Literature DB >> 18621748

Experience using web services for biological sequence analysis.

Heinz Stockinger1, Teresa Attwood, Shahid Nadeem Chohan, Richard Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro Fernandes, Robert D Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurelie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman.   

Abstract

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

Mesh：

Year:  2008        PMID： 18621748      PMCID： PMC2989672          DOI： 10.1093/bib/bbn029

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  18 in total

1.  ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.

Authors:  Pål Puntervoll; Rune Linding; Christine Gemünd; Sophie Chabanis-Davidson; Morten Mattingsdal; Scott Cameron; David M A Martin; Gabriele Ausiello; Barbara Brannetti; Anna Costantini; Fabrizio Ferrè; Vincenza Maselli; Allegra Via; Gianni Cesareni; Francesca Diella; Giulio Superti-Furga; Lucjan Wyrwicz; Chenna Ramu; Caroline McGuigan; Rambabu Gudavalli; Ivica Letunic; Peer Bork; Leszek Rychlewski; Bernhard Küster; Manuela Helmer-Citterich; William N Hunter; Rein Aasland; Toby J Gibson
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

Authors:  Richard G Côté; Philip Jones; Rolf Apweiler; Henning Hermjakob
Journal:  BMC Bioinformatics       Date:  2006-02-28       Impact factor: 3.169

3.  Genome re-annotation: a wiki solution?

Authors:  Steven L Salzberg
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

4.  The Universal Protein Resource (UniProt).

Authors: 
Journal:  Nucleic Acids Res       Date:  2006-11-16       Impact factor: 16.971

5.  The distributed annotation system.

Authors:  R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal:  BMC Bioinformatics       Date:  2001-10-10       Impact factor: 3.169

6.  HitKeeper, a generic software package for hit list management.

Authors:  Jörg Hau; Michael Muller; Marco Pagni
Journal:  Source Code Biol Med       Date:  2007-03-28

7.  PairsDB atlas of protein sequence space.

Authors:  Andreas Heger; Eija Korpelainen; Taavi Hupponen; Kimmo Mattila; Vesa Ollikainen; Liisa Holm
Journal:  Nucleic Acids Res       Date:  2007-11-05       Impact factor: 16.971

8.  The Pfam protein families database.

Authors:  Robert D Finn; John Tate; Jaina Mistry; Penny C Coggill; Stephen John Sammut; Hans-Rudolf Hotz; Goran Ceric; Kristoffer Forslund; Sean R Eddy; Erik L L Sonnhammer; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2007-11-26       Impact factor: 16.971

9.  The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

Authors:  Richard G Côté; Philip Jones; Lennart Martens; Samuel Kerrien; Florian Reisinger; Quan Lin; Rasko Leinonen; Rolf Apweiler; Henning Hermjakob
Journal:  BMC Bioinformatics       Date:  2007-10-18       Impact factor: 3.169

10.  Integrating sequence and structural biology with DAS.

Authors:  Andreas Prlić; Thomas A Down; Eugene Kulesha; Robert D Finn; Andreas Kähäri; Tim J P Hubbard
Journal:  BMC Bioinformatics       Date:  2007-09-12       Impact factor: 3.169
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  13 in total

1.  KBWS: an EMBOSS associated package for accessing bioinformatics web services.

Authors:  Kazuki Oshita; Kazuharu Arakawa; Masaru Tomita
Journal:  Source Code Biol Med       Date:  2011-04-29

2.  G-language genome analysis environment with REST and SOAP web service interfaces.

Authors:  Kazuharu Arakawa; Nobuhiro Kido; Kazuki Oshita; Masaru Tomita
Journal:  Nucleic Acids Res       Date:  2010-05-03       Impact factor: 16.971

3.  An active registry for bioinformatics web services.

Authors:  S Pettifer; D Thorne; P McDermott; T Attwood; J Baran; J C Bryne; T Hupponen; D Mowbray; G Vriend
Journal:  Bioinformatics       Date:  2009-05-21       Impact factor: 6.937

4.  myExperiment: a repository and social network for the sharing of bioinformatics workflows.

Authors:  Carole A Goble; Jiten Bhagat; Sergejs Aleksejevs; Don Cruickshank; Danius Michaelides; David Newman; Mark Borkum; Sean Bechhofer; Marco Roos; Peter Li; David De Roure
Journal:  Nucleic Acids Res       Date:  2010-05-25       Impact factor: 16.971

5.  TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services.

Authors:  Toshiaki Katayama; Mitsuteru Nakao; Toshihisa Takagi
Journal:  Nucleic Acids Res       Date:  2010-05-14       Impact factor: 16.971

6.  A quick guide to large-scale genomic data mining.

Authors:  Curtis Huttenhower; Oliver Hofmann
Journal:  PLoS Comput Biol       Date:  2010-05-27       Impact factor: 4.475

7.  The EMBRACE web service collection.

Authors:  Steve Pettifer; Jon Ison; Matús Kalas; Dave Thorne; Philip McDermott; Inge Jonassen; Ali Liaquat; José M Fernández; Jose M Rodriguez; David G Pisano; Christophe Blanchet; Mahmut Uludag; Peter Rice; Edita Bartaseviciute; Kristoffer Rapacki; Maarten Hekkelman; Olivier Sand; Heinz Stockinger; Andrew B Clegg; Erik Bongcam-Rudloff; Jean Salzemann; Vincent Breton; Teresa K Attwood; Graham Cameron; Gert Vriend
Journal:  Nucleic Acids Res       Date:  2010-05-12       Impact factor: 16.971

8.  The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Authors:  Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord Hendrix Barboza; Raoul Jp Bonnal; Richard Bruskiewich; Jan C Bryne; José M Fernández; Akira Funahashi; Paul Mk Gordon; Naohisa Goto; Andreas Groscurth; Alex Gutteridge; Richard Holland; Yoshinobu Kano; Edward A Kawas; Arnaud Kerhornou; Eri Kibukawa; Akira R Kinjo; Michael Kuhn; Hilmar Lapp; Heikki Lehvaslaiho; Hiroyuki Nakamura; Yasukazu Nakamura; Tatsuya Nishizawa; Chikashi Nobata; Tamotsu Noguchi; Thomas M Oinn; Shinobu Okamoto; Stuart Owen; Evangelos Pafilis; Matthew Pocock; Pjotr Prins; René Ranzinger; Florian Reisinger; Lukasz Salwinski; Mark Schreiber; Martin Senger; Yasumasa Shigemoto; Daron M Standley; Hideaki Sugawara; Toshiyuki Tashiro; Oswaldo Trelles; Rutger A Vos; Mark D Wilkinson; William York; Christian M Zmasek; Kiyoshi Asai; Toshihisa Takagi
Journal:  J Biomed Semantics       Date:  2010-08-21

9.  BioXSD: the common data-exchange format for everyday bioinformatics web services.

Authors:  Matús Kalas; Pål Puntervoll; Alexandre Joseph; Edita Bartaseviciūte; Armin Töpfer; Prabakar Venkataraman; Steve Pettifer; Jan Christian Bryne; Jon Ison; Christophe Blanchet; Kristoffer Rapacki; Inge Jonassen
Journal:  Bioinformatics       Date:  2010-09-15       Impact factor: 6.937

10.  A web server for interactive and zoomable Chaos Game Representation images.

Authors:  Kazuharu Arakawa; Kazuki Oshita; Masaru Tomita
Journal:  Source Code Biol Med       Date:  2009-09-17
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