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The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.
Arnaud E, Laporte MA, Kim S, Aubert C, Leonelli S, Miro B, Cooper L, Jaiswal P, Kruseman G, Shrestha R, Buttigieg PL, Mungall CJ, Pietragalla J, Agbona A, Muliro J, Detras J, Hualla V, Rathore A, Das RR, Dieng I, Bauchet G, Menda N, Pommier C, Shaw F, Lyon D, Mwanzia L, Juarez H, Bonaiuti E, Chiputwa B, Obileye O, Auzoux S, Yeumo ED, Mueller LA, Silverstein K, Lafargue A, Antezana E, Devare M, King B. Arnaud E, et al. Among authors: buttigieg pl. Patterns (N Y). 2020 Sep 25;1(7):100105. doi: 10.1016/j.patter.2020.100105. eCollection 2020 Oct 9. Patterns (N Y). 2020. PMID: 33205138 Free PMC article.
Emerging semantics to link phenotype and environment.
Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. Thessen AE, et al. Among authors: buttigieg pl. PeerJ. 2015 Dec 14;3:e1470. doi: 10.7717/peerj.1470. eCollection 2015. PeerJ. 2015. PMID: 26713234 Free PMC article.
Transforming the study of organisms: Phenomic data models and knowledge bases.
Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Thessen AE, et al. Among authors: buttigieg pl. PLoS Comput Biol. 2020 Nov 24;16(11):e1008376. doi: 10.1371/journal.pcbi.1008376. eCollection 2020 Nov. PLoS Comput Biol. 2020. PMID: 33232313 Free PMC article. Review.
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: buttigieg pl. Database (Oxford). 2021 Oct 26;2021:baab069. doi: 10.1093/database/baab069. Database (Oxford). 2021. PMID: 34697637 Free PMC article.
Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability.
Meyer R, Appeltans W, Duncan WD, Dimitrova M, Gan YM, Stjernegaard Jeppesen T, Mungall C, Paul DL, Provoost P, Robertson T, Schriml L, Suominen S, Walls R, Sweetlove M, Ung V, Van de Putte A, Wallis E, Wieczorek J, Buttigieg PL. Meyer R, et al. Among authors: buttigieg pl. Biodivers Data J. 2023 Oct 3;11:e112420. doi: 10.3897/BDJ.11.e112420. eCollection 2023. Biodivers Data J. 2023. PMID: 37829294 Free PMC article.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. Yilmaz P, et al. Among authors: buttigieg pl. Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823. Nat Biotechnol. 2011. PMID: 21552244 Free PMC article.
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.
Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, Bowers S, Buttigieg PL, Davies N, Endresen D, Gandolfo MA, Hanner R, Janning A, Krishtalka L, Matsunaga A, Midford P, Morrison N, Ó Tuama É, Schildhauer M, Smith B, Stucky BJ, Thomer A, Wieczorek J, Whitacre J, Wooley J. Walls RL, et al. Among authors: buttigieg pl. PLoS One. 2014 Mar 3;9(3):e89606. doi: 10.1371/journal.pone.0089606. eCollection 2014. PLoS One. 2014. PMID: 24595056 Free PMC article.
Value, but high costs in post-deposition data curation.
ten Hoopen P, Amid C, Buttigieg PL, Pafilis E, Bravakos P, Cerdeño-Tárraga AM, Gibson R, Kahlke T, Legaki A, Narayana Murthy K, Papastefanou G, Pereira E, Rossello M, Luisa Toribio A, Cochrane G. ten Hoopen P, et al. Among authors: buttigieg pl. Database (Oxford). 2016 Feb 9;2016:bav126. doi: 10.1093/database/bav126. Print 2016. Database (Oxford). 2016. PMID: 26861660 Free PMC article.
39 results