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OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B. Jackson R, et al. Among authors: ruttenberg a. Database (Oxford). 2021 Oct 26;2021:baab069. doi: 10.1093/database/baab069. Database (Oxford). 2021. PMID: 34697637 Free PMC article.
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium; Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. Smith B, et al. Among authors: ruttenberg a. Nat Biotechnol. 2007 Nov;25(11):1251-5. doi: 10.1038/nbt1346. Nat Biotechnol. 2007. PMID: 17989687 Free PMC article.
OntoFox: web-based support for ontology reuse.
Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. Xiang Z, et al. Among authors: ruttenberg a. BMC Res Notes. 2010 Jun 22;3:175. doi: 10.1186/1756-0500-3-175. BMC Res Notes. 2010. PMID: 20569493 Free PMC article.
Modeling biomedical experimental processes with OBI.
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J; OBI consortium. Brinkman RR, et al. Among authors: ruttenberg a. J Biomed Semantics. 2010 Jun 22;1 Suppl 1(Suppl 1):S7. doi: 10.1186/2041-1480-1-S1-S7. J Biomed Semantics. 2010. PMID: 20626927 Free PMC article.
A strategy for building neuroanatomy ontologies.
Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD. Osumi-Sutherland D, et al. Among authors: ruttenberg a. Bioinformatics. 2012 May 1;28(9):1262-9. doi: 10.1093/bioinformatics/bts113. Epub 2012 Mar 7. Bioinformatics. 2012. PMID: 22402613 Free article.
Protein Ontology: a controlled structured network of protein entities.
Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. Natale DA, et al. Among authors: ruttenberg a. Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24270789 Free PMC article.
An ontology-based method for secondary use of electronic dental record data.
Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, Song M, Thyvalikakath TP, Liu K, Hernandez P. Schleyer TK, et al. Among authors: ruttenberg a. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:234-8. eCollection 2013. AMIA Jt Summits Transl Sci Proc. 2013. PMID: 24303273 Free PMC article.
The neurological disease ontology.
Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD. Jensen M, et al. Among authors: ruttenberg a. J Biomed Semantics. 2013 Dec 6;4(1):42. doi: 10.1186/2041-1480-4-42. J Biomed Semantics. 2013. PMID: 24314207 Free PMC article.
flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR. Courtot M, et al. Among authors: ruttenberg a. Bioinformatics. 2015 Apr 15;31(8):1337-9. doi: 10.1093/bioinformatics/btu807. Epub 2014 Dec 6. Bioinformatics. 2015. PMID: 25481008 Free PMC article.
38 results