title: The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
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.
authors.affiliation: Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. ktym@hgc.jp.
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Katayama
authors.forename: Mark D
authors.initials: MD
authors.lastname: Wilkinson
authors.forename: Rutger
authors.initials: R
authors.lastname: Vos
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawashima
authors.forename: Shuichi
authors.initials: S
authors.lastname: Kawashima
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Yamamoto
authors.forename: Hong-Woo
authors.initials: HW
authors.lastname: Chun
authors.forename: Atsuko
authors.initials: A
authors.lastname: Yamaguchi
authors.forename: Shin
authors.initials: S
authors.lastname: Kawano
authors.forename: Jan
authors.initials: J
authors.lastname: Aerts
authors.forename: Kiyoko F
authors.initials: KF
authors.lastname: Aoki-Kinoshita
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Arakawa
authors.forename: Bruno
authors.initials: B
authors.lastname: Aranda
authors.forename: Raoul Jp
authors.initials: RJ
authors.lastname: Bonnal
authors.forename: José M
authors.initials: JM
authors.lastname: Fernández
authors.forename: Takatomo
authors.initials: T
authors.lastname: Fujisawa
authors.forename: Paul Mk
authors.initials: PM
authors.lastname: Gordon
authors.forename: Naohisa
authors.initials: N
authors.lastname: Goto
authors.forename: Syed
authors.initials: S
authors.lastname: Haider
authors.forename: Todd
authors.initials: T
authors.lastname: Harris
authors.forename: Takashi
authors.initials: T
authors.lastname: Hatakeyama
authors.forename: Isaac
authors.initials: I
authors.lastname: Ho
authors.forename: Masumi
authors.initials: M
authors.lastname: Itoh
authors.forename: Arek
authors.initials: A
authors.lastname: Kasprzyk
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Kido
authors.forename: Young-Joo
authors.initials: YJ
authors.lastname: Kim
authors.forename: Akira R
authors.initials: AR
authors.lastname: Kinjo
authors.forename: Fumikazu
authors.initials: F
authors.lastname: Konishi
authors.forename: Yulia
authors.initials: Y
authors.lastname: Kovarskaya
authors.forename: Greg
authors.initials: G
authors.lastname: von Kuster
authors.forename: Alberto
authors.initials: A
authors.lastname: Labarga
authors.forename: Vachiranee
authors.initials: V
authors.lastname: Limviphuvadh
authors.forename: Luke
authors.initials: L
authors.lastname: McCarthy
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Yunsun
authors.initials: Y
authors.lastname: Nam
authors.forename: Kozo
authors.initials: K
authors.lastname: Nishida
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Nishimura
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Nishizawa
authors.forename: Soichi
authors.initials: S
authors.lastname: Ogishima
authors.forename: Tom
authors.initials: T
authors.lastname: Oinn
authors.forename: Shinobu
authors.initials: S
authors.lastname: Okamoto
authors.forename: Shujiro
authors.initials: S
authors.lastname: Okuda
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Ono
authors.forename: Kazuki
authors.initials: K
authors.lastname: Oshita
authors.forename: Keun-Joon
authors.initials: KJ
authors.lastname: Park
authors.forename: Nicholas
authors.initials: N
authors.lastname: Putnam
authors.forename: Martin
authors.initials: M
authors.lastname: Senger
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Yasumasa
authors.initials: Y
authors.lastname: Shigemoto
authors.forename: Hideaki
authors.initials: H
authors.lastname: Sugawara
authors.forename: James
authors.initials: J
authors.lastname: Taylor
authors.forename: Oswaldo
authors.initials: O
authors.lastname: Trelles
authors.forename: Chisato
authors.initials: C
authors.lastname: Yamasaki
authors.forename: Riu
authors.initials: R
authors.lastname: Yamashita
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Satoh
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Takagi