Jump to content

List of OBO Foundry ontologies

Add links
From Wikipedia, the free encyclopedia

This is the current revision of this page, as edited by OAbot (talk | contribs) at 04:03, 4 January 2024 (Open access bot: hdl updated in citation with #oabot.). The present address (URL) is a permanent link to this version.

(diff) ← Previous revision | Latest revision (diff) | Newer revision → (diff)

This is a list of ontologies that are part of the OBO Foundry as of January 2020.

OBO Foundry ontologies

[edit]
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]
Evidence & Conclusion Ontology[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]

[43]

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

[edit]
  1. ^ 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.
  2. ^ Arp R. Building ontologies with basic formal ontology. ISBN 978-0-262-32958-3. OCLC 951562682.
  3. ^ 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.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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.
  7. ^ 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.
  8. ^ 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. Vol. 6. Springer London. pp. 327–349. doi:10.1007/978-1-84628-885-2_16. ISBN 978-1-84628-884-5. S2CID 14660678.
  9. ^ 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.
  10. ^ 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.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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.
  18. ^ 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.
  19. ^ 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.
  20. ^ 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.
  21. ^ 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.
  22. ^ 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.
  23. ^ 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. pp. 317–326. doi:10.1145/1135777.1135826. ISBN 1-59593-323-9. S2CID 10764748.
  24. ^ 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.
  25. ^ 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]
  26. ^ Yoder MJ, Mikó I, Seltmann KC, Bertone MA, Deans AR (December 2010). "A gross anatomy ontology for hymenoptera". PLOS ONE. 5 (12). Public Library of Science: e15991. Bibcode:2010PLoSO...515991Y. doi:10.1371/journal.pone.0015991. OCLC 719846058. PMC 3012123. PMID 21209921.
  27. ^ 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)
  28. ^ 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
  29. ^ 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.
  30. ^ 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.
  31. ^ 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.
  32. ^ 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.
  33. ^ 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.
  34. ^ 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.
  35. ^ 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.
  36. ^ 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.
  37. ^ 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.
  38. ^ 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.
  39. ^ 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.
  40. ^ 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.
  41. ^ 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.
  42. ^ 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.
  43. ^ 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.
  44. ^ 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.
  45. ^ 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.
  46. ^ 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.
  47. ^ 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.
  48. ^ 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.
  49. ^ 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.
  50. ^ 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.
  51. ^ 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.
  52. ^ 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.
  53. ^ 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.
  54. ^ 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. hdl:11336/120759. ISSN 1424-2818.
  55. ^ Midford P, Balhoff J, Dahdul W, Kothari C, Lapp H, Lundberg J, et al. (2010-07-06). "The Teleost Taxonomy Ontology". Nature Precedings: 1. doi:10.1038/npre.2010.4629.1.
  56. ^ 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.
  57. ^ 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.
  58. ^ 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.
  59. ^ 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. S2CID 53442324.
  60. ^ 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.
  61. ^ 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.
  62. ^ He Y, Cowell L, Diehl A, Mobley H, Peters B, et al. (2009-08-05). "VO: Vaccine Ontology". Nature Precedings. doi:10.1038/npre.2009.3553.
  63. ^ 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.
Retrieved from "https://en.wikipedia.org/w/index.php?title=List_of_OBO_Foundry_ontologies&oldid=1193502120"