List of OBO Foundry ontologies
This is a list of ontologies that are part of the OBO Foundry as of January 2020.
OBO Foundry ontologies[]
Title | Prefix | Description | Official page |
---|---|---|---|
Agronomy Ontology | AGRO | Ontology of concepts relevant to agronomy experiments. | [1] |
An ontology of core ecological entities | ECOCORE | An ontology for ecological entities. | [2] |
Anatomical Entity Ontology | AEO | Ontology of anatomical structures that expand CARO, the Common Anatomy Reference Ontology. | [3] |
Antibiotic Resistance Ontology | ARO | Ontology for antibiotic resistance genes and mutations. | [4] |
Apollo Structured Vocabulary [1] | APOLLO-SV | Ontology for enabling interoperability of epidemic models and public health application software. | [5] |
Ascomycete phenotype ontology | APO | A structured controlled vocabulary for the phenotypes of Ascomycete fungi. | [6] |
Basic Formal Ontology[2] | BFO | The upper-level ontology upon which OBO Foundry ontologies are built. | [7] |
Beta Cell Genomics Ontology | BCGO | An application ontology built for beta cell genomic studies. | [8] |
Biological Collections Ontology [3] | BCO | An ontology for biodiversity data. | [9] |
Biological Imaging Methods Ontology | FBBI | Ontology for methods involved in biomedical imaging, including preparation and acquisition. | [10] |
Biological Spatial Ontology | BSPO | An ontology for representing spatial concepts used in biology. | [11] |
BRENDA tissue / enzyme source | BTO | An ontology for the source of enzymes. | [12] |
C. elegans development ontology (see WormBase) | WBLS | An ontology for the development of Caenorhabditis elegans. | [13] |
C. elegans Gross Anatomy Ontology (see WormBase) | WBBT | An ontology for the anatomy of Caenorhabditis elegans. | [14] |
C. elegans phenotype (see WormBase) | WBPHENOTYPE | An ontology for the phenotypes of Caenorhabditis elegans. | [15] |
Cardiovascular Disease Ontology | CVDO | An ontology for concepts related to cardiovascular diseases. | [16] [17] |
Cell Line Ontology [4] | CLO | Ontology to describe cell lines. | [18] [19] |
Cell Ontology [5] | CL | Ontology for metazoan cell types. | [20] [21] |
Chemical Entities of Biological Interest | CHEBI | Ontology of small molecular entities of biological interest. | [22] |
Chemical Information Ontology [6] | CHEMINF | Ontology for descriptors used in chemoinformatics databases. | [23] [24] |
Chemical Methods Ontology | CHMO | An ontology for the methods used in chemical experiments. | [25] |
Clinical LABoratory Ontology | LABO | An ontology of prescriptions and reports in clinical laboratories. | [26] |
Clinical measurement ontology [7] | CMO | Ontology to classify clinical measurements of experimental animals. | [27] |
Common Anatomy Reference Ontology [8] | CARO | An ontology to improve interoperability between anatomy ontologies for different organisms. | [28] |
Comparative Data Analysis Ontology [9] | CDAO | Ontology of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees. | [29] [30] |
Confidence Information Ontology [10] | CIO | An ontology to describe confidence information in sequence annotations. | [31] |
Contributor Role Ontology | CRO | An ontology for the diverse roles behind a scientific research article. | [32] [33] |
Ctenophore Ontology | CTENO | An anatomical and developmental ontology for ctenophores (Comb Jellies). | [34] |
Dictyostelium discoideum anatomy[11] | DDANAT | A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum. | [35] |
Dictyostelium discoideum phenotype ontology | DDPHENO | An ontology for phenotypes of the slime-mould Dictyostelium discoideum. | [36] |
Drosophila development | FBDV | An ontology of the development of Drosophila melanogaster. | [37] |
Drosophila gross anatomy[12] | FBBT | An ontology for the anatomy of Drosophila melanogaster. | [38] |
Drosophila Phenotype Ontology | FBCV | An ontology of common Drosophila phenotypes. | [39] |
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology [13] | DIDEO | Ontology for drug–drug interaction evidence. | [40] |
[14] | ECO | An ontology for types evidence used to support scientific claims. | [41] |
eagle-i resource ontology | ERO | An ontology of research equipment, protocols and consumables. | [42] |
Emotion Ontology [15] | MFOEM | An ontology of emotions, moods, and other kinds of feelings. | [44] |
Environment Ontology [16] | ENVO | Ontology of environmental features and habitats. | [45] |
Experimental condition ontology [17] | XCO | An ontology for the different conditions in which experimental measurements are taken. | [46] |
Exposure Ontology [18] | EXO | Ontology to describe exposure to environmental factors (such as cigarette smoke) that might influence clinical outcomes. | [47] |
Fission Yeast Phenotype Ontology[19] | FYPO | An ontology of phenotypes of fission yeast. | [48] [49] |
Flora Phenotype Ontology [20] | FLOPO | An ontology for traits and phenotypes of flowering plants. | [50] |
FlyBase Controlled Vocabulary | FBCV | An ontology to support the FlyBase project. | [51] |
Food Ontology [21] | FOODON | An ontology to represent entities that play a food role or related to foods. | [52] |
Foundational Model of Anatomy Ontology (subset) | FMAO | Subset of the Foundational Model of Anatomy Ontology. | [53] |
Fungal Anatomy Ontology | FAO | An ontology for the anatomy of fungi. | [54] |
Gazetteer | GAZ | An ontology that acts as a gazetteer (geographical dictionary). | [55] |
Gene Ontology | GO | An ontology for describing the function of genes and gene products. | [56] [57] |
Genomic Epidemiology Ontology [22] | GENEPIO | An ontology for foodborne pathogens and associated outbreaks. | [58] |
Genotype Ontology | GENO | An ontology for genotypes and their related phenotypes and diseases. | [59] |
Geographical Entity Ontology | GEO | An ontology of geographical entities. | [60] |
Glycan Naming Ontology [23] | GNOME | An ontology for glycans based on GlyTouCan. | [61] |
Homology Ontology [24] | HOM | An ontology for concepts related to homology. | [62] |
Human Ancestry Ontology [25] | HANCESTRO | An ontology of ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. | [63] |
Human Developmental Stages | HSAPDV | An ontology of stages of the human life. | [64] |
Human Disease Ontology | DO | An ontology for describing human diseases. | [65] |
Human Phenotype Ontology | HPO | An ontology for human phenotypes in hereditary and non-hereditary diseases. | [66] [67] |
HUPO-PSI cross-linking and derivatization reagents controlled vocabulary | PSI-MS | An ontology for reagents used to cross-link molecules in mass spectrometry experiments. | [68] |
Hymenoptera Anatomy Ontology [26] | HAO | An ontology of the anatomy of the Hymenoptera (bees, wasps, and ants). | [69] |
Hypertension Ontology | HTN | An ontology for clinical data about hypertension. | [70] |
Infectious Disease Ontology [27] | IDO | A set of ontologies related to infectious diseases. | [71] |
Information Artifact Ontology [28] | IAO | An ontology of information entities. | [72] |
Informed Consent Ontology | ICO | An ontology for concepts related to informed consent, such as forms and policies. | [73] |
Integrative and Conjugative Element Ontology | ICEO | An ontology of bacterial integrative and conjugative elements (ICEs). | [74] |
Interaction Network Ontology [29] | INO | An ontology for gene-gene interactions. | [75] |
Malaria Ontology [30] | IDOMAL | An ontology for concepts related to malaria. | [76] |
Mammalian Feeding Muscle Ontology | MFMO | An ontology for the mammalian muscles that play a role in feeding behavior. | [77] |
Mammalian Phenotype Ontology | MP | Standard terms for annotating mammalian phenotypic data. | [78] |
Mass spectrometry ontology | MI | An ontology for concepts to describe mass spectrometry in the context of proteomics. | [79] |
Measurement method ontology | MMO | An ontology for methods of clinical and laboratory measurements. | [80] |
Medaka Developmental Stages | OlatDv | An ontology of life stages for the medaka fish. | [81] |
Mental Disease Ontology [31] | MFOMD | An ontology for mental diseases. | [82] |
Mental Functioning Ontology [31] | MFO | An ontology for concepts related to mental functioning. | [83] [84] |
MHC Restriction Ontology [32] | MRO | An ontology for Major Histocompatibility Complex (MHC) restriction in experiments. | [85] |
MIAPA Ontology [33] | MIAPA | An ontology for phylogenetic data. | [86] |
Microbial Conditions Ontology [34] | MCO | An ontology for microbial growth conditions. | [87] |
Minimum PDDI Information Ontology | MPIO | An ontology of the minimum information to describe drug–drug interactions. | [88] |
Molecular Interactions Controlled Vocabulary | MI | An ontology for concepts related to the study of protein-protein interactions. | [89] |
Mondo Disease Ontology | MONDO | An ontology for the integration of information on disease. | [90] |
Mosquito gross anatomy ontology (VectorBase) | TGMA | An ontology for the anatomy of mosquitoes. | [91] |
Mouse adult gross anatomy ontology | EMAPA | An ontology for the adult anatomy of the mouse (Mus). | [92] |
Mouse Developmental Stages | MmusDv | An ontology of stages of the mouse (Mus) life. | [93] |
Mouse gross anatomy and development, timed | EMAP | Ontology of anatomical structures of the mouse (Mus musculus). | [94] |
Mouse Pathology Ontology [35] | MPATH | An ontology of mouse pathology phenotypes. | [95] |
Name Reaction Ontology | RXNO | An ontology for organic reactions in organic synthesis. | [96] |
NCBI organismal classification [36] | NCBITaxon | An ontology representation of the NCBI organismal taxonomy. | [97] |
Neuro Behavior Ontology | NBO | An ontology of behavioral phenotypes of animals. | [98] |
NOMEN - A nomenclatural ontology for biological names [37] | NOMEN | An ontology of the rules of nomenclature for biological names. | [99] |
Non-Coding RNA Ontology [38] | NCRO | An ontology for non-coding RNA function. | [100] |
Ontologized MIABIS | OMIABIS | An ontological version of MIABIS (Minimum Information About BIobank data Sharing). | [101] |
Ontology for Biobanking [39] | OBIB | An ontology for concepts related to biobanks. | [102] |
Ontology for Biomedical Investigations | OBI | An ontology which describes biological processes, cellular components and molecular functions in living organisms. | [103] |
Ontology for General Medical Science | OGMS | An ontology for general aspects of medicine, with a focus on cancer. | [104] |
Ontology for Parasite LifeCycle [40] | OPL | A reference ontology for parasite life cycle stages. | [105] |
Ontology of Adverse Events [41] | OAE | An ontology for adverse events of drug regimens. | [106] |
Ontology of Arthropod Circulatory Systems [42] | OARCS | An ontology for the circulatory systems of arthropods. | [107] |
Ontology of Biological and Clinical Statistics [43] | OBCS | An ontology to describe statistical tools and methods used in biomedical investigation. | [108] |
Ontology of Biological Attributes | OBA | An ontology for biological traits. | [109] |
Ontology of Medically Related Social Entities [44] | OMRSE | An ontology for entities (roles and organizations) related to healthcare. | [110] [111] |
Ontology of Microbial Phenotypes [45] | OMP | An ontology of phenotypes of microorganisms. | [112] |
Ontology of Organizational Structures of Trauma centers and Trauma systems | OOSTT | An ontology for the organizational structures of trauma centers and trauma systems. | [113] |
Ontology of Precision Medicine and Investigation | OPMI | An ontology for concepts related to precision medicine. | [114] |
Ontology of Prokaryotic Phenotypic and Metabolic Characters [46] | MICRO | An ontology of prokaryotic phenotypic and metabolic characters. | [115] |
Ontology of RNA Sequencing | ORNASEQ | An ontology to annotate RNA Sequencing experiments. | [116] |
Ontology of Vaccine Adverse Events [47] | OVAE | An ontology for adverse events of vaccines. | [117] [118] |
Pathogen Host Interaction Phenotype Ontology | PHIPO | An ontology of phenotypes that occur in pathogen-host interactions. | [119] |
Pathogen Transmission Ontology | TRANS | An ontology for disease transmission processes. | [120] |
Pathway ontology | PW | An ontology for annotating gene products to pathways. | [121] |
Performance Summary Display Ontology | PSDO | An ontology for concepts related to performance information for teams and organizations. | [122] |
Phenotype And Trait Ontology | FOBI | FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data. | [123] |
Planaria Ontology | PLANA | An ontology for the anatomy and developmental stages of the planaria (Schmidtea mediterranea). | [124] |
Planarian Phenotype Ontology | PLANP | An ontology for phenotypes of the planaria (Schmidtea mediterranea). | [125] |
Plant Experimental Conditions Ontology | PECO | An ontology for concepts related to plant biology experiments. | [126] |
Plant ontology | PO | An ontology and database resource that links plant traits to genomics data. | [127] |
Plant Phenology Ontology | PPO | An ontology for describing the cyclic phenomena of plants. | [128] |
Plant Trait Ontology | TO | An ontology for phenotypic traits in plants. | [129] |
Platynereis Developmental Stages | PDUMDV | An ontology for life stages of the annelid Platynereis dumerilii. | [130] |
Population and Community Ontology | PCO | An ontology for describing groups of interacting organisms. | [131] |
Porifera Ontology [48] | PORO | An ontology for the anatomy of sponges (Porifera) | [132] |
Protein modification [49] | MOD | An ontology for protein chemical modifications. | [133] |
Protein Ontology [50] | PRO | An ontological representation of protein-related entities. | [134] |
Rat Strain Ontology [51] | RS | An ontology for laboratorial rat strains. | [135] |
Relation Ontology [52] | RO | An ontology for relations between terms in the ontologies. | [136] |
Scientific Evidence and Provenance Information Ontology | SEPIO | An ontology for the provenance of scientific claims and supporting evidence. | [137] |
Sequence types and features ontology | SO | An ontology for annotation of sequences. | [138] |
Software Ontology[53] | SWO | An ontology to describe software applications with a focus on bioinformatics tools. | [139] |
Spider Ontology[54] | SPD | An ontology for anatomy and behavior of spiders as well as spider-derived products. | [140] |
Symptom Ontology | SYMP | An ontology of disease symptoms. | [141] |
Taxonomic rank vocabulary | TAXRANK | An ontology of taxonomic ranks in systematics. | [142] |
Teleost taxonomy ontology [55] | TTO | An ontology for the taxonomy of teleost fish. | [143] |
The Data Use Ontology [56] | DUO | Ontology for conditions of data use. | [144] |
The Drug Ontology [57] | DRON | An ontology for drug products. | [145] |
The Ontology of Genes and Genomes | OGG | An ontology of genes and genomes of biological organisms. | [146] |
The Oral Health and Disease Ontology [58] | OHD | An ontology for the content of teeth-related health records. | [147] |
The Prescription of Drugs Ontology [59] | PDRO | An ontology for concepts related to prescription of drugs. | [148] |
The Statistical Methods Ontology | STATO | An ontology for statistical methods, such as tests and experimental designs. | [149] |
Tick Anatomy Ontology [60] | TADS | An ontology for the anatomy of the tick families Ixodidae and Argasidae. | [150] |
Uberon multi-species anatomy ontology | UBERON | An integrative, cross species ontology for anatomical terms. | [151] |
Unified phenotype ontology (uPheno) | UPHENO | An ontology for unified phenotypical descriptictions. | [152] |
Units of measurement ontology | UO | An ontology of metrical units, couplet to the PATO ontology. | [153] |
Vaccination Informed Consent Ontology [61] | VICO | An ontology of clinical informed consents focused on vaccination procedures. | [154] |
Vaccine Ontology [62] | VO | An ontology for concepts related to vaccines and vaccination. | [155] |
Vertebrate Taxonomy Ontology | VTO | An ontology for the taxonomy of vertebrates. | [156] |
Vertebrate Trait Ontology | VT | An ontology for traits covering vertebrates | [157] |
VEuPathDB ontology | EUPATH | An ontology for the support of the Eukaryotic Pathogen, Host & Vector Genomics Resource. | [158] |
Xenopus Anatomy Ontology [63] | XAO | Ontology of the anatomy of the African clawed frog (Xenopus laevis). | [159] |
Xenopus Phenotype Ontology | XPO | An ontology for anatomical, cellular, and gene function phenotypes in African clawed frogs (Xenopus laevis). | [160] |
Zebrafish anatomy and development ontology | ZFA | Ontology for the anatomy and development of the zebrafish (Danio rerio). | [161] |
Zebrafish developmental stages ontology | ZFS | An ontology for developmental stages of the zebrafish (Danio rerio). | [162] |
Zebrafish Experimental Conditions Ontology | ZECO | An ontology for experimental conditions used in zebrafish research and described in ZFIN. | [163] |
Zebrafish Phenotype Ontology | ZP | An ontology for the phenotypes of the zebrafish (Danio rerio). | [164] |
References[]
- ^ Hogan WR, Wagner MM, Brochhausen M, Levander J, Brown ST, Millett N, et al. (August 2016). "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation". Journal of Biomedical Semantics. 7 (1): 50. doi:10.1186/s13326-016-0092-y. PMC 4989460. PMID 27538448.
- ^ Arp R. Building ontologies with basic formal ontology. ISBN 978-0-262-32958-3. OCLC 951562682.
- ^ Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, et al. (2014-03-03). "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies". PLOS ONE. 9 (3): e89606. Bibcode:2014PLoSO...989606W. doi:10.1371/journal.pone.0089606. PMC 3940615. PMID 24595056.
- ^ Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, et al. (2014-08-13). "CLO: The cell line ontology". Journal of Biomedical Semantics. 5 (1): 37. doi:10.1186/2041-1480-5-37. PMC 4387853. PMID 25852852.
- ^ Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, et al. (July 2016). "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability". Journal of Biomedical Semantics. 7 (1): 44. doi:10.1186/s13326-016-0088-7. PMC 4932724. PMID 27377652.
- ^ Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M (2011-10-03). "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web". PLOS ONE. 6 (10): e25513. Bibcode:2011PLoSO...625513H. doi:10.1371/journal.pone.0025513. PMC 3184996. PMID 21991315.
- ^ Smith, Jennifer R; Park, Carissa A; Nigam, Rajni; Laulederkind, Stanley JF; Hayman, G; Wang, Shur-Jen; Lowry, Timothy F; Petri, Victoria; Pons, Jeff; Tutaj, Marek; Liu, Weisong (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. ISSN 2041-1480. PMC 3882879. PMID 24103152.
- ^ Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JL, Mungall CJ, Smith B (2008). "CARO – The Common Anatomy Reference Ontology". Anatomy Ontologies for Bioinformatics. Computational Biology. 6. Springer London. pp. 327–349. doi:10.1007/978-1-84628-885-2_16. ISBN 978-1-84628-884-5.
- ^ Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A (July 2009). "Initial implementation of a comparative data analysis ontology". Evolutionary Bioinformatics Online. 5: 47–66. doi:10.4137/ebo.s2320. PMC 2747124. PMID 19812726.
- ^ Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, et al. (2015-05-09). "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations". Database. 2015: bav043. doi:10.1093/database/bav043. PMC 4425939. PMID 25957950.
- ^ Gaudet P, Williams JG, Fey P, Chisholm RL (March 2008). "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum". BMC Genomics. 9 (1): 130. doi:10.1186/1471-2164-9-130. PMC 2323390. PMID 18366659.
- ^ Costa M, Reeve S, Grumbling G, Osumi-Sutherland D (October 2013). "The Drosophila anatomy ontology". Journal of Biomedical Semantics. 4 (1): 32. doi:10.1186/2041-1480-4-32. PMC 4015547. PMID 24139062.
- ^ Utecht J, Brochhausen M, Judkins J, Schneider J, Boyce RD (2017). "Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation". Studies in Health Technology and Informatics. 245: 960–964. PMC 5765984. PMID 29295242.
- ^ Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, et al. (January 2019). "ECO, the Evidence & Conclusion Ontology: community standard for evidence information". Nucleic Acids Research. 47 (D1): D1186–D1194. doi:10.1093/nar/gky1036. PMC 6323956. PMID 30407590.
- ^ Hastings J, Brass A, Caine C, Jay C, Stevens R (2014). "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference". Journal of Biomedical Semantics. 5: 38. doi:10.1186/2041-1480-5-38. PMC 4417517. PMID 25937879.
- ^ Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE (December 2013). "The environment ontology: contextualising biological and biomedical entities". Journal of Biomedical Semantics. 4 (1): 43. doi:10.1186/2041-1480-4-43. PMC 3904460. PMID 24330602.
- ^ 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.
- ^ Harris MA, Lock A, Bähler J, Oliver SG, Wood V (July 2013). "FYPO: the fission yeast phenotype ontology". Bioinformatics. 29 (13): 1671–8. doi:10.1093/bioinformatics/btt266. PMC 3694669. PMID 23658422.
- ^ Hoehndorf R, Alshahrani M, Gkoutos GV, Gosline G, Groom Q, Hamann T, et al. (November 2016). "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants". Journal of Biomedical Semantics. 7 (1): 65. doi:10.1186/s13326-016-0107-8. PMC 5109718. PMID 27842607.
- ^ Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, et al. (December 2018). "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration". NPJ Science of Food. 2 (1): 23. doi:10.1038/s41538-018-0032-6. PMC 6550238. PMID 31304272.
- ^ Griffiths, Emma; Dooley, Damion; Graham, Morag; Van Domselaar, Gary; Brinkman, Fiona S. L.; Hsiao, William W. L. (2017-06-26). "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance". Frontiers in Microbiology. 8: 1068. doi:10.3389/fmicb.2017.01068. ISSN 1664-302X. PMC 5483436. PMID 28694792.
- ^ Sahoo SS, Thomas C, Sheth A, York WS, Tartir S (2006). "Knowledge modeling and its application in life sciences". Proceedings of the 15th International Conference on World Wide Web - WWW '06. New York, New York, USA: ACM Press: 317. doi:10.1145/1135777.1135826. ISBN 1-59593-323-9. S2CID 10764748.
- ^ 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. 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. Public Library of Science. 5 (12): e15991. 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. Infectious Disease Informatics. Springer New York. pp. 373–395. doi:10.1007/978-1-4419-1327-2_19. ISBN 978-1-4419-1326-5.
- ^ 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.
- ^ a b 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.
- ^ Parikh PP, Zheng J, Logan-Klumpler F, Stoeckert CJ, Louis C, Topalis P, et al. (May 2012). "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms". Journal of Biomedical Semantics. 3 (1): 5. doi:10.1186/2041-1480-3-5. PMC 3488002. PMID 22621763.
- ^ He Y, Sarntivijai S, Lin Y, Xiang Z, Guo A, Zhang S, et al. (2014). "OAE: The Ontology of Adverse Events". Journal of Biomedical Semantics. 5 (1): 29. doi:10.1186/2041-1480-5-29. PMC 4120740. PMID 25093068.
- ^ Wirkner CS, Göpel T, Runge J, Keiler J, Klussmann-Fricke BJ, Huckstorf K, et al. (September 2017). "The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions". Systematic Biology. 66 (5): 754–768. doi:10.1093/sysbio/syw108. PMID 28123116.
- ^ Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y (September 2016). "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis". Journal of Biomedical Semantics. 7 (1): 53. doi:10.1186/s13326-016-0100-2. PMC 5024438. PMID 27627881.
- ^ Hicks A, Hanna J, Welch D, Brochhausen M, Hogan WR (July 2016). "The ontology of medically related social entities: recent developments". Journal of Biomedical Semantics. 7 (1): 47. doi:10.1186/s13326-016-0087-8. PMC 4942889. PMID 27406187.
- ^ Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, et al. (November 2014). "An ontology for microbial phenotypes". BMC Microbiology. 14 (1): 294. doi:10.1186/s12866-014-0294-3. PMC 4287307. PMID 25433798.
- ^ Blank CE, Cui H, Moore LR, Walls RL (December 2016). "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions". Journal of Biomedical Semantics. 7 (1): 18. doi:10.1186/s13326-016-0060-6. PMC 4830071. PMID 27076900.
- ^ Marcos E, Zhao B, He Y (November 2013). "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines". Journal of Biomedical Semantics. 4 (1): 40. doi:10.1186/2041-1480-4-40. PMC 4177204. PMID 24279920.
- ^ Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ (2014-09-08). "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology". Journal of Biomedical Semantics. 5 (1): 39. doi:10.1186/2041-1480-5-39. PMC 4177528. PMID 25276334.
- ^ Montecchi-Palazzi, Luisa; Beavis, Ron; Binz, Pierre-Alain; Chalkley, Robert J; Cottrell, John; Creasy, David; Shofstahl, Jim; Seymour, Sean L; Garavelli, John S (August 2008). "The PSI-MOD community standard for representation of protein modification data". Nature Biotechnology. 26 (8): 864–866. doi:10.1038/nbt0808-864. ISSN 1087-0156. PMID 18688235. S2CID 205270043.
- ^ Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, et al. (January 2017). "Protein Ontology (PRO): enhancing and scaling up the representation of protein entities". Nucleic Acids Research. 45 (D1): D339–D346. doi:10.1093/nar/gkw1075. PMC 5210558. PMID 27899649.
- ^ Nigam, Rajni; Munzenmaier, Diane H; Worthey, Elizabeth A; Dwinell, Melinda R; Shimoyama, Mary; Jacob, Howard J (2013). "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD". Journal of Biomedical Semantics. 4 (1): 36. doi:10.1186/2041-1480-4-36. ISSN 2041-1480. PMC 4177145. PMID 24267899.
- ^ Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, et al. (2005). "Relations in biomedical ontologies". Genome Biology. 6 (5): R46. doi:10.1186/gb-2005-6-5-r46. PMC 1175958. PMID 15892874.
- ^ Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R (2014). "The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation". Journal of Biomedical Semantics. 5 (1): 25. doi:10.1186/2041-1480-5-25. PMC 4098953. PMID 25068035.
- ^ Ramírez MJ, Michalik P (2019-10-22). "The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data". Diversity. 11 (10): 202. doi:10.3390/d11100202. ISSN 1424-2818.
- ^ Midford P, Balhoff J, Dahdul W, Kothari C, Lapp H, Lundberg J, et al. (2010-07-06). "The Teleost Taxonomy Ontology". Nature Precedings. doi:10.1038/npre.2010.4629.1.
- ^ Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, et al. (January 2016). Barsh GS (ed.). "Consent Codes: Upholding Standard Data Use Conditions". PLOS Genetics. 12 (1): e1005772. doi:10.1371/journal.pgen.1005772. PMC 4721915. PMID 26796797.
- ^ Hanna J, Joseph E, Brochhausen M, Hogan WR (December 2013). "Building a drug ontology based on RxNorm and other sources". Journal of Biomedical Semantics. 4 (1): 44. doi:10.1186/2041-1480-4-44. PMC 3931349. PMID 24345026.
- ^ Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, et al. (2013-03-18). "An ontology-based method for secondary use of electronic dental record data". AMIA Joint Summits on Translational Science Proceedings. AMIA Joint Summits on Translational Science. 2013: 234–8. PMC 3845770. PMID 24303273.
- ^ Ethier JF, Barton A, Taseen R (2018-11-09). "An ontological analysis of drug prescriptions". Applied Ontology. 13 (4): 273–294. doi:10.3233/ao-180202.
- ^ Topalis P, Tzavlaki C, Vestaki K, Dialynas E, Sonenshine DE, Butler R, et al. (February 2008). "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase". Insect Molecular Biology. 17 (1): 87–9. doi:10.1111/j.1365-2583.2008.00781.x. PMID 18237287. S2CID 8618269.
- ^ Lin Y, Zheng J, He Y (2016-04-19). "VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms". Journal of Biomedical Semantics. 7 (1): 20. doi:10.1186/s13326-016-0062-4. PMC 4837519. PMID 27099700.
- ^ He Y, Cowell L, Diehl A, Mobley H, Peters B, Ruttenberg A, et al. (2009-08-05). "VO: Vaccine Ontology". Nature Precedings. doi:10.1038/npre.2009.3553. Missing
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(help) - ^ Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, et al. (October 2013). "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase". Journal of Biomedical Semantics. 4 (1): 31. doi:10.1186/2041-1480-4-31. PMC 3816597. PMID 24139024.
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