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dc.contributor.authorKatayama, Toshiaki
Wilkinson, Mark D.
Vos, Rutger
Kawashima, Takeshi
Kawashima, Shuichi
Nakao, Mitsuteru
Yamamoto, Yasunori
Chun, Hong-Woo
Yamaguchi, Atsuko
Kawano, Shin
Aerts, Jan
Aoki-Kinoshita, Kiyoko F.
Arakawa, Kazuharu
Aranda, Bruno
Bonnal, Raoul J.
Fernández, José M.
Fujisawa, Takatomo
Gordon, Paul M.
Goto, Naohisa
Haider, Syed
Harris, Todd
Hatakeyama, Takashi
Ho, Isaac
Itoh, Masumi
Kasprzyk, Arek
Kido, Nobuhiro
Kim, Young-Joo
Kinjo, Akira R.
Konishi, Fumikazu
Kovarskaya, Yulia
von Kuster, Greg
Labarga, Alberto
Limviphuvadh, Vachiranee
McCarthy, Luke
Nakamura, Yasukazu
Nam, Yunsun
Nishida, Kozo
Nishimura, Kunihiro
Nishizawa, Tatsuya
Ogishima, Soichi
Oinn, Tom
Okamoto, Shinobu
Okuda, Shujiro
Ono, Keiichiro
Oshita, Kazuki
Park, Keun-Joon
Putnam, Nicholas
Senger, Martin
Severin, Jessica
Shigemoto, Yasumasa
Sugawara, Hideaki
Taylor, James
Trelles, Oswaldo
Yamasaki, Chisato
Yamashita, Riu
Satoh, Noriyuki
Takagi, Toshihisa
dc.date.accessioned 2015-10-25T08:05:04Z
dc.date.available 2015-10-25T08:05:04Z
dc.date.issued 2011
dc.identifier.citation Katayama, Toshiaki, Wilkinson, Mark D., Vos, Rutger, et al.. "The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications." Journal of Biomedical Semantics, (2011) BioMed Central: http://dx.doi.org/10.1186/2041-1480-2-4.
dc.identifier.urihttps://hdl.handle.net/1911/81892
dc.description.abstract Background: 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.publisher BioMed Central
dc.rights Article 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.title The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
dc.type Journal article
dc.citation.journalTitle Journal of Biomedical Semantics
dc.date.updated 2015-10-25T08:06:04Z
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1186/2041-1480-2-4
dc.language.rfc3066 en
dc.type.publication publisher version
dc.rights.holder Katayama et al; licensee BioMed Central Ltd.


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