Literature DB >> 17893861

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.

Sandra Orchard1, Samuel Kerrien, Philip Jones, Arnaud Ceol, Andrew Chatr-Aryamontri, Lukasz Salwinski, Jason Nerothin, Henning Hermjakob.   

Abstract

The ever-increasing generation of, and corresponding interest in, molecular interaction data has lead to the establishment of a number of high-quality molecular interaction databases which manually curate interaction data extracted from the literature. In order to effectively share the curation load, and ensure that data is stored in and accessible from multiple sources, these databases have united to form the IMEx consortium. All of the IMEx databases also accept direct deposition of interaction data from authors prior to publication, thus both assisting the scientist in preparing the dataset for publication and ensuring that its subsequent representation in the public domain databases is fully accurate. This article walks the potential submitter through the various routes by which data may be deposited with the databases and describes the tools which have been developed to assist in this process.

Mesh:

Year:  2007        PMID: 17893861     DOI: 10.1002/pmic.200700286

Source DB:  PubMed          Journal:  Proteomics        ISSN: 1615-9853            Impact factor:   3.984


  27 in total

1.  Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.

Authors:  KiYoung Lee; David Thorneycroft; Premanand Achuthan; Henning Hermjakob; Trey Ideker
Journal:  Plant Cell       Date:  2010-04-06       Impact factor: 11.277

2.  Recurated protein interaction datasets.

Authors:  Lukasz Salwinski; Luana Licata; Andrew Winter; David Thorneycroft; Jyoti Khadake; Arnaud Ceol; Andrew Chatr Aryamontri; Rose Oughtred; Michael Livstone; Lorrie Boucher; David Botstein; Kara Dolinski; Tanya Berardini; Eva Huala; Mike Tyers; David Eisenberg; Gianni Cesareni; Henning Hermjakob
Journal:  Nat Methods       Date:  2009-12       Impact factor: 28.547

3.  Interaction databases on the same page.

Authors:  Andrei L Turinsky; Sabry Razick; Brian Turner; Ian M Donaldson; Shoshana J Wodak
Journal:  Nat Biotechnol       Date:  2011-05       Impact factor: 54.908

Review 4.  Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.

Authors:  Juan Antonio Vizcaíno; Joseph M Foster; Lennart Martens
Journal:  J Proteomics       Date:  2010-07-06       Impact factor: 4.044

5.  Literature-curated protein interaction datasets.

Authors:  Michael E Cusick; Haiyuan Yu; Alex Smolyar; Kavitha Venkatesan; Anne-Ruxandra Carvunis; Nicolas Simonis; Jean-François Rual; Heather Borick; Pascal Braun; Matija Dreze; Jean Vandenhaute; Mary Galli; Junshi Yazaki; David E Hill; Joseph R Ecker; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

6.  DASMIweb: online integration, analysis and assessment of distributed protein interaction data.

Authors:  Hagen Blankenburg; Fidel Ramírez; Joachim Büch; Mario Albrecht
Journal:  Nucleic Acids Res       Date:  2009-06-05       Impact factor: 16.971

7.  The European Bioinformatics Institute's data resources.

Authors:  Catherine Brooksbank; Graham Cameron; Janet Thornton
Journal:  Nucleic Acids Res       Date:  2009-11-24       Impact factor: 16.971

8.  MINT, the molecular interaction database: 2009 update.

Authors:  Arnaud Ceol; Andrew Chatr Aryamontri; Luana Licata; Daniele Peluso; Leonardo Briganti; Livia Perfetto; Luisa Castagnoli; Gianni Cesareni
Journal:  Nucleic Acids Res       Date:  2009-11-06       Impact factor: 16.971

9.  The IntAct molecular interaction database in 2010.

Authors:  B Aranda; P Achuthan; Y Alam-Faruque; I Armean; A Bridge; C Derow; M Feuermann; A T Ghanbarian; S Kerrien; J Khadake; J Kerssemakers; C Leroy; M Menden; M Michaut; L Montecchi-Palazzi; S N Neuhauser; S Orchard; V Perreau; B Roechert; K van Eijk; H Hermjakob
Journal:  Nucleic Acids Res       Date:  2009-10-22       Impact factor: 16.971

10.  myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks.

Authors:  Jamil Bacha; James S Brodie; Matthew W Loose
Journal:  BMC Dev Biol       Date:  2009-06-06       Impact factor: 1.978

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