Publications

2011-2016

  1. Bolleman JT, Mungall CJ, Strozzi F, Baran J, Dumontier M, Bonnal RJP, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJA (2016). FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation. J Biomed Semantics. In Press (preprint at bioRxiv doi:10.1101/002121).
  2. 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. The health care and life sciences community profile for dataset descriptions PeerJ Preprints 4:e1982v1 https://doi.org/10.7287/peerj.preprints.1982v1 (2016)
  3. SIB Swiss Institute of Bioinformatics Members. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases Nucleic Acids Res. 44:D27-D37 (2016). doi:10.1093/nar/gkv1310
  4. The UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 43:D204-D212 (2015). doi:10.1093/nar/gku989
  5. Alocci D, Mariethoz J, Horlacher O, Bolleman JT, Campbell MP, Lisacek F Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search PLOS http://dx.doi.org/10.1371/journal.pone.0144578 (2015)
  6. Wimalaratne SM, Bolleman JT, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H and Laibe C. SPARQL-enabled identifier conversion with Identifiers. org Bioinformatics 31:1875-1877 (2015). doi:10.1093/bioinformatics/btv064
  7. Famiglietti ML, Estreicher A, Gos A, Bolleman JT, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I; UniProt Consortium. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation Hum Mutat. 35:927-935 (2014). doi:10.1002/humu.22594
  8. Wu H, Fujiwara T, Yamamoto Y, Bolleman JT and Yamaguchi A BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data J of Biomedical Semantics 2014 5:32 doi:10.1186/2041-1480-5-32
  9. Jupp S, Malone J, Bolleman JT, 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. The EBI RDF platform: linked open data for the life sciences Bioinformatics 30:1338-1339 (2014). doi:10.1093/bioinformatics/btt765
  10. 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 JT, Bonnal TJP, Luigi Buttigieg P, Campbell MP, Chen Y, Chiba H, Cock PJA, K Bretonnel Cohen, 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, H Packer N, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin S, 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 and Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains J of Biomedical Semantics 2014 5:5 doi:10.1186/2041-1480-5-5
  11. The UniProt Consortium Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 42:D191-D198 doi:10.1093/nar/gkt1140
  12. Aoki-Kinoshita KF, Bolleman JT, Campbell MP, Kawano S, Kim Jin, Lütteke T, Matsubara M, Okuda S, Ranzinger R, Sawaki H, Shikanai T, Shinmachi D, Suzuki Y, Toukach P, Yamada I, Packer NH and Narimatsu H Introducing glycomics data into the Semantic Web J of Biomedical Semantics 2013 4:39 doi:10.1186/2041-1480-4-39
  13. 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 JT, Bonnal JPR, Chapman B, Cock PJA, Eriksson T, Gordon MKP, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim JY, 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. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies J of Biomedical Semantics 2013 4:6 doi: 10.1186/2041-1480-4-6
  14. The UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013
    15. Nucl. Acids Res. (2013) 41 (D1): D43-D47. doi: 10.1093/nar/gks1068
  15. Bolleman JT, Géhant S, Redaschi N. Catching inconsistencies with the semantic web: a biocuration case study. Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences Paris, France, November 28-30, 2012.