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Page 1
Finding our way through phenotypes.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. Deans AR, et al. Among authors: smith ad, smith b. PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan. PLoS Biol. 2015. PMID: 25562316 Free PMC article.
Ontologies as integrative tools for plant science.
Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW. Walls RL, et al. Among authors: smith b. Am J Bot. 2012 Aug;99(8):1263-75. doi: 10.3732/ajb.1200222. Epub 2012 Jul 30. Am J Bot. 2012. PMID: 22847540 Free PMC article.
The plant ontology as a tool for comparative plant anatomy and genomic analyses.
Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. Cooper L, et al. Among authors: smith b. Plant Cell Physiol. 2013 Feb;54(2):e1. doi: 10.1093/pcp/pcs163. Epub 2012 Dec 5. Plant Cell Physiol. 2013. PMID: 23220694 Free PMC article.
The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. Bandrowski A, et al. Among authors: smith b. PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016. PLoS One. 2016. PMID: 27128319 Free PMC article.
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: smith b. Database (Oxford). 2021 Oct 26;2021:baab069. doi: 10.1093/database/baab069. Database (Oxford). 2021. PMID: 34697637 Free PMC article.
OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.
Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva Nd, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A. Huang J, et al. Among authors: smith b. J Biomed Semantics. 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016. J Biomed Semantics. 2016. PMID: 27175225 Free PMC article.
The representation of protein complexes in the Protein Ontology (PRO).
Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C. Bult CJ, et al. Among authors: smith b. BMC Bioinformatics. 2011 Sep 19;12:371. doi: 10.1186/1471-2105-12-371. BMC Bioinformatics. 2011. PMID: 21929785 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. Nat Biotechnol. 2007 Nov;25(11):1251-5. doi: 10.1038/nbt1346. Nat Biotechnol. 2007. PMID: 17989687 Free PMC article.
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