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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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LexGrid Resource Report Resource Website 1+ mentions |
LexGrid (RRID:SCR_006627) | LexGrid | software resource | LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, parse, ontology |
is listed by: BioPortal is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: European Bioinformatics Institute has parent organization: National Cancer Institute |
NIH ; Cancer Biomedical Informatics Grid ; NLM LM07319 |
PMID:19261933 | Free for academic use | nlx_149194 | http://www.lexgrid.org/ | SCR_006627 | Lexical Grid | 2026-02-07 02:07:13 | 1 | ||||
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Phylogenetic Ontology Resource Report Resource Website |
Phylogenetic Ontology (RRID:SCR_000912) | PHYLONT | data or information resource, ontology, controlled vocabulary | Ontology for Phylogenetic Analysis | owl | is listed by: BioPortal | nlx_157550 | SCR_000912 | 2026-02-12 09:43:04 | 0 | |||||||||
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Bleeding History Phenotype Ontology Resource Report Resource Website |
Bleeding History Phenotype Ontology (RRID:SCR_001165) | BHO | data or information resource, ontology, controlled vocabulary | An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders. | owl | is listed by: BioPortal | Hemorrhagic disorder | nlx_157338 | SCR_001165 | 2026-02-12 09:43:06 | 0 | ||||||||
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Amphibian Taxonomy Ontology Resource Report Resource Website |
Amphibian Taxonomy Ontology (RRID:SCR_000906) | ATO | data or information resource, ontology, controlled vocabulary | A taxonomy of Amphibia | obo | is listed by: BioPortal | nlx_157317 | SCR_000906 | 2026-02-12 09:43:04 | 0 | |||||||||
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Anatomic Pathology Lexicon Resource Report Resource Website |
Anatomic Pathology Lexicon (RRID:SCR_000907) | PATHLEX | data or information resource, ontology, controlled vocabulary | A comprehensive lexicon - a unified language of anatomic pathology terms - for standardized indexing and retrieval of anatomic pathology information resources. | owl | is listed by: BioPortal | nlx_157318 | SCR_000907 | 2026-02-12 09:43:04 | 0 | |||||||||
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HIV ontology Resource Report Resource Website |
HIV ontology (RRID:SCR_000908) | HIV | data or information resource, ontology, controlled vocabulary | Ontology that encompasses all knowledge about HIV | obo | is listed by: BioPortal | HIV | nlx_157422 | SCR_000908 | 2026-02-12 09:43:04 | 0 | ||||||||
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Body System Terms from ICD11 Resource Report Resource Website |
Body System Terms from ICD11 (RRID:SCR_001252) | ICD11-BODYSYSTEM | data or information resource, ontology, controlled vocabulary | Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157339 | SCR_001252 | 2026-02-12 09:43:07 | 0 | ||||||||
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Teleost Anatomy Ontology Resource Report Resource Website 1+ mentions |
Teleost Anatomy Ontology (RRID:SCR_001610) | TAO | data or information resource, ontology, controlled vocabulary | A multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase. | homology, anatomy, morphology, fish, obo, organismal, zebrafish anatomy |
uses: Zebrafish Anatomical Ontology uses: Common Anatomy Reference Ontology uses: Vertebrate Skeletal Anatomy Ontology is used by: Phenoscape Knowledgebase is listed by: BioPortal is listed by: OBO has parent organization: Phenoscape |
PMID:20547776 | Free, Freely available | nlx_153876 | http://purl.obolibrary.org/obo/tao.obo http://bioportal.bioontology.org/ontologies/38362?p=terms |
https://www.nescent.org/phenoscape/ | SCR_001610 | 2026-02-12 09:43:12 | 1 | |||||
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Bioassay Ontology Resource Report Resource Website 1+ mentions |
Bioassay Ontology (RRID:SCR_002638) | BAO | data or information resource, ontology, controlled vocabulary | Ontology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation. | chemical biology, drug screening, assay, perturbation, high-throughput screening, owl |
is used by: LINCS Information Framework is listed by: BioPortal is parent organization of: G Protein-Coupled Receptor BioAssays Ontology |
Free, Freely available | nlx_156065 | SCR_002638 | 2026-02-12 09:43:25 | 7 | ||||||||
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Ascomycete Phenotype Ontology Resource Report Resource Website |
Ascomycete Phenotype Ontology (RRID:SCR_003254) | APO | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary for the phenotypes of Ascomycete fungi. | obo, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: SGD |
Free, Freely available | nlx_157321 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo | SCR_003254 | 2026-02-12 09:43:33 | 0 | |||||||
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Beta Cell Genomics Ontology Resource Report Resource Website |
Beta Cell Genomics Ontology (RRID:SCR_003259) | OBI BCGO, BCGO | data or information resource, ontology, controlled vocabulary | An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc. | owl, cell type, classification, ontology, beta cell genomics |
uses: BFO uses: Ontology for Biomedical Investigations is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology has parent organization: Beta Cell Biology Consortium |
Free, Available for download, Freely available | nlx_157324 | https://github.com/obi-bcgo/bcgo | SCR_003259 | 2026-02-12 09:43:33 | 0 | |||||||
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Dictyostelium Discoideum Anatomy Ontology Resource Report Resource Website |
Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) | DDANAT | data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. | obo, anatomy, organismal, cellular |
is listed by: BioPortal is listed by: OBO has parent organization: Dictyostelium discoideum genome database |
Free, Available for download, Freely available | nlx_157387 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo | SCR_003309 | Dictyostelium discoideum anatomy | 2026-02-12 09:43:34 | 0 | ||||||
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Biological Collections Ontology Resource Report Resource Website |
Biological Collections Ontology (RRID:SCR_003262) | BCO | data or information resource, ontology, controlled vocabulary | Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. | owl, interoperability, biodiversity, museum collection, environmental sample, metagenomic sample, ecological survey |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
PMID:24595056 | Free, Available for download, Freely available | nlx_157333 | http://purl.obolibrary.org/obo/bco.owl http://purl.bioontology.org/ontology/BCO |
SCR_003262 | 2026-02-12 09:43:33 | 0 | ||||||
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Common Anatomy Reference Ontology Resource Report Resource Website |
Common Anatomy Reference Ontology (RRID:SCR_003296) | CARO | data or information resource, ontology, controlled vocabulary | An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies. | obo, anatomy, organismal, ontology, interoperability, template |
is used by: Teleost Anatomy Ontology is listed by: BioPortal is listed by: OBO |
Free, Freely available | nlx_157369 | https://bioportal.bioontology.org/ontologies/CARO | SCR_003296 | 2026-02-12 09:43:34 | 0 | |||||||
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Clinical Measurement Ontology Resource Report Resource Website |
Clinical Measurement Ontology (RRID:SCR_003291) | CMO | data or information resource, ontology, controlled vocabulary | An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. | obo, phenotype, clinical, measurement, morphology, physiology |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO has parent organization: Medical College of Wisconsin; Wisconsin; USA |
PMID:22654893 | Free, Freely available | nlx_157364 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo |
SCR_003291 | 2026-02-12 09:43:34 | 0 | ||||||
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Chemical Methods Ontology Resource Report Resource Website 1+ mentions |
Chemical Methods Ontology (RRID:SCR_003286) | CHMO, RSC CMO | data or information resource, ontology, controlled vocabulary | An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). | obo, chemistry, analytical chemistry, physical chemistry, material chemistry, method, health, mass spectrometry, electron microscopy, chemical experiment, sample ionization, chromatography, electrophoresis, instrument |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is listed by: Ontobee is related to: Information Artifact Ontology is related to: Ontology for Biomedical Investigations has parent organization: Royal Society of Chemistry |
Free, Available for download, Freely available | nlx_157363 | http://purl.bioontology.org/ontology/CHMO http://purl.obolibrary.org/obo/chmo.owl http://www.ontobee.org/browser/index.php?o=CHMO |
https://code.google.com/p/rsc-cmo/ | SCR_003286 | RSC Chemical Methods Ontology | 2026-02-12 09:43:33 | 1 | |||||
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FlyBase Controlled Vocabulary Resource Report Resource Website |
FlyBase Controlled Vocabulary (RRID:SCR_003318) | FB-CV, FBcv | data or information resource, controlled vocabulary | A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them. | obo |
is listed by: BioPortal is listed by: OBO has parent organization: FlyBase |
Free, Available for download, Freely available | nlx_157408 | http://sourceforge.net/p/fbcv/code-0/HEAD/tree/releases/latest/fbcv-simple.obo?format=raw | SCR_003318 | 2026-02-12 09:43:34 | 0 | |||||||
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Fission Yeast Phenotype Ontology Resource Report Resource Website |
Fission Yeast Phenotype Ontology (RRID:SCR_003315) | FYPO | data or information resource, ontology, controlled vocabulary | A formal ontology of phenotypes observed in fission yeast that is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions. | obo, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: PomBase |
Free, Available for download, Freely available | nlx_157405 | https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/releases/latest/fypo.obo?format=raw | https://sourceforge.net/apps/trac/pombase/wiki/FissionYeastPhenotypeOntology | SCR_003315 | 2026-02-12 09:43:35 | 0 | ||||||
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Lipid Ontology Resource Report Resource Website |
Lipid Ontology (RRID:SCR_003349) | LiPrO | data or information resource, ontology, controlled vocabulary | An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. | owl, lipid, ontology |
is listed by: BioPortal is listed by: OBO |
Free, Available for download, Freely available | nlx_157458 | http://www.lipidprofiles.com/LipidOntology | SCR_003349 | 2026-02-12 09:43:35 | 0 | |||||||
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Population and Community Ontology Resource Report Resource Website |
Population and Community Ontology (RRID:SCR_003462) | PCO | data or information resource, ontology, controlled vocabulary | An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO). | owl, community, population, biomedical, evolution, ecology |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
New BSD License, (Code) | nlx_157557 | http://purl.bioontology.org/ontology/PCO http://purl.obolibrary.org/obo/pco.owl |
SCR_003462 | 2026-02-12 09:43:37 | 0 |
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