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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Fly Taxonomy Resource Report Resource Website |
Fly Taxonomy (RRID:SCR_003317) | FB-SP, FBsp | controlled vocabulary, data or information resource | The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. | obo, taxonomy, organismal |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge has parent organization: FlyBase |
Free, Available for download, Freely available | nlx_157407 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo | SCR_003317 | FlyBase Taxa | 2026-09-05 06:25:01 | 0 | ||||||
|
Plant Trait Ontology Resource Report Resource Website |
Plant Trait Ontology (RRID:SCR_003461) | PTO, TO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. | obo, phenotype, trait |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157556 | http://purl.bioontology.org/ontology/PTO, http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=co, http://www.gramene.org/plant_ontology/index.html#to, http://www.gramene.org/plant_ontology/ | SCR_003461 | 2026-09-05 06:25:04 | 0 | ||||||||
|
Suggested Ontology for Pharmacogenomics Resource Report Resource Website |
Suggested Ontology for Pharmacogenomics (RRID:SCR_003497) | SOPHARM, SO-Pharm | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:25:04 | 0 | ||||||||
|
Physico-Chemical Process Resource Report Resource Website |
Physico-Chemical Process (RRID:SCR_003530) | REX | controlled vocabulary, data or information resource, ontology | 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) | 2026-09-05 06:25:05 | 0 | ||||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:25:04 | 2 | ||||||
|
Subcellular Anatomy Ontology Resource Report Resource Website 1+ mentions |
Subcellular Anatomy Ontology (RRID:SCR_003486) | SAO, NIF Subcellular | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:25:04 | 1 | |||||
|
Vertebrate Taxonomy Ontology Resource Report Resource Website |
Vertebrate Taxonomy Ontology (RRID:SCR_003518) | VTO | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:25:05 | 0 | ||||||
|
International Classification for Patient Safety Resource Report Resource Website |
International Classification for Patient Safety (RRID:SCR_003553) | ICPS | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:25:05 | 0 | ||||||||
|
eagle-i research resource ontology Resource Report Resource Website 1+ mentions |
eagle-i research resource ontology (RRID:SCR_008784) | ERO | controlled vocabulary, data or information resource, data repository, database, ontology, service resource, software application, software resource, source code, storage service 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 | 2026-09-05 06:26:28 | 1 | |||||||
|
Alzheimer's disease ontology Resource Report Resource Website 1+ mentions |
Alzheimer's disease ontology (RRID:SCR_010289) | ADO | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:26:38 | 1 | ||||||
|
Fungal Gross Anatomy Ontology Resource Report Resource Website |
Fungal Gross Anatomy Ontology (RRID:SCR_010322) | FAO | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:26:39 | 0 | ||||||||
|
Human Developmental Anatomy Ontology abstract version 1 Resource Report Resource Website |
Human Developmental Anatomy Ontology abstract version 1 (RRID:SCR_010323) | EHDAA | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:26:39 | 0 | |||||||||
|
G Protein-Coupled Receptor BioAssays Ontology Resource Report Resource Website 1+ mentions |
G Protein-Coupled Receptor BioAssays Ontology (RRID:SCR_010324) | BAO-GPCR | controlled vocabulary, data or information resource, ontology | Ontology (http://www.bioassayontology.org/bao_gpcr) that describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies. | owl |
is listed by: BioPortal has parent organization: Bioassay Ontology |
nlx_157410 | SCR_010324 | 2026-09-05 06:26:39 | 5 | |||||||||
|
Galen Ontology Resource Report Resource Website |
Galen Ontology (RRID:SCR_010325) | GALEN | controlled vocabulary, data or information resource, ontology | A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic. | owl | is listed by: BioPortal | nlx_157411 | SCR_010325 | 2026-09-05 06:26:39 | 0 | |||||||||
|
Gene Ontology Extension Resource Report Resource Website |
Gene Ontology Extension (RRID:SCR_010327) | GO-EXT | controlled vocabulary, data or information resource, ontology | An extension of the Gene Ontology. | obo |
is listed by: BioPortal has parent organization: Gene Ontology |
nlx_157414 | SCR_010327 | 2026-09-05 06:26:39 | 0 | |||||||||
|
Crop Ontology Resource Report Resource Website 10+ mentions |
Crop Ontology (RRID:SCR_010299) | CO | controlled vocabulary, data or information resource, ontology | Ontology that includes crop-specific trait ontologies for several economically important plants like rice, wheat, maize, potato, musa, chickpea and sorghum along with other important domains for crop research such as germplasm, passport, trait measurement scales, experimental design factors etc. | obo | is listed by: BioPortal | nlx_157378 | http://cropontology.org/ | SCR_010299 | 2026-09-05 06:26:38 | 12 | ||||||||
|
Amino Acid Ontology Resource Report Resource Website |
Amino Acid Ontology (RRID:SCR_010290) | AMINO-ACID | controlled vocabulary, data or information resource, ontology | An ontology of amino acids and their properties. Inferred version. | owl | is listed by: BioPortal | nlx_157315 | SCR_010290 | 2026-09-05 06:26:38 | 0 | |||||||||
|
Biochemical Substructure Ontology Resource Report Resource Website |
Biochemical Substructure Ontology (RRID:SCR_010185) | BICSO | controlled vocabulary, data or information resource, ontology | Biochemical Substructure Ontology | protege | is listed by: BioPortal | nlx_157330 | SCR_010185 | 2026-09-05 06:26:37 | 0 | |||||||||
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KB Bio 101 Resource Report Resource Website |
KB Bio 101 (RRID:SCR_010268) | AURA | controlled vocabulary, data or information resource, ontology | Ontology of the AURA + Inquire project at SRI International, Menlo Park. | owl | is listed by: BioPortal | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | nlx_157455 | SCR_010268 | KB_Bio_101 | 2026-09-05 06:26:38 | 0 | |||||||
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Current Procedural Terminology Resource Report Resource Website |
Current Procedural Terminology (RRID:SCR_010301) | CPT | controlled vocabulary, data or information resource, ontology | Ontology of current procedural terminology. | umls | is listed by: BioPortal | nlx_157380 | SCR_010301 | 2026-09-05 06:26:38 | 0 |
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