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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Plant Trait Ontology Resource Report Resource Website |
Plant Trait Ontology (RRID:SCR_003461) | PTO, TO | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:06 | 0 | ||||||||
|
Suggested Ontology for Pharmacogenomics Resource Report Resource Website |
Suggested Ontology for Pharmacogenomics (RRID:SCR_003497) | SOPHARM, SO-Pharm | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:07 | 0 | ||||||||
|
Physico-Chemical Process Resource Report Resource Website |
Physico-Chemical Process (RRID:SCR_003530) | REX | data or information resource, controlled vocabulary, 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) | 2025-05-15 10:37:07 | 0 | ||||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:06 | 2 | ||||||
|
Subcellular Anatomy Ontology Resource Report Resource Website 1+ mentions |
Subcellular Anatomy Ontology (RRID:SCR_003486) | SAO, NIF Subcellular | data or information resource, controlled vocabulary, ontology | An 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 | nif-0000-00206 | http://ccdb.ucsd.edu/SAO/1.2/SAO.owl http://ccdb.ucsd.edu/CCDBWebSite/sao.html http://bioportal.bioontology.org/ontologies/SAO |
SCR_003486 | 2025-05-15 10:37:06 | 1 | ||||||
|
Kinetic Simulation Algorithm Ontology Resource Report Resource Website |
Kinetic Simulation Algorithm Ontology (RRID:SCR_003361) | KISAO | data or information resource, controlled vocabulary, ontology | An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use. | owl, algorithm, simulation |
is listed by: BioPortal is listed by: OBO has parent organization: BioModels |
PMID:22027554 | Acknowledgement requested | nlx_157456 | http://purl.bioontology.org/ontology/KISAO http://biomodels.net/kisao/KISAO |
SCR_003361 | 2025-05-15 10:37:05 | 0 | ||||||
|
Vertebrate Taxonomy Ontology Resource Report Resource Website |
Vertebrate Taxonomy Ontology (RRID:SCR_003518) | VTO | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:07 | 0 | ||||||
|
International Classification for Patient Safety Resource Report Resource Website |
International Classification for Patient Safety (RRID:SCR_003553) | ICPS | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:08 | 0 | ||||||||
|
NEMO Ontology Resource Report Resource Website |
NEMO Ontology (RRID:SCR_003386) | NEMO Ontology | data or information resource, controlled vocabulary, ontology | Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG). | eeg, meg, owl, event-related potential, cognitive, behavioral, data sharing, erp |
is listed by: BioPortal is related to: NEMO Analysis Toolkit has parent organization: Neural ElectroMagnetic Ontologies (NEMO) Project has parent organization: SourceForge |
NIH | Freely available | nif-0000-32927 | http://purl.bioontology.org/ontology/NEMO http://sourceforge.net/projects/nemoontologies/ |
http://nemo.nic.uoregon.edu/wiki/NEMO#NEMO_Ontology | SCR_003386 | Neural ElectroMagnetic Ontology | 2025-05-15 10:37:05 | 0 | ||||
|
Synthetic Biology Open Language Visual Ontology Resource Report Resource Website |
Synthetic Biology Open Language Visual Ontology (RRID:SCR_001261) | SBOL | data or information resource, controlled vocabulary, ontology | Ontology to represent standardized graphical notation for synthetic biology. | obo | is listed by: BioPortal | nlx_157601 | SCR_001261 | 2025-05-15 10:36:08 | 0 | |||||||||
|
Teleost Taxonomy Ontology Resource Report Resource Website |
Teleost Taxonomy Ontology (RRID:SCR_001611) | TTO | data or information resource, controlled vocabulary, ontology | 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 |
Creative Commons Zero License | nlx_153877 | https://www.nescent.org/phenoscape/ | SCR_001611 | 2025-05-15 10:36:17 | 0 | |||||||
|
Sleep Domain Ontology Resource Report Resource Website |
Sleep Domain Ontology (RRID:SCR_006808) | SDO | data or information resource, controlled vocabulary, ontology | An application ontology for the domain of Sleep Medicine. | owl | is listed by: BioPortal | nlx_157590 | SCR_006808 | 2025-05-15 10:38:42 | 0 | |||||||||
|
Cell Behavior Ontology Resource Report Resource Website 1+ mentions |
Cell Behavior Ontology (RRID:SCR_007055) | CBO | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:38:46 | 1 | ||||||||
|
Cerebrotendinous Xanthomatosis Ontology Resource Report Resource Website |
Cerebrotendinous Xanthomatosis Ontology (RRID:SCR_007067) | CTX | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:38:46 | 0 | |||||||||
|
Cancer Chemoprevention Ontology Resource Report Resource Website |
Cancer Chemoprevention Ontology (RRID:SCR_006966) | CANCO | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:38:44 | 0 | ||||||||
|
Clusters of Orthologous Groups Analysis Ontology Resource Report Resource Website 1+ mentions |
Clusters of Orthologous Groups Analysis Ontology (RRID:SCR_007232) | CAO | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:38:49 | 3 | |||||||
|
BFO Resource Report Resource Website 1+ mentions |
BFO (RRID:SCR_004818) | BFO | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:37:46 | 4 | ||||||
|
Bioinformatics Web Service Ontology Resource Report Resource Website |
Bioinformatics Web Service Ontology (RRID:SCR_004529) | OBIWS | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:37:34 | 0 | ||||||||
|
PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:37:55 | 1 | |||||||||
|
MPO Resource Report Resource Website 10+ mentions |
MPO (RRID:SCR_004855) | MPO, MP | data or information resource, controlled vocabulary, ontology | 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 | 2025-05-15 10:37:47 | 19 |
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