1+ mentions |
Reference Sequence Annotation (RRID:SCR_006095) | RSA | data or information resource, ontology, controlled vocabulary | An ontology for sequence annotations and how to preserve them with reference sequences. | owl | is listed by: BioPortal | nlx_157571 | SCR_006095 | 2026-02-14 02:01:02 | 2 | |||||||||
|
Vaccine Ontology Resource Report Resource Website 1+ mentions |
Vaccine Ontology (RRID:SCR_006271) | VO | data or information resource, ontology, controlled vocabulary | A biomedical ontology in the vaccine domain | owl |
is used by: Ontology of Vaccine Adverse Events is listed by: BioPortal |
PMID:21871085 | nlx_157621 | SCR_006271 | 2026-02-14 02:01:15 | 1 | ||||||||
|
Master Drug Data Base Clinical Drugs Resource Report Resource Website |
Master Drug Data Base Clinical Drugs (RRID:SCR_003668) | MDDB | data or information resource, ontology, controlled vocabulary | Ontology of master drug data base, 2009_08_05 | umls | is listed by: BioPortal | nlx_157466 | SCR_003668 | 2026-02-14 02:00:29 | 0 | |||||||||
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Medaka Fish Anatomy and Development Ontology Resource Report Resource Website |
Medaka Fish Anatomy and Development Ontology (RRID:SCR_003719) | MFO | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. | obo | is listed by: BioPortal | nlx_157469 | SCR_003719 | 2026-02-14 02:00:51 | 0 | |||||||||
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Minimal Standard Terminology of Digestive Endoscopy Resource Report Resource Website |
Minimal Standard Terminology of Digestive Endoscopy (RRID:SCR_003785) | MSTDE | data or information resource, ontology, controlled vocabulary | Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001. | umls | is listed by: BioPortal | nlx_157483 | SCR_003785 | 2026-02-14 02:00:51 | 0 | |||||||||
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Systematized Nomenclature of Medicine - International Version Resource Report Resource Website |
Systematized Nomenclature of Medicine - International Version (RRID:SCR_003849) | SNMI | data or information resource, ontology, controlled vocabulary | Ontology of systematized nomenclature of human and veterinary medicine: SNOMED International. Cote, Roger A., editor. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998. | umls | is listed by: BioPortal | nlx_157604 | SCR_003849 | Systematized Nomenclature of Medicine International Version | 2026-02-14 02:00:52 | 0 | ||||||||
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Neural-Immune Gene Ontology Resource Report Resource Website 1+ mentions |
Neural-Immune Gene Ontology (RRID:SCR_004120) | NIGO | data or information resource, ontology, controlled vocabulary | Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains. | obo |
is listed by: BioPortal is related to: Gene Ontology |
nlx_157506 | SCR_004120 | 2026-02-14 02:00:37 | 1 | |||||||||
|
MeGO Resource Report Resource Website |
MeGO (RRID:SCR_000110) | MeGO | data or information resource, ontology, 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 | 2026-02-14 01:59:37 | 0 | |||||||
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EnvO Resource Report Resource Website 10+ mentions |
EnvO (RRID:SCR_000182) | EnvO | data or information resource, ontology, 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 | 2026-02-14 01:59:39 | 20 | |||||||
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Epoch Clinical Trial Ontology Resource Report Resource Website |
Epoch Clinical Trial Ontology (RRID:SCR_000366) | CTONT | data or information resource, ontology, controlled vocabulary | Ontology of clinical trial terminology. | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157400 | SCR_000366 | 2026-02-14 01:59:43 | 0 | ||||||||
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Vertebrate Skeletal Anatomy Ontology Resource Report Resource Website |
Vertebrate Skeletal Anatomy Ontology (RRID:SCR_000313) | VSAO | data or information resource, ontology, 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 | 2026-02-14 01:59:41 | 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 | data or information resource, ontology, 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 | 2026-02-14 01:59:40 | 0 | |||||||||
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Information Artifact Ontology Resource Report Resource Website 1+ mentions |
Information Artifact Ontology (RRID:SCR_000477) | IAO | data or information resource, ontology, 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 | 2026-02-14 01:59:47 | 2 | ||||||
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PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | data or information resource, ontology, 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 | 2026-02-14 02:00:52 | 1 | |||||||||
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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 | data or information resource, ontology, controlled vocabulary | Ontology of Computer retrieval of Information on Scientific Projects (CRISP). | umls | is listed by: BioPortal | nlx_157374 | SCR_005301 | 2026-02-14 02:01:04 | 41 |
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