The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

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dc.citation.journalTitleJournal of Biomedical Semanticsen_US
dc.contributor.authorKatayama, Toshiakien_US
dc.contributor.authorWilkinson, Mark D.en_US
dc.contributor.authorVos, Rutgeren_US
dc.contributor.authorKawashima, Takeshien_US
dc.contributor.authorKawashima, Shuichien_US
dc.contributor.authorNakao, Mitsuteruen_US
dc.contributor.authorYamamoto, Yasunorien_US
dc.contributor.authorChun, Hong-Wooen_US
dc.contributor.authorYamaguchi, Atsukoen_US
dc.contributor.authorKawano, Shinen_US
dc.contributor.authorAerts, Janen_US
dc.contributor.authorAoki-Kinoshita, Kiyoko F.en_US
dc.contributor.authorArakawa, Kazuharuen_US
dc.contributor.authorAranda, Brunoen_US
dc.contributor.authorBonnal, Raoul J.en_US
dc.contributor.authorFernández, José M.en_US
dc.contributor.authorFujisawa, Takatomoen_US
dc.contributor.authorGordon, Paul M.en_US
dc.contributor.authorGoto, Naohisaen_US
dc.contributor.authorHaider, Syeden_US
dc.contributor.authorHarris, Todden_US
dc.contributor.authorHatakeyama, Takashien_US
dc.contributor.authorHo, Isaacen_US
dc.contributor.authorItoh, Masumien_US
dc.contributor.authorKasprzyk, Areken_US
dc.contributor.authorKido, Nobuhiroen_US
dc.contributor.authorKim, Young-Jooen_US
dc.contributor.authorKinjo, Akira R.en_US
dc.contributor.authorKonishi, Fumikazuen_US
dc.contributor.authorKovarskaya, Yuliaen_US
dc.contributor.authorvon Kuster, Gregen_US
dc.contributor.authorLabarga, Albertoen_US
dc.contributor.authorLimviphuvadh, Vachiraneeen_US
dc.contributor.authorMcCarthy, Lukeen_US
dc.contributor.authorNakamura, Yasukazuen_US
dc.contributor.authorNam, Yunsunen_US
dc.contributor.authorNishida, Kozoen_US
dc.contributor.authorNishimura, Kunihiroen_US
dc.contributor.authorNishizawa, Tatsuyaen_US
dc.contributor.authorOgishima, Soichien_US
dc.contributor.authorOinn, Tomen_US
dc.contributor.authorOkamoto, Shinobuen_US
dc.contributor.authorOkuda, Shujiroen_US
dc.contributor.authorOno, Keiichiroen_US
dc.contributor.authorOshita, Kazukien_US
dc.contributor.authorPark, Keun-Joonen_US
dc.contributor.authorPutnam, Nicholasen_US
dc.contributor.authorSenger, Martinen_US
dc.contributor.authorSeverin, Jessicaen_US
dc.contributor.authorShigemoto, Yasumasaen_US
dc.contributor.authorSugawara, Hideakien_US
dc.contributor.authorTaylor, Jamesen_US
dc.contributor.authorTrelles, Oswaldoen_US
dc.contributor.authorYamasaki, Chisatoen_US
dc.contributor.authorYamashita, Riuen_US
dc.contributor.authorSatoh, Noriyukien_US
dc.contributor.authorTakagi, Toshihisaen_US
dc.date.accessioned2015-10-25T08:05:04Zen_US
dc.date.available2015-10-25T08:05:04Zen_US
dc.date.issued2011en_US
dc.date.updated2015-10-25T08:06:04Zen_US
dc.description.abstractBackground: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Results: Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Conclusions: Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.en_US
dc.identifier.citationKatayama, Toshiaki, Wilkinson, Mark D., Vos, Rutger, et al.. "The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications." <i>Journal of Biomedical Semantics,</i> (2011) BioMed Central: http://dx.doi.org/10.1186/2041-1480-2-4.en_US
dc.identifier.doihttp://dx.doi.org/10.1186/2041-1480-2-4en_US
dc.identifier.urihttps://hdl.handle.net/1911/81892en_US
dc.language.isoengen_US
dc.publisherBioMed Centralen_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.titleThe 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applicationsen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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