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BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. Katayama T, et al. Among authors: dumontier m. J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5. J Biomed Semantics. 2014. PMID: 24495517 Free PMC article.
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. Vos RA, et al. Among authors: dumontier m. F1000Res. 2020 Feb 24;9:136. doi: 10.12688/f1000research.18236.1. eCollection 2020. F1000Res. 2020. PMID: 32308977 Free PMC article.
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.
Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R. Dumontier M, et al. J Biomed Semantics. 2014 Mar 6;5(1):14. doi: 10.1186/2041-1480-5-14. J Biomed Semantics. 2014. PMID: 24602174 Free PMC article.
SPARQL-enabled identifier conversion with Identifiers.org.
Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. Wimalaratne SM, et al. Among authors: dumontier m. Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31. Bioinformatics. 2015. PMID: 25638809 Free PMC article.
The health care and life sciences community profile for dataset descriptions.
Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A. Dumontier M, et al. PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331. eCollection 2016. PeerJ. 2016. PMID: 27602295 Free PMC article.
Automatically exposing OpenLifeData via SADI semantic Web Services.
González AR, Callahan A, Cruz-Toledo J, Garcia A, Egaña Aranguren M, Dumontier M, Wilkinson MD. González AR, et al. Among authors: dumontier m. J Biomed Semantics. 2014 Nov 19;5:46. doi: 10.1186/2041-1480-5-46. eCollection 2014. J Biomed Semantics. 2014. PMID: 25937881 Free PMC article.
GFVO: the Genomic Feature and Variation Ontology.
Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M. Baran J, et al. Among authors: dumontier m. PeerJ. 2015 May 5;3:e933. doi: 10.7717/peerj.933. eCollection 2015. PeerJ. 2015. PMID: 26019997 Free PMC article.
Special issue on bio-ontologies and phenotypes.
Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH. Soldatova LN, et al. Among authors: dumontier m. J Biomed Semantics. 2015 Dec 17;6:40. doi: 10.1186/s13326-015-0040-2. eCollection 2015. J Biomed Semantics. 2015. PMID: 26682035 Free PMC article.
164 results