List of OBO Foundry ontologies
From Wikipedia, the free encyclopedia
This is a list of ontologies that are part of the OBO Foundry as of January 2020.[update]
| Title | Prefix | Description | Official page |
|---|---|---|---|
| Agronomy Ontology | AGRO | Ontology of concepts relevant to agronomy experiments. | |
| An ontology of core ecological entities | ECOCORE | An ontology for ecological entities. | |
| Anatomical Entity Ontology | AEO | Ontology of anatomical structures that expand CARO, the Common Anatomy Reference Ontology. | |
| Antibiotic Resistance Ontology | ARO | Ontology for antibiotic resistance genes and mutations. | |
| Apollo Structured Vocabulary [1] | APOLLO-SV | Ontology for enabling interoperability of epidemic models and public health application software. | |
| Ascomycete phenotype ontology | APO | A structured controlled vocabulary for the phenotypes of Ascomycete fungi. | |
| Basic Formal Ontology[2] | BFO | The upper-level ontology upon which OBO Foundry ontologies are built. | |
| Beta Cell Genomics Ontology | BCGO | An application ontology built for beta cell genomic studies. | |
| Biological Collections Ontology [3] | BCO | An ontology for biodiversity data. | |
| Biological Imaging Methods Ontology | FBBI | Ontology for methods involved in biomedical imaging, including preparation and acquisition. | |
| Biological Spatial Ontology | BSPO | An ontology for representing spatial concepts used in biology. | |
| BRENDA tissue / enzyme source | BTO | An ontology for the source of enzymes. | |
| C. elegans development ontology (see WormBase) | WBLS | An ontology for the development of Caenorhabditis elegans. | |
| C. elegans Gross Anatomy Ontology (see WormBase) | WBBT | An ontology for the anatomy of Caenorhabditis elegans. | |
| C. elegans phenotype (see WormBase) | WBPHENOTYPE | An ontology for the phenotypes of Caenorhabditis elegans. | |
| Cardiovascular Disease Ontology | CVDO | An ontology for concepts related to cardiovascular diseases. | |
| Cell Line Ontology [4] | CLO | Ontology to describe cell lines. | |
| Cell Ontology [5] | CL | Ontology for metazoan cell types. | |
| Chemical Entities of Biological Interest | CHEBI | Ontology of small molecular entities of biological interest. | |
| Chemical Information Ontology [6] | CHEMINF | Ontology for descriptors used in chemoinformatics databases. | |
| Chemical Methods Ontology | CHMO | An ontology for the methods used in chemical experiments. | |
| Clinical LABoratory Ontology | LABO | An ontology of prescriptions and reports in clinical laboratories. | |
| Clinical measurement ontology [7] | CMO | Ontology to classify clinical measurements of experimental animals. | |
| Common Anatomy Reference Ontology [8] | CARO | An ontology to improve interoperability between anatomy ontologies for different organisms. | |
| Comparative Data Analysis Ontology [9] | CDAO | Ontology of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees. | |
| Confidence Information Ontology [10] | CIO | An ontology to describe confidence information in sequence annotations. | |
| Contributor Role Ontology | CRO | An ontology for the diverse roles behind a scientific research article. | |
| Ctenophore Ontology | CTENO | An anatomical and developmental ontology for ctenophores (Comb Jellies). | |
| Dictyostelium discoideum anatomy[11] | DDANAT | A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum. | |
| Dictyostelium discoideum phenotype ontology | DDPHENO | An ontology for phenotypes of the slime-mould Dictyostelium discoideum. | |
| Drosophila development | FBDV | An ontology of the development of Drosophila melanogaster. | |
| Drosophila gross anatomy[12] | FBBT | An ontology for the anatomy of Drosophila melanogaster. | |
| Drosophila Phenotype Ontology | FBCV | An ontology of common Drosophila phenotypes. | |
| Drug-drug Interaction and Drug-drug Interaction Evidence Ontology [13] | DIDEO | Ontology for drug–drug interaction evidence. | |
| Evidence & Conclusion Ontology[14] | ECO | An ontology for types evidence used to support scientific claims. | |
| eagle-i resource ontology | ERO | An ontology of research equipment, protocols and consumables. | |
| Emotion Ontology [15] | MFOEM | An ontology of emotions, moods, and other kinds of feelings. | |
| Environment Ontology [16] | ENVO | Ontology of environmental features and habitats. | |
| Experimental condition ontology [17] | XCO | An ontology for the different conditions in which experimental measurements are taken. | |
| Exposure Ontology [18] | EXO | Ontology to describe exposure to environmental factors (such as cigarette smoke) that might influence clinical outcomes. | |
| Fission Yeast Phenotype Ontology[19] | FYPO | An ontology of phenotypes of fission yeast. | |
| Flora Phenotype Ontology [20] | FLOPO | An ontology for traits and phenotypes of flowering plants. | |
| FlyBase Controlled Vocabulary | FBCV | An ontology to support the FlyBase project. | |
| Food Ontology [21] | FOODON | An ontology to represent entities that play a food role or related to foods. | |
| Foundational Model of Anatomy Ontology (subset) | FMAO | Subset of the Foundational Model of Anatomy Ontology. | |
| Fungal Anatomy Ontology | FAO | An ontology for the anatomy of fungi. | |
| Gazetteer | GAZ | An ontology that acts as a gazetteer (geographical dictionary). | |
| Gene Ontology | GO | An ontology for describing the function of genes and gene products. | |
| Genomic Epidemiology Ontology [22] | GENEPIO | An ontology for foodborne pathogens and associated outbreaks. | |
| Genotype Ontology | GENO | An ontology for genotypes and their related phenotypes and diseases. | |
| Geographical Entity Ontology | GEO | An ontology of geographical entities. | |
| Glycan Naming Ontology [23] | GNOME | An ontology for glycans based on GlyTouCan. | |
| Homology Ontology [24] | HOM | An ontology for concepts related to homology. | |
| Human Ancestry Ontology [25] | HANCESTRO | An ontology of ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. | |
| Human Developmental Stages | HSAPDV | An ontology of stages of the human life. | |
| Human Disease Ontology | DO | An ontology for describing human diseases. | |
| Human Phenotype Ontology | HPO | An ontology for human phenotypes in hereditary and non-hereditary diseases. | |
| HUPO-PSI cross-linking and derivatization reagents controlled vocabulary | PSI-MS | An ontology for reagents used to cross-link molecules in mass spectrometry experiments. | |
| Hymenoptera Anatomy Ontology [26] | HAO | An ontology of the anatomy of the Hymenoptera (bees, wasps, and ants). | |
| Hypertension Ontology | HTN | An ontology for clinical data about hypertension. | |
| Infectious Disease Ontology [27] | IDO | A set of ontologies related to infectious diseases. | |
| Information Artifact Ontology [28] | IAO | An ontology of information entities. | |
| Informed Consent Ontology | ICO | An ontology for concepts related to informed consent, such as forms and policies. | |
| Integrative and Conjugative Element Ontology | ICEO | An ontology of bacterial integrative and conjugative elements (ICEs). | |
| Interaction Network Ontology [29] | INO | An ontology for gene-gene interactions. | |
| Malaria Ontology [30] | IDOMAL | An ontology for concepts related to malaria. | |
| Mammalian Feeding Muscle Ontology | MFMO | An ontology for the mammalian muscles that play a role in feeding behavior. | |
| Mammalian Phenotype Ontology | MP | Standard terms for annotating mammalian phenotypic data. | |
| Mass spectrometry ontology | MI | An ontology for concepts to describe mass spectrometry in the context of proteomics. | |
| Measurement method ontology | MMO | An ontology for methods of clinical and laboratory measurements. | |
| Medaka Developmental Stages | OlatDv | An ontology of life stages for the medaka fish. | |
| Mental Disease Ontology [31] | MFOMD | An ontology for mental diseases. | |
| Mental Functioning Ontology [31] | MFO | An ontology for concepts related to mental functioning. | |
| MHC Restriction Ontology [32] | MRO | An ontology for Major Histocompatibility Complex (MHC) restriction in experiments. | |
| MIAPA Ontology [33] | MIAPA | An ontology for phylogenetic data. | |
| Microbial Conditions Ontology [34] | MCO | An ontology for microbial growth conditions. | |
| Minimum PDDI Information Ontology | MPIO | An ontology of the minimum information to describe drug–drug interactions. | |
| Molecular Interactions Controlled Vocabulary | MI | An ontology for concepts related to the study of protein-protein interactions. | |
| Mondo Disease Ontology | MONDO | An ontology for the integration of information on disease. | |
| Mosquito gross anatomy ontology (VectorBase) | TGMA | An ontology for the anatomy of mosquitoes. | |
| Mouse adult gross anatomy ontology | EMAPA | An ontology for the adult anatomy of the mouse (Mus). | |
| Mouse Developmental Stages | MmusDv | An ontology of stages of the mouse (Mus) life. | |
| Mouse gross anatomy and development, timed | EMAP | Ontology of anatomical structures of the mouse (Mus musculus). | |
| Mouse Pathology Ontology [35] | MPATH | An ontology of mouse pathology phenotypes. | |
| Name Reaction Ontology | RXNO | An ontology for organic reactions in organic synthesis. | |
| NCBI organismal classification [36] | NCBITaxon | An ontology representation of the NCBI organismal taxonomy. | |
| Neuro Behavior Ontology | NBO | An ontology of behavioral phenotypes of animals. | |
| NOMEN - A nomenclatural ontology for biological names [37] | NOMEN | An ontology of the rules of nomenclature for biological names. | |
| Non-Coding RNA Ontology [38] | NCRO | An ontology for non-coding RNA function. | |
| Ontologized MIABIS | OMIABIS | An ontological version of MIABIS (Minimum Information About BIobank data Sharing). | |
| Ontology for Biobanking [39] | OBIB | An ontology for concepts related to biobanks. | |
| Ontology for Biomedical Investigations | OBI | An ontology which describes biological processes, cellular components and molecular functions in living organisms. | |
| Ontology for General Medical Science | OGMS | An ontology for general aspects of medicine, with a focus on cancer. | |
| Ontology for Parasite LifeCycle [40] | OPL | A reference ontology for parasite life cycle stages. | |
| Ontology of Adverse Events [41] | OAE | An ontology for adverse events of drug regimens. | |
| Ontology of Arthropod Circulatory Systems [42] | OARCS | An ontology for the circulatory systems of arthropods. | |
| Ontology of Biological and Clinical Statistics [43] | OBCS | An ontology to describe statistical tools and methods used in biomedical investigation. | |
| Ontology of Biological Attributes | OBA | An ontology for biological traits. | |
| Ontology of Medically Related Social Entities [44] | OMRSE | An ontology for entities (roles and organizations) related to healthcare. | |
| Ontology of Microbial Phenotypes [45] | OMP | An ontology of phenotypes of microorganisms. | |
| Ontology of Organizational Structures of Trauma centers and Trauma systems | OOSTT | An ontology for the organizational structures of trauma centers and trauma systems. | |
| Ontology of Precision Medicine and Investigation | OPMI | An ontology for concepts related to precision medicine. | |
| Ontology of Prokaryotic Phenotypic and Metabolic Characters [46] | MICRO | An ontology of prokaryotic phenotypic and metabolic characters. | |
| Ontology of RNA Sequencing | ORNASEQ | An ontology to annotate RNA Sequencing experiments. | |
| Ontology of Vaccine Adverse Events [47] | OVAE | An ontology for adverse events of vaccines. | |
| Pathogen Host Interaction Phenotype Ontology | PHIPO | An ontology of phenotypes that occur in pathogen-host interactions. | |
| Pathogen Transmission Ontology | TRANS | An ontology for disease transmission processes. | |
| Pathway ontology | PW | An ontology for annotating gene products to pathways. | |
| Performance Summary Display Ontology | PSDO | An ontology for concepts related to performance information for teams and organizations. | |
| Phenotype And Trait Ontology | FOBI | FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data. | |
| Planaria Ontology | PLANA | An ontology for the anatomy and developmental stages of the planaria (Schmidtea mediterranea). | |
| Planarian Phenotype Ontology | PLANP | An ontology for phenotypes of the planaria (Schmidtea mediterranea). | |
| Plant Experimental Conditions Ontology | PECO | An ontology for concepts related to plant biology experiments. | |
| Plant ontology | PO | An ontology and database resource that links plant traits to genomics data. | |
| Plant Phenology Ontology | PPO | An ontology for describing the cyclic phenomena of plants. | |
| Plant Trait Ontology | TO | An ontology for phenotypic traits in plants. | |
| Platynereis Developmental Stages | PDUMDV | An ontology for life stages of the annelid Platynereis dumerilii. | |
| Population and Community Ontology | PCO | An ontology for describing groups of interacting organisms. | |
| Porifera Ontology [48] | PORO | An ontology for the anatomy of sponges (Porifera) | |
| Protein modification [49] | MOD | An ontology for protein chemical modifications. | |
| Protein Ontology [50] | PRO | An ontological representation of protein-related entities. | |
| Rat Strain Ontology [51] | RS | An ontology for laboratorial rat strains. | |
| Relation Ontology [52] | RO | An ontology for relations between terms in the ontologies. | |
| Scientific Evidence and Provenance Information Ontology | SEPIO | An ontology for the provenance of scientific claims and supporting evidence. | |
| Sequence types and features ontology | SO | An ontology for annotation of sequences. | |
| Software Ontology[53] | SWO | An ontology to describe software applications with a focus on bioinformatics tools. | |
| Spider Ontology[54] | SPD | An ontology for anatomy and behavior of spiders as well as spider-derived products. | |
| Symptom Ontology | SYMP | An ontology of disease symptoms. | |
| Taxonomic rank vocabulary | TAXRANK | An ontology of taxonomic ranks in systematics. | |
| Teleost taxonomy ontology [55] | TTO | An ontology for the taxonomy of teleost fish. | |
| The Data Use Ontology [56] | DUO | Ontology for conditions of data use. | |
| The Drug Ontology [57] | DRON | An ontology for drug products. | |
| The Ontology of Genes and Genomes | OGG | An ontology of genes and genomes of biological organisms. | |
| The Oral Health and Disease Ontology [58] | OHD | An ontology for the content of teeth-related health records. | |
| The Prescription of Drugs Ontology [59] | PDRO | An ontology for concepts related to prescription of drugs. | |
| The Statistical Methods Ontology | STATO | An ontology for statistical methods, such as tests and experimental designs. | |
| Tick Anatomy Ontology [60] | TADS | An ontology for the anatomy of the tick families Ixodidae and Argasidae. | |
| Uberon multi-species anatomy ontology | UBERON | An integrative, cross species ontology for anatomical terms. | |
| Unified phenotype ontology (uPheno) | UPHENO | An ontology for unified phenotypical descriptictions. | |
| Units of measurement ontology | UO | An ontology of metrical units, couplet to the PATO ontology. | |
| Vaccination Informed Consent Ontology [61] | VICO | An ontology of clinical informed consents focused on vaccination procedures. | |
| Vaccine Ontology [62] | VO | An ontology for concepts related to vaccines and vaccination. | |
| Vertebrate Taxonomy Ontology | VTO | An ontology for the taxonomy of vertebrates. | |
| Vertebrate Trait Ontology | VT | An ontology for traits covering vertebrates | |
| VEuPathDB ontology | EUPATH | An ontology for the support of the Eukaryotic Pathogen, Host & Vector Genomics Resource. | |
| Xenopus Anatomy Ontology [63] | XAO | Ontology of the anatomy of the African clawed frog (Xenopus laevis). | |
| Xenopus Phenotype Ontology | XPO | An ontology for anatomical, cellular, and gene function phenotypes in African clawed frogs (Xenopus laevis). | |
| Zebrafish anatomy and development ontology | ZFA | Ontology for the anatomy and development of the zebrafish (Danio rerio). | |
| Zebrafish developmental stages ontology | ZFS | An ontology for developmental stages of the zebrafish (Danio rerio). | |
| Zebrafish Experimental Conditions Ontology | ZECO | An ontology for experimental conditions used in zebrafish research and described in ZFIN. | |
| Zebrafish Phenotype Ontology | ZP | An ontology for the phenotypes of the zebrafish (Danio rerio). |
References
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- ↑ Smith JR, Park CA, Nigam R, Laulederkind SJ, Hayman GT, Wang SJ, et al. (October 2013). "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications". Journal of Biomedical Semantics. 4 (1): 26. doi:10.1186/2041-1480-4-26. PMC 3882879. PMID 24103152.
- ↑ Younesi E, Ansari S, Guendel M, Ahmadi S, Coggins C, Hoeng J, et al. (2014). "CSEO - the Cigarette Smoke Exposure Ontology". Journal of Biomedical Semantics. 5 (1): 31. doi:10.1186/2041-1480-5-31. PMC 4120729. PMID 25093069.
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- ↑ Roux, Julien; Robinson-Rechavi, Marc (March 2010). "An ontology to clarify homology-related concepts" (PDF). Trends in Genetics. 26 (3): 99–102. doi:10.1016/j.tig.2009.12.012. ISSN 0168-9525. PMID 20116127.
- ↑ Mulder N (2018-09-16). "Faculty of 1000 evaluation for A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog". doi:10.3410/f.732698975.793550674. S2CID 69505888.
{{cite journal}}: Cite journal requires|journal=(help)[clarification needed] - ↑ Yoder MJ, Mikó I, Seltmann KC, Bertone MA, Deans AR (December 2010). "A gross anatomy ontology for hymenoptera". PLOS ONE. 5 (12) e15991. Public Library of Science. Bibcode:2010PLoSO...515991Y. doi:10.1371/journal.pone.0015991. OCLC 719846058. PMC 3012123. PMID 21209921.
- ↑ Cowell LG, Smith B (2009-10-03). Infectious Disease Ontology. Springer New York. pp. 373–395. doi:10.1007/978-1-4419-1327-2_19. ISBN 978-1-4419-1326-5.
{{cite book}}:|work=ignored (help) - ↑ Ceusters W, Smith B (2015), "Aboutness: Towards Foundations for the Information Artifact Ontology", Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO), CEUR vol. 1515, pp. 1–5, retrieved 2020-02-15
- ↑ Hur J, Özgür A, Xiang Z, He Y (2015-01-06). "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions". Journal of Biomedical Semantics. 6 (1): 2. doi:10.1186/2041-1480-6-2. PMC 4362819. PMID 25785184.
- ↑ Topalis P, Mitraka E, Bujila I, Deligianni E, Dialynas E, Siden-Kiamos I, et al. (August 2010). "IDOMAL: an ontology for malaria". Malaria Journal. 9: 230. doi:10.1186/1475-2875-9-230. PMC 2925367. PMID 20698959.
- 1 2 Ceusters W, Smith B (December 2010). "Foundations for a realist ontology of mental disease". Journal of Biomedical Semantics. 1 (1): 10. doi:10.1186/2041-1480-1-10. PMC 3017014. PMID 21143905.
- ↑ Vita R, Overton JA, Seymour E, Sidney J, Kaufman J, Tallmadge RL, et al. (2016). "An ontology for major histocompatibility restriction". Journal of Biomedical Semantics. 7: 1. doi:10.1186/s13326-016-0045-5. PMC 4709943. PMID 26759709.
- ↑ Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, et al. (June 2006). "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)". Omics. 10 (2): 231–7. doi:10.1089/omi.2006.10.231. PMC 3167193. PMID 16901231.
- ↑ Tierrafría VH, Mejía-Almonte C, Camacho-Zaragoza JM, Salgado H, Alquicira K, Ishida C, et al. (March 2019). Wren J (ed.). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions". Bioinformatics. 35 (5): 856–864. doi:10.1093/bioinformatics/bty689. PMC 7963087. PMID 30137210.
- ↑ Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV (September 2013). "The mouse pathology ontology, MPATH; structure and applications". Journal of Biomedical Semantics. 4 (1): 18. doi:10.1186/2041-1480-4-18. PMC 3851164. PMID 24033988.
- ↑ Federhen S (January 2012). "The NCBI Taxonomy database". Nucleic Acids Research. 40 (Database issue): D136-43. doi:10.1093/nar/gkr1178. PMC 3245000. PMID 22139910.
- ↑ Yoder, Matthew; Dmitriev, Dmitry; Pereira, José Luis; Cigliano, Maria Marta (2017-08-14). "Design and use of NOMEN, an ontology defining the rules of biological nomenclature". Proceedings of TDWG. 1 e20284. doi:10.3897/tdwgproceedings.1.20284. ISSN 2535-0897.
- ↑ Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, et al. (2016-05-04). "The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology". Journal of Biomedical Semantics. 7 (1): 24. doi:10.1186/s13326-016-0066-0. PMC 4857245. PMID 27152146.
- ↑ Brochhausen M, Zheng J, Birtwell D, Williams H, Masci AM, Ellis HJ, Stoeckert CJ (2016-05-02). "OBIB-a novel ontology for biobanking". Journal of Biomedical Semantics. 7 (1): 23. doi:10.1186/s13326-016-0068-y. PMC 4855778. PMID 27148435.
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