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

Simple item page
dc.citation.journalTitleJournal of Biomedical Semantics
dc.contributor.authorKatayama, Toshiaki
dc.contributor.authorWilkinson, Mark D.
dc.contributor.authorVos, Rutger
dc.contributor.authorKawashima, Takeshi
dc.contributor.authorKawashima, Shuichi
dc.contributor.authorNakao, Mitsuteru
dc.contributor.authorYamamoto, Yasunori
dc.contributor.authorChun, Hong-Woo
dc.contributor.authorYamaguchi, Atsuko
dc.contributor.authorKawano, Shin
dc.contributor.authorAerts, Jan
dc.contributor.authorAoki-Kinoshita, Kiyoko F.
dc.contributor.authorArakawa, Kazuharu
dc.contributor.authorAranda, Bruno
dc.contributor.authorBonnal, Raoul J.
dc.contributor.authorFernández, José M.
dc.contributor.authorFujisawa, Takatomo
dc.contributor.authorGordon, Paul M.
dc.contributor.authorGoto, Naohisa
dc.contributor.authorHaider, Syed
dc.contributor.authorHarris, Todd
dc.contributor.authorHatakeyama, Takashi
dc.contributor.authorHo, Isaac
dc.contributor.authorItoh, Masumi
dc.contributor.authorKasprzyk, Arek
dc.contributor.authorKido, Nobuhiro
dc.contributor.authorKim, Young-Joo
dc.contributor.authorKinjo, Akira R.
dc.contributor.authorKonishi, Fumikazu
dc.contributor.authorKovarskaya, Yulia
dc.contributor.authorvon Kuster, Greg
dc.contributor.authorLabarga, Alberto
dc.contributor.authorLimviphuvadh, Vachiranee
dc.contributor.authorMcCarthy, Luke
dc.contributor.authorNakamura, Yasukazu
dc.contributor.authorNam, Yunsun
dc.contributor.authorNishida, Kozo
dc.contributor.authorNishimura, Kunihiro
dc.contributor.authorNishizawa, Tatsuya
dc.contributor.authorOgishima, Soichi
dc.contributor.authorOinn, Tom
dc.contributor.authorOkamoto, Shinobu
dc.contributor.authorOkuda, Shujiro
dc.contributor.authorOno, Keiichiro
dc.contributor.authorOshita, Kazuki
dc.contributor.authorPark, Keun-Joon
dc.contributor.authorPutnam, Nicholas
dc.contributor.authorSenger, Martin
dc.contributor.authorSeverin, Jessica
dc.contributor.authorShigemoto, Yasumasa
dc.contributor.authorSugawara, Hideaki
dc.contributor.authorTaylor, James
dc.contributor.authorTrelles, Oswaldo
dc.contributor.authorYamasaki, Chisato
dc.contributor.authorYamashita, Riu
dc.contributor.authorSatoh, Noriyuki
dc.contributor.authorTakagi, Toshihisa
dc.date.accessioned2015-10-25T08:05:04Z
dc.date.available2015-10-25T08:05:04Z
dc.date.issued2011
dc.date.updated2015-10-25T08:06:04Z
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.
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.
dc.identifier.doihttp://dx.doi.org/10.1186/2041-1480-2-4
dc.identifier.urihttps://hdl.handle.net/1911/81892
dc.language.isoeng
dc.publisherBioMed Central
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.
dc.titleThe 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
13326_2011_Article_51.pdf
Size:
662.41 KB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.61 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Faculty Publications