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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. McMurry JA, et al. Among authors: jimenez rc. PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun. PLoS Biol. 2017. PMID: 28662064 Free PMC article.
Uniform resolution of compact identifiers for biomedical data.
Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Wimalaratne SM, et al. Sci Data. 2018 May 8;5:180029. doi: 10.1038/sdata.2018.29. Sci Data. 2018. PMID: 29737976 Free PMC article.
Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H. Villaveces JM, et al. Among authors: jimenez rc. Bioinformatics. 2011 Sep 15;27(18):2616-7. doi: 10.1093/bioinformatics/btr433. Epub 2011 Jul 28. Bioinformatics. 2011. PMID: 21798964 Free PMC article.
Tools and data services registry: a community effort to document bioinformatics resources.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Ison J, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3. Nucleic Acids Res. 2016. PMID: 26538599 Free PMC article.
Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Perez-Riverol Y, et al. Among authors: jimenez rc. Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. Nat Biotechnol. 2017. PMID: 28486464 Free PMC article. No abstract available.
Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H. Jimenez RC, et al. Bioinformatics. 2008 Sep 15;24(18):2119-21. doi: 10.1093/bioinformatics/btn387. Epub 2008 Aug 11. Bioinformatics. 2008. PMID: 18694895
General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J. Silva LB, et al. Among authors: jimenez rc. F1000Res. 2017 Mar 15;6:273. doi: 10.12688/f1000research.10750.2. eCollection 2017. F1000Res. 2017. PMID: 28443186 Free PMC article. Review.
MyDas, an extensible Java DAS server.
Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H. Salazar GA, et al. Among authors: jimenez rc. PLoS One. 2012;7(9):e44180. doi: 10.1371/journal.pone.0044180. Epub 2012 Sep 13. PLoS One. 2012. PMID: 23028496 Free PMC article.
The bio.tools registry of software tools and data resources for the life sciences.
Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. Ison J, et al. Genome Biol. 2019 Aug 12;20(1):164. doi: 10.1186/s13059-019-1772-6. Genome Biol. 2019. PMID: 31405382 Free PMC article.
57 results