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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

References

  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.
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  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.
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  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.