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

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• 作者：Toshiaki Katayama (1)
  Mark D Wilkinson (1)
  Gos Micklem (1)
  Shuichi Kawashima (1)
  Atsuko Yamaguchi (1)
  Mitsuteru Nakao (1)
  Yasunori Yamamoto (1)
  Shinobu Okamoto (1)
  Kenta Oouchida (1)
  Hong-Woo Chun (1)
  Jan Aerts (1)
  Hammad Afzal (1)
  Erick Antezana (1)
  Kazuharu Arakawa (1)
  Bruno Aranda (1)
  Francois Belleau (1)
  Jerven Bolleman (1)
  Raoul JP Bonnal (1)
  Brad Chapman (1)
  Peter JA Cock (1)
  Tore Eriksson (1)
  Paul MK Gordon (1)
  Naohisa Goto (1)
  Kazuhiro Hayashi (1)
  Heiko Horn (1)
  Ryosuke Ishiwata (1)
  Eli Kaminuma (1)
  Arek Kasprzyk (1)
  Hideya Kawaji (1)
  Nobuhiro Kido (1)
  Young Joo Kim (1)
  Akira R Kinjo (1)
  Fumikazu Konishi (1)
  Kyung-Hoon Kwon (1)
  Alberto Labarga (1)
  Anna-Lena Lamprecht (1)
  Yu Lin (1)
  Pierre Lindenbaum (1)
  Luke McCarthy (1)
  Hideyuki Morita (1)
  Katsuhiko Murakami (1)
  Koji Nagao (1)
  Kozo Nishida (1)
  Kunihiro Nishimura (1)
  Tatsuya Nishizawa (1)
  Soichi Ogishima (1)
  Keiichiro Ono (1)
  Kazuki Oshita (1)
  Keun-Joon Park (1)
  Pjotr Prins (1)
  Taro L Saito (1)
  Matthias Samwald (1)
  Venkata P Satagopam (1)
  Yasumasa Shigemoto (1)
  Richard Smith (1)
  Andrea Splendiani (1)
  Hideaki Sugawara (1)
  James Taylor (1)
  Rutger A Vos (1)
  David Withers (1)
  Chisato Yamasaki (1)
  Christian M Zmasek (1)
  Shoko Kawamoto (1)
  Kosaku Okubo (1)
  Kiyoshi Asai (1)
  Toshihisa Takagi (1)
  
• 关键词：BioHackathon ; Open source ; Software ; Semantic Web ; Databases ; Data integration ; Data visualization ; Web services ; Interfaces
• 刊名：Journal of Biomedical Semantics
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：4
• 期：1
• 全文大小：619KB
• 参考文献：1. Smedley D, Haider S, Ballester B, / et al.: BioMart鈥揵iological queries made easy. / BMC Genomics 2009, 10:22. CrossRef
  2. Smith RN, Aleksic J, Butano D, / et al.: InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. / Bioinformatics 2012, 28:3163鈥?165. CrossRef
  3. Antezana E, Kuiper M, Mironov V: Biological knowledge management: the emerging role of the Semantic Web technologies. / Brief Bioinform 2009, 10:392鈥?07. CrossRef
  4. / Clinical Observations Interoperability. http://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability
  5. Samwald M, Jentzsch A, Bouton C, / et al.: Linked open drug data for pharmaceutical research and development. / J Cheminformatics 2011, 3:19. CrossRef
  6. Belleau F, Nolin M-A, Tourigny N, Rigault P, Morissette J: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. / J Biomed Inform 2008, 41:706鈥?16. CrossRef
  7. Bio2RDFhttp://bio2rdf.org/
  8. Bizer C, Heath T, Berners-Lee T: Linked data - The story so far. / J Semantic Web Inf Syst 2009, 5:1鈥?2.
  9. Goto N, Prins P, Nakao M, / et al.: BioRuby: bioinformatics software for the Ruby programming language. / Bioinformatics 2010, 26:2617鈥?619. CrossRef
  10. BioRubyhttp://bioruby.org/
  11. Cock PJA, Antao T, Chang JT, / et al.: Biopython: freely available Python tools for computational molecular biology and bioinformatics. / Bioinformatics 2009, 25:1422鈥?423. CrossRef
  12. / BioPython. http://biopython.org/
  13. Wilkinson MD, McCarthy L, Vandervalk B, / et al.: SADI, SHARE, and the in silico scientific method. / BMC Bioinformatics 2010,11(Suppl 1):S7. CrossRef
  14. SADIhttp://sadiframework.org/
  15. Arakawa K, Kido N, Oshita K, Tomita M: G-language genome analysis environment with REST and SOAP web service interfaces. / Nucleic Acids Res 2010, 38:W700-W705. CrossRef
  16. / G-language. http://www.g-language.org/
  17. Hull D, Wolstencroft K, Stevens R, / et al.: Taverna: a tool for building and running workflows of services. / Nucleic Acids Res 2006, 34:W729-W732. CrossRef
  18. Lyne R, Smith R, Rutherford K, / et al.: FlyMine: an integrated database for Drosophila and Anopheles genomics. / Genome Biol 2007, 8:R129. CrossRef
  19. FlyMinehttp://www.flymine.org/
  20. Lamprecht A-L, Margaria T, Steffen B: Bio-jETI: a framework for semantics-based service composition. / BMC Bioinformatics 2009,10(Suppl 1):S8. CrossRef
  21. Bio-jETIhttp://biojeti.cs.tu-dortmund.de/
  22. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. / Bioinformatics 2011, 27:431鈥?32. CrossRef
  23. / Cytoscape. http://www.cytoscape.org/
  24. / BioHackathon 2010 participants. http://hackathon3.dbcls.jp/wiki/Participants
  25. Magrane M, Uniprot Consortium: UniProt Knowledgebase: a hub of integrated protein data. / Database 2011, 2011:bar009. CrossRef
  26. UniProthttp://www.uniprot.org/
  27. / Korean HapMap Project. http://www.khapmap.org/
  28. TreeBasehttp://www.treebase.org/
  29. Kaminuma E, Kosuge T, Kodama Y, / et al.: DDBJ progress report. / Nucleic Acids Res 2011, 39:D22-D27. CrossRef
  30. INSCDhttp://www.insdc.org/
  31. PDBjhttp://www.pdbj.org/
  32. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. / Nucleic Acids Res 2010, 38:D355-D360. CrossRef
  33. KEGGhttp://www.kegg.jp/
  34. DBCLShttp://dbcls.rois.ac.jp/
  35. Aranda B, Achuthan P, Alam-Faruque Y, / et al.: The IntAct molecular interaction database in 2010. / Nucleic Acids Res 2010, 38:D525-D531. CrossRef
  36. / IntAct. http://www.ebi.ac.uk/intact/
  37. Antezana E, Blond茅 W, Ega帽a M, / et al.: BioGateway: a semantic systems biology tool for the life sciences. / BMC Bioinformatics 2009,10(Suppl 1):S11. CrossRef
  38. / BioGateway. http://www.semantic-systems-biology.org/biogateway
  39. DERIhttp://www.deri.org/
  40. Aranda B, Blankenburg H, Kerrien S, / et al.: PSICQUIC and PSISCORE: accessing and scoring molecular interactions. / Nat Methods 2011, 8:528鈥?29. CrossRef
  41. PSICQUIChttp://psicquic.googlecode.com/
  42. / The HUPO Proteomics Standards Initiative. http://www.psidev.info/
  43. Stearns MQ, Price C, Spackman KA, Wang AY: / SNOMED clinical terms: overview of the development process and project status. 2001, 662鈥?66. [ / Proceedings of AMIA Symposium]
  44. Rogers J, Roberts A, Solomon D, / et al.: GALEN Ten Years On: Tasks and Supporting Tools. / Proc Medinfo 2001, 256鈥?60.
  45. Ashburner M, Ball CA, Blake JA, / et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. / Nat Genet 2000, 25:25鈥?9. CrossRef
  46. Gruber TR: A translation approach to portable ontology specifications. / Knowledge Acquisition 1993, 5:199鈥?20. CrossRef
  47. Chandrasekaran B, Josephson JR, Benjamins VR: What are ontologies, and why do we need them? / IEEE Intell Syst 1999, 14:20鈥?6. CrossRef
  48. Walls RL, Athreya B, Cooper L, / et al.: Ontologies as integrative tools for plant science. / Am J Bot 2012, 99:1263鈥?275. CrossRef
  49. Courtot M, Juty N, Kn眉pfer C, / et al.: Controlled vocabularies and semantics in systems biology. / Mol Syst Biol 2011, 7:543. CrossRef
  50. Abidi SR, Abidi SSR, Hussain S, Shepherd M: Ontology-based modeling of clinical practice guidelines: a clinical decision support system for breast cancer follow-up interventions at primary care settings. / Stud Health Technol Inform 2007, 129:845鈥?49.
  51. / RDF/XML Syntax Specification (Revised). http://www.w3.org/TR/REC-rdf-syntax/
  52. / Notation3 (N3): A readable RDF syntax. http://www.w3.org/TeamSubmission/n3/
  53. SPARQLhttp://www.w3.org/TR/rdf-sparql-query/
  54. Antezana E, Ega帽a M, Blond茅 W, / et al.: The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. / Genome Biol 2009, 10:R58. CrossRef
  55. UniProt ftpftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/
  56. Kosuge T, Abe T, Okido T, / et al.: Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS). / DNA Res 2006, 13:245鈥?54. CrossRef
  57. Kinjo AR, Suzuki H, Yamashita R, / et al.: Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. / Nucleic Acids Res 2012, 40:D453-D460. CrossRef
  58. Katayama T, Nakao M, Takagi T: TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. / Nucleic Acids Res 2010, 38:W706-W711. CrossRef
  59. TogoWShttp://togows.dbcls.jp/
  60. TogoDBhttp://togodb.dbcls.jp/
  61. W3C Cool URIhttp://www.w3.org/TR/cooluris/
  62. Polite URIhttp://hackathon3.dbcls.jp/wiki/URI
  63. FreeBasehttp://www.freebase.com/view/base/politeuri/views/9202a8c04000641f8000000013e0f893
  64. LSRNhttp://lsrn.org/
  65. Identifiers.orghttp://identifiers.org/
  66. / Semanticscience Integrated Ontology. http://code.google.com/p/semanticscience/wiki/SIO
  67. Ceol A, Chatr Aryamontri A, Licata L, / et al.: MINT, the molecular interaction database: 2009 update. / Nucleic Acids Res 2010, 38:D532-D539. CrossRef
  68. Stark C, Breitkreutz B-J, Chatr-Aryamontri A, / et al.: The BioGRID Interaction Database: 2011 update. / Nucleic Acids Res 2011, 39:D698-D704. CrossRef
  69. Razick S, Magklaras G, Donaldson IM: iRefIndex: a consolidated protein interaction database with provenance. / BMC Bioinformatics 2008, 9:405. CrossRef
  70. Chautard E, Fatoux-Ardore M, Ballut L, Thierry-Mieg N, Ricard-Blum S: MatrixDB, the extracellular matrix interaction database. / Nucleic Acids Res 2011, 39:D235-D240. CrossRef
  71. Croft D, O鈥橩elly G, Wu G, / et al.: Reactome: a database of reactions, pathways and biological processes. / Nucleic Acids Res 2011, 39:D691-D697. CrossRef
  72. Goll J, Rajagopala SV, Shiau SC, / et al.: MPIDB: the microbial protein interaction database. / Bioinformatics 2008, 24:1743鈥?744. CrossRef
  73. ChEMBLhttps://www.ebi.ac.uk/chembl/
  74. / PSICQUIC Registry. http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
  75. Demir E, Cary MP, Paley S, / et al.: The BioPAX community standard for pathway data sharing. / Nat Biotechnol 2010, 28:935鈥?42. CrossRef
  76. / PSI-MI XML. http://www.psidev.info/mif
  77. / Apache Jena. http://jena.apache.org/
  78. Funahashi A, Matsuoka Y, Jouraku A, / et al.: CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. / Proc IEEE 2008, 96:1254鈥?265. CrossRef
  79. Hucka M, Finney A, Sauro HM, / et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. / Bioinformatics 2003, 19:524鈥?31. CrossRef
  80. Mizuno S, Iijima R, Ogishima S, Kikuchi M, Matsuoka Y, Ghosh S, Miyamoto T, Miyashita A, Kuwano RTH: AlzPathway: a comprehensive map of signaling pathways of Alzheimer鈥檚 disease. / BMC Syst Biol 2012, 6:52. CrossRef
  81. / AlzPathway. http://alzpathway.org/
  82. / SBML to BioPax. http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLtoBioPax.html
  83. Oda K, Matsuoka Y, Funahashi A, Kitano H: A comprehensive pathway map of epidermal growth factor receptor signaling. / Mol Syst Biol 2005, 2005.0010:1鈥?7. CrossRef
  84. / 4store. http://4store.org/
  85. Page RDM: Taxonomic names, metadata, and the semantc web. / Biodiversity Inform 2006, 3:1鈥?5.
  86. Sober贸n J, Peterson AT: Biodiversity informatics: managing and applying primary biodiversity data. / Philos Trans R Soc Lond B Biol Sci 2004, 359:689鈥?98. CrossRef
  87. Ley RE, Turnbaugh PJ, Klein S, Gordon JI: Human gut microbes associated with obesity. / Nature 2006, 444:1022鈥?023. CrossRef
  88. Rusch DB, Halpern AL, Sutton G, / et al.: The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. / PLoS Biol 2007, 5:e77. CrossRef
  89. / TDWG ontology. http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology
  90. / DarwinCore. http://rs.tdwg.org/dwc/
  91. Prosdocimi F, Chisham B, Pontelli E, Thompson J, Stoltzfus A: Initial Implementation of a comparative Data Analysis Ontology. / Evol Bioinformatics 2009, 5:47鈥?6.
  92. Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A: Text processing through Web services: calling Whatizit. / Bioinformatics 2008, 24:296鈥?98. CrossRef
  93. / Whatizit. http://www.ebi.ac.uk/webservices/whatizit
  94. O鈥橠onoghue SI, Horn H, Pafilis E, / et al.: Reflect: A practical approach to web semantics. / Web Semantics 2010, 8:182鈥?89. CrossRef
  95. Prosdocimi F, Chisham B, Pontelli E, Thompson J, Stoltzfus A: Initial Implementation of a comparative Data Analysis Ontology. / EvolBioinformatics 2009, 5:47鈥?6.
  96. / Reflect. http://reflect.ws/
  97. Ananiadou S, Kell DB, Tsujii J: Text mining and its potential applications in systems biology. / Trends Biotechnol 2006, 24:571鈥?79. CrossRef
  98. / Medie. http://www.nactem.ac.uk/medie/
  99. / RDFa. http://rdfa.info/
  100. Splendiani A: RDFScape: Semantic Web meets systems biology. / BMC Bioinformatics 2008,9(Suppl 4):S6. CrossRef
  101. Goecks J, Nekrutenko A, Taylor J: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. / Genome Biol 2010, 11:R86. CrossRef
  102. / Galaxy. http://main.g2.bx.psu.edu/
  103. / EBI Ontology Lookup Service. http://www.ebi.ac.uk/ontology-lookup/
  104. Flicek P, Amode MR, Barrell D, / et al.: Ensembl 2011. / Nucleic Acids Res 2011, 39:D800-D806. CrossRef
  105. / Ensembl. http://www.ensembl.org/
  106. Dreszer TR, Karolchik D, Zweig AS, / et al.: The UCSC Genome Browser database: extensions and updates 2011. / Nucleic Acids Res 2012, 40:D918-D923. CrossRef
  107. Contrino S, Smith RN, Butano D, / et al.: modMine: flexible access to modENCODE data. / Nucleic Acids Res 2012, 40:D1082-D1088. CrossRef
  108. / EDAM Ontology. http://edamontology.org/
  109. Wilkinson MD, Senger M, Kawas E, / et al.: Interoperability with Moby 1.0--it鈥檚 better than sharing your toothbrush! / Brief Bioinform 2008, 9:220鈥?31. CrossRef
  110. Heim P, Hellmann S, Lehmann J, Lohmann S: RelFinder: Revealing Relationships in RDF Knowledge Bases. / Proc 4th Int Conf Semantic Digital Media Technol, (Lecture Notes Comput Sci) 2009, 5887:182鈥?87. CrossRef
  111. RelFinderhttp://www.visualdataweb.org/relfinder.php
  112. / G-language Bookmarklet. http://www.g-language.org/wiki/bookmarklet
  113. Wilkinson MD, Vandervalk B, McCarthy L: The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation. / J Biomed Semantics 2011, 2:8. CrossRef
  114. CPANhttp://www.cpan.org/
  115. / SADI framework. http://code.google.com/p/sadi/
  116. / Daggoo. http://www.daggoo.net/
  117. / Evidence ontology. http://code.google.com/p/evidenceontology/
  
• 作者单位：Toshiaki Katayama (1)
  Mark D Wilkinson (1)
  Gos Micklem (1)
  Shuichi Kawashima (1)
  Atsuko Yamaguchi (1)
  Mitsuteru Nakao (1)
  Yasunori Yamamoto (1)
  Shinobu Okamoto (1)
  Kenta Oouchida (1)
  Hong-Woo Chun (1)
  Jan Aerts (1)
  Hammad Afzal (1)
  Erick Antezana (1)
  Kazuharu Arakawa (1)
  Bruno Aranda (1)
  Francois Belleau (1)
  Jerven Bolleman (1)
  Raoul JP Bonnal (1)
  Brad Chapman (1)
  Peter JA Cock (1)
  Tore Eriksson (1)
  Paul MK Gordon (1)
  Naohisa Goto (1)
  Kazuhiro Hayashi (1)
  Heiko Horn (1)
  Ryosuke Ishiwata (1)
  Eli Kaminuma (1)
  Arek Kasprzyk (1)
  Hideya Kawaji (1)
  Nobuhiro Kido (1)
  Young Joo Kim (1)
  Akira R Kinjo (1)
  Fumikazu Konishi (1)
  Kyung-Hoon Kwon (1)
  Alberto Labarga (1)
  Anna-Lena Lamprecht (1)
  Yu Lin (1)
  Pierre Lindenbaum (1)
  Luke McCarthy (1)
  Hideyuki Morita (1)
  Katsuhiko Murakami (1)
  Koji Nagao (1)
  Kozo Nishida (1)
  Kunihiro Nishimura (1)
  Tatsuya Nishizawa (1)
  Soichi Ogishima (1)
  Keiichiro Ono (1)
  Kazuki Oshita (1)
  Keun-Joon Park (1)
  Pjotr Prins (1)
  Taro L Saito (1)
  Matthias Samwald (1)
  Venkata P Satagopam (1)
  Yasumasa Shigemoto (1)
  Richard Smith (1)
  Andrea Splendiani (1)
  Hideaki Sugawara (1)
  James Taylor (1)
  Rutger A Vos (1)
  David Withers (1)
  Chisato Yamasaki (1)
  Christian M Zmasek (1)
  Shoko Kawamoto (1)
  Kosaku Okubo (1)
  Kiyoshi Asai (1)
  Toshihisa Takagi (1)
  
  1. Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
  
• ISSN：2041-1480

文摘

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.