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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Portfolio Management Application Resource Report Resource Website |
Portfolio Management Application (RRID:SCR_010411) | PMA | data or information resource, ontology, controlled vocabulary | Ontology of a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports. | owl | is listed by: BioPortal | nlx_157559 | SCR_010411 | 2026-02-17 10:01:29 | 0 | |||||||||
|
Protein-Protein Interaction Ontology Resource Report Resource Website |
Protein-Protein Interaction Ontology (RRID:SCR_010413) | PPIO | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. | obo |
is listed by: BioPortal has parent organization: HUPO Proteomics Standards Initiative |
nlx_157561 | SCR_010413 | 2026-02-17 10:01:44 | 0 | |||||||||
|
Proteomics Data and Process Provenance Ontology Resource Report Resource Website |
Proteomics Data and Process Provenance Ontology (RRID:SCR_010414) | PROPREO | data or information resource, ontology, controlled vocabulary | A comprehensive proteomics data and process provenance ontology. | owl | is listed by: BioPortal | nlx_157562 | SCR_010414 | 2026-02-17 10:01:52 | 0 | |||||||||
|
Provenance Ontology Resource Report Resource Website 10+ mentions |
Provenance Ontology (RRID:SCR_010415) | PROVO | data or information resource, ontology, controlled vocabulary | Ontology that expresses the PROV Data Model using the OWL2 Web Ontology Language (OWL2) providing a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains. | owl | is listed by: BioPortal | nlx_157563 | SCR_010415 | PROV-O | 2026-02-17 10:01:29 | 10 | ||||||||
|
Quantitative Imaging Biomarker Ontology Resource Report Resource Website |
Quantitative Imaging Biomarker Ontology (RRID:SCR_010417) | QIBO | data or information resource, ontology, controlled vocabulary | An ontology that describes various concepts in quantitative imaging biomarkers. | owl | is listed by: BioPortal | nlx_157565 | SCR_010417 | 2026-02-17 10:01:45 | 0 | |||||||||
|
Gene Regulation Ontology Resource Report Resource Website |
Gene Regulation Ontology (RRID:SCR_010590) | GRO, BOOTStrep | data or information resource, ontology, controlled vocabulary | Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). | owl, genomic, proteomic, biological process, gene regulation, gene expression, gene, transcription factor, process, molecule, biological_process |
is listed by: BioPortal is listed by: OBO has parent organization: European Bioinformatics Institute |
nlx_157415, nlx_46399 | http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest |
SCR_010590 | Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events | 2026-02-17 10:01:32 | 0 | |||||||
|
HGNC Resource Report Resource Website 500+ mentions |
HGNC (RRID:SCR_002827) | data or information resource, controlled vocabulary, database | Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs. | gene, owl, gene symbol, phenotype, nomenclature, gene family, gene groups, genomic, proteomic, ortholog, web service, locus, protein coding, genetics, gold standard, bio.tools, FASEB list, GCBR, ELIXIR Core Data Resource |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: INFEVERS is related to: VGNC has parent organization: University of Cambridge School of Clinical Medicine; Cambridge; United Kingdom |
NHGRI U24HG003345 | PMID:36243972 PMID:32747822 PMID:34615987 PMID:33152070 |
Free, Freely available | biotools:genenames.org, nif-0000-02955, r3d100010901 | http://bioportal.bioontology.org/ontologies/HUGO https://bio.tools/genenames.org https://doi.org/10.17616/R3XC80 |
SCR_002827 | HUGO symbols, HGNC Database, HGNC - HUGO Gene Nomenclature Committee, HUGO Gene Nomenclature Committee, Human Genome Organization Gene Symbols | 2026-02-17 10:00:05 | 974 | |||||
|
International Classification for Nursing Practice Resource Report Resource Website |
International Classification for Nursing Practice (RRID:SCR_003099) | ICNP | data or information resource, ontology, controlled vocabulary | Ontology of the international classification for nursing practice. | owl | is listed by: BioPortal | Free, Available for download, Freely available | nlx_157445 | SCR_003099 | 2026-02-17 09:59:55 | 0 | ||||||||
|
Spider Ontology Resource Report Resource Website |
Spider Ontology (RRID:SCR_003117) | SPD | data or information resource, ontology, controlled vocabulary | An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). | obo, anatomy, organismal, behavior, product, spider |
is listed by: BioPortal is listed by: OBO has parent organization: Tree of Life: Phylogeny of Spiders |
Free, Freely available | nlx_157595 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo | SCR_003117 | 2026-02-17 10:00:10 | 0 | |||||||
|
Interaction Ontology Resource Report Resource Website |
Interaction Ontology (RRID:SCR_003055) | IXNO | data or information resource, ontology, controlled vocabulary | Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health. | obo |
is listed by: BioPortal has parent organization: Comparative Toxicogenomics Database (CTD) |
Free, Freely available | nlx_157444 | SCR_003055 | 2026-02-17 09:59:55 | 0 | ||||||||
|
Mental Functioning Ontology Resource Report Resource Website 1+ mentions |
Mental Functioning Ontology (RRID:SCR_003245) | MF, MFO | data or information resource, ontology, controlled vocabulary | An ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies. | mental functioning, mental process, cognition, trait, psychology, neuroscience, owl |
is listed by: BioPortal is listed by: Google Code is listed by: OBO is related to: Information Artifact Ontology is related to: Emotion Ontology is related to: Emotion Ontology has parent organization: University at Buffalo; New York; USA |
Free, Freely available | nlx_157305 | http://purl.obolibrary.org/obo/mf.owl | SCR_003245 | mental-functioning-ontology | 2026-02-17 10:00:07 | 1 | ||||||
|
Emotion Ontology Resource Report Resource Website |
Emotion Ontology (RRID:SCR_003272) | MFOEM | data or information resource, ontology, controlled vocabulary | An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialization of the broader Mental Functioning Ontology. | owl, affect, emotion, mood, appraisal, feeling, health, ontology |
is listed by: Google Code is listed by: OBO is listed by: BioPortal is related to: Mental Functioning Ontology is related to: Mental Functioning Ontology |
Free, Available for download, Freely available | nlx_157396 | https://github.com/jannahastings/emotion-ontology | SCR_003272 | 2026-02-17 10:00:15 | 0 | |||||||
|
Experimental Conditions Ontology Resource Report Resource Website 1+ mentions |
Experimental Conditions Ontology (RRID:SCR_003306) | XCO | data or information resource, ontology, controlled vocabulary | An ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. | obo, clinical, physiology, morphology, measurement |
is listed by: BioPortal is listed by: OBO has parent organization: Medical College of Wisconsin; Wisconsin; USA |
PMID:22654893 | Free, Available for download, Freely available | nlx_157401 | ftp://rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo http://sourceforge.net/projects/phenoonto/ |
SCR_003306 | Experimental condition ontology | 2026-02-17 09:59:59 | 1 | |||||
|
National Center for Biomedical Ontology Resource Report Resource Website 10+ mentions |
National Center for Biomedical Ontology (RRID:SCR_003304) | NCBO | organization portal, data or information resource, training resource, database, portal | Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments. | biomedical ontology, biomedical software tools |
is used by: DisGeNET is related to: Protege is related to: National Centers for Biomedical Computing has parent organization: National Centers for Biomedical Computing is parent organization of: BioPortal is parent organization of: PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate Ontologies is parent organization of: Bio-Mixer |
NHGRI U54 HG004028 | PMID:21672956 PMID:23734708 |
Free, Freely available | nif-0000-31891 | SCR_003304 | 2026-02-17 10:00:14 | 27 | ||||||
|
Vertebrate Trait Ontology Resource Report Resource Website |
Vertebrate Trait Ontology (RRID:SCR_003214) | VT | data or information resource, ontology, controlled vocabulary | A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. | trait, morphology, physiology, development, obo |
is listed by: BioPortal is related to: monarch-ontologies is related to: Rat Genome Database (RGD) is related to: Animal QTLdb is related to: Mouse Phenome Database (MPD) has parent organization: SourceForge |
PMID:23937709 | Free, Available for download, Freely available | nlx_156940 | SCR_003214 | VT Ontology | 2026-02-17 09:59:57 | 0 | ||||||
|
Chemical Information Ontology Resource Report Resource Website 1+ mentions |
Chemical Information Ontology (RRID:SCR_003290) | CHEMINF | data or information resource, ontology, controlled vocabulary | An ontology that aims to establish a standard in representing chemical information including chemical structure and the ability to richly describe chemical properties, whether intrinsic or computed. It includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. | owl, biochemistry, chemistry, chemical structure, chemical property, structure, property, molecular |
is listed by: BioPortal is listed by: OBO is listed by: Google Code has parent organization: European Bioinformatics Institute |
PMID:21991315 | Free, Available for download, Freely available | nlx_157362 | http://purl.bioontology.org/ontology/CHEMINF http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl |
SCR_003290 | 2026-02-17 09:59:58 | 2 | ||||||
|
Fly Taxonomy Resource Report Resource Website |
Fly Taxonomy (RRID:SCR_003317) | FB-SP, FBsp | data or information resource, controlled vocabulary | 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 | 2026-02-17 10:00:14 | 0 | ||||||
|
Plant Trait Ontology Resource Report Resource Website |
Plant Trait Ontology (RRID:SCR_003461) | PTO, TO | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-17 10:00:19 | 0 | ||||||||
|
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 | 2026-02-17 10:00:20 | 0 | ||||||||
|
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) | 2026-02-17 10:00:02 | 0 |
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