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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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RightField Resource Report Resource Website 1+ mentions |
RightField (RRID:SCR_002649) | RightField | software resource, software application | An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies. | annotation, semantic, ontology, term selection, excel, java, bio.tools |
is listed by: BioPortal is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: SEEK is related to: Workflow4Ever has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:21622664 | Free, Available for download, Freely available | biotools:rightfield, nlx_156077 | https://bio.tools/rightfield | SCR_002649 | 2026-02-07 02:14:15 | 3 | ||||||
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Lipid Ontology Resource Report Resource Website |
Lipid Ontology (RRID:SCR_003349) | LiPrO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | |||||||
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Ascomycete Phenotype Ontology Resource Report Resource Website |
Ascomycete Phenotype Ontology (RRID:SCR_003254) | APO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:40 | 0 | |||||||
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Measurement Method Ontology Resource Report Resource Website |
Measurement Method Ontology (RRID:SCR_003373) | MMO | ontology, controlled vocabulary, data or information resource | An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. | obo, phenotype, clinical |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO |
PMID:22654893 | Free, Available for download, Freely available | nlx_157468 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo |
SCR_003373 | 2026-02-11 10:56:40 | 0 | ||||||
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Beta Cell Genomics Ontology Resource Report Resource Website |
Beta Cell Genomics Ontology (RRID:SCR_003259) | OBI BCGO, BCGO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:40 | 0 | |||||||
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Malaria Ontology Resource Report Resource Website |
Malaria Ontology (RRID:SCR_003369) | IDOMAL | ontology, controlled vocabulary, data or information resource | An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO). | obo, health, pathological, clinical, epidemiological, biological, intervention |
is listed by: BioPortal is listed by: OBO has parent organization: AnoBase: An Anopheles database |
Malaria | Free, Available for download, Freely available | nlx_157464 | http://purl.obolibrary.org/obo/idomal.obo http://anobase.vectorbase.org/idomal/IDOMAL.obo |
SCR_003369 | 2026-02-11 10:56:40 | 0 | ||||||
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Dictyostelium Discoideum Anatomy Ontology Resource Report Resource Website |
Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) | DDANAT | controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | ||||||
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Biological Collections Ontology Resource Report Resource Website |
Biological Collections Ontology (RRID:SCR_003262) | BCO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | ||||||
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Common Anatomy Reference Ontology Resource Report Resource Website |
Common Anatomy Reference Ontology (RRID:SCR_003296) | CARO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | |||||||
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Clinical Measurement Ontology Resource Report Resource Website |
Clinical Measurement Ontology (RRID:SCR_003291) | CMO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | ||||||
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Chemical Methods Ontology Resource Report Resource Website 1+ mentions |
Chemical Methods Ontology (RRID:SCR_003286) | CHMO, RSC CMO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 1 | |||||
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FlyBase Controlled Vocabulary Resource Report Resource Website |
FlyBase Controlled Vocabulary (RRID:SCR_003318) | FB-CV, FBcv | controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:41 | 0 | |||||||
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Fission Yeast Phenotype Ontology Resource Report Resource Website |
Fission Yeast Phenotype Ontology (RRID:SCR_003315) | FYPO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:43 | 0 | ||||||
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Population and Community Ontology Resource Report Resource Website |
Population and Community Ontology (RRID:SCR_003462) | PCO | ontology, controlled vocabulary, data or information resource | 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 | 2026-02-11 10:56:41 | 0 | |||||||
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Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | controlled vocabulary, data or information resource | A structured controlled vocabulary for the representation of plant environmental conditions. | obo, environment, gene expression, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157554 | http://purl.bioontology.org/ontology/PECO http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo http://www.gramene.org/plant_ontology/index.html#eo |
SCR_003460 | 2026-02-11 10:56:43 | 0 | ||||||||
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FMA Resource Report Resource Website 1+ mentions |
FMA (RRID:SCR_003379) | FMA | software application, ontology, data or information resource, database, software resource, data analysis software, data processing software, controlled vocabulary | A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model. | anatomy, informatics, model, neuroanatomy, protg, reference, standard, structural, taxonomy, owl, phenotype |
is listed by: BioPortal is related to: T3DB is related to: HIV Brain Sequence Database is related to: CELDA Ontology has parent organization: University of Washington; Seattle; USA |
RSNA-NIBIB ; University of Washington; Washington; USA ; Murdock Charitable Trust ; Microsoft ; Intel Corporation ; NLM LM006822; NLM LM06316; NLM contract LM03528; NHLBI HL08770 |
PMID:18688289 PMID:18360535 PMID:16779026 |
Free, Freely available | nif-0000-00066 | http://bioportal.bioontology.org/ontologies/FMA | SCR_003379 | Foundational Model of Anatomy Ontology, Foundational Model of Anatomy | 2026-02-11 10:56:40 | 8 | ||||
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PharmGKB Ontology Resource Report Resource Website |
PharmGKB Ontology (RRID:SCR_003529) | pharmgkb-owl | ontology, controlled vocabulary, data or information resource | An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner. | owl, medical, drug |
is listed by: BioPortal is related to: Comparative Toxicogenomics Database (CTD) is related to: DrugBank is related to: MeSH is related to: Human Disease Ontology has parent organization: PharmGKB |
PMID:11928517 | New BSD License | nlx_157636 | SCR_003529 | 2026-02-11 10:56:44 | 0 | |||||||
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Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | ontology, controlled vocabulary, data or information resource | Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles. | adverse event, health, pathological, molecular, cellular, organismal, multi-organismal |
is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Ontology of Vaccine Adverse Events has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:25093068 | Free, Freely available | nlx_157522 | http://purl.bioontology.org/ontology/OAE http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl |
SCR_003428 | 2026-02-11 10:56:44 | 2 | ||||||
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Minimal Anatomical Terminology Resource Report Resource Website |
Minimal Anatomical Terminology (RRID:SCR_003385) | MAT | ontology, controlled vocabulary, data or information resource | An ontology of minimal set of terms for anatomy. | obo, anatomy, organismal, ontology |
is listed by: BioPortal is listed by: OBO has parent organization: eMouseAtlas |
Free, Available for download, Freely available | nlx_157480 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo | SCR_003385 | 2026-02-11 10:56:44 | 0 |
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