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Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.

Key challenges for the creation and maintenance of specialist protein resources.

Author information

1
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158.
2
SIB-Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland.
3
Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35100, Greece.
4
INRA, Umr866 Dynamique Musculaire Et Métabolisme, Montpellier, F-34000, France.
5
Université Montpellier, Montpellier, F-34000, France.
6
Institute for Molecular Bioscience. The University of Queensland, Brisbane, Queensland, 4072, Australia.
7
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom.
8
Architecture Et Fonction Des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France.
9
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
10
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20892.
11
Department of Bioinformatics & Computational Biology, Genentech, 1 DNA Way, South San Francisco, California, 98010.
12
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan.
13
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom.
14
Department of Molecular Biology, University of California at San Diego, La Jolla, California, 92093.
15
National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore, 560065, India.
16
Chair NC-IUPHAR, Spedding Research Solutions SARL, 6 Rue Ampere, Le Vesinet, 78110, France.
17
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
18
Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA, Nijmegen, The Netherlands.

Abstract

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value.

KEYWORDS:

big data; biocuration; key challenges; longevity; misannotation; specialist protein resource

PMID:
25820941
PMCID:
PMC4446195
DOI:
10.1002/prot.24803
[Indexed for MEDLINE]
Free PMC Article

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