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Items: 20

1.

The health care and life sciences community profile for dataset descriptions.

Dumontier M, Gray AJ, 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.

PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331.

2.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Bolleman JT, Mungall CJ, Strozzi F, Baran J, Dumontier M, Bonnal RJ, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJ.

J Biomed Semantics. 2016 Jun 13;7:39. doi: 10.1186/s13326-016-0067-z.

3.

Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search.

Alocci D, Mariethoz J, Horlacher O, Bolleman JT, Campbell MP, Lisacek F.

PLoS One. 2015 Dec 14;10(12):e0144578. doi: 10.1371/journal.pone.0144578.

4.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members..

Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310.

5.

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.

Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064.

6.

UniProt: a hub for protein information.

UniProt Consortium..

Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12. doi: 10.1093/nar/gku989.

7.

BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data.

Wu H, Fujiwara T, Yamamoto Y, Bolleman J, Yamaguchi A.

J Biomed Semantics. 2014 Jul 10;5:32. doi: 10.1186/2041-1480-5-32.

8.

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.

Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I; UniProt Consortium..

Hum Mutat. 2014 Aug;35(8):927-35. doi: 10.1002/humu.22594. Review.

9.

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.

Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K; UniProt Consortium..

Database (Oxford). 2014 Mar 12;2014:bau016. doi: 10.1093/database/bau016.

10.

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.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

11.

The EBI RDF platform: linked open data for the life sciences.

Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.

Bioinformatics. 2014 May 1;30(9):1338-9. doi: 10.1093/bioinformatics/btt765.

12.

Introducing glycomics data into the Semantic Web.

Aoki-Kinoshita KF, Bolleman J, Campbell MP, Kawano S, Kim JD, Lütteke T, Matsubara M, Okuda S, Ranzinger R, Sawaki H, Shikanai T, Shinmachi D, Suzuki Y, Toukach P, Yamada I, Packer NH, Narimatsu H.

J Biomed Semantics. 2013 Nov 26;4(1):39. doi: 10.1186/2041-1480-4-39.

13.

Activities at the Universal Protein Resource (UniProt).

UniProt Consortium..

Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8. doi: 10.1093/nar/gkt1140.

14.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

15.

Reorganizing the protein space at the Universal Protein Resource (UniProt).

UniProt Consortium..

Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. doi: 10.1093/nar/gkr981.

16.

UniProt Knowledgebase: a hub of integrated protein data.

Magrane M; UniProt Consortium..

Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009.

17.

Ongoing and future developments at the Universal Protein Resource.

UniProt Consortium..

Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. doi: 10.1093/nar/gkq1020.

18.

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.

Hinz U; UniProt Consortium..

Cell Mol Life Sci. 2010 Apr;67(7):1049-64. doi: 10.1007/s00018-009-0229-6. Review.

19.

The Universal Protein Resource (UniProt) in 2010.

UniProt Consortium..

Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. doi: 10.1093/nar/gkp846.

20.

The Universal Protein Resource (UniProt) 2009.

UniProt Consortium..

Nucleic Acids Res. 2009 Jan;37(Database issue):D169-74. doi: 10.1093/nar/gkn664.

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