Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Patricia C Babbitt; Pantelis G Bagos; Amos Bairoch; Alex Bateman; Arnaud Chatonnet; Mark Jinan Chen; David J Craik; Robert D Finn; David Gloriam; Daniel H Haft; Bernard Henrissat; Gemma L Holliday; Vignir Isberg; Quentin Kaas; David Landsman; Nicolas Lenfant; Gerard Manning; Nozomi Nagano; Narayanaswamy Srinivasan; Claire O'Donovan; Kim D Pruitt; Ramanathan Sowdhamini; Neil D Rawlings; Milton H Saier Jr; Joanna L Sharman; Michael Spedding; Konstantinos D Tsirigos; Ake Vastermark; Gerrit Vriend

doi:10.1093/database/bav063

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Database (Oxford). 2015 Jul 11:2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.

Authors

Patricia C Babbitt¹, Pantelis G Bagos², Amos Bairoch³, Alex Bateman⁴, Arnaud Chatonnet⁵, Mark Jinan Chen⁶, David J Craik⁷, Robert D Finn⁴, David Gloriam⁸, Daniel H Haft⁹, Bernard Henrissat¹⁰, Gemma L Holliday¹, Vignir Isberg¹¹, Quentin Kaas⁷, David Landsman⁹, Nicolas Lenfant⁵, Gerard Manning⁶, Nozomi Nagano¹², Narayanaswamy Srinivasan¹³, Claire O'Donovan⁴, Kim D Pruitt⁹, Ramanathan Sowdhamini¹⁴, Neil D Rawlings⁴, Milton H Saier Jr¹⁵, Joanna L Sharman¹⁶, Michael Spedding¹⁷, Konstantinos D Tsirigos¹⁸, Ake Vastermark¹⁵, Gerrit Vriend¹⁹

Affiliations

¹ Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
² Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, Lamia, 35100, Greece.
³ SIB-Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
⁴ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁵ INRA, UMR866 Dynamique Musculaire et Métabolisme, F-34000 Montpellier, France.
⁶ Razavi Newman Center for Bioinformatics, Salk Institute, 10010 North Torrey Pines Rd., La Jolla, CA 92037, USA, ; Bioinformatics & Computational Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
⁷ Queensland Bioscience Precinct, 306 Carmody Rd, Building 80, The University of Queensland, Australia.
⁸ Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 København Ø, Denmark.
⁹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
¹⁰ Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France, ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
¹¹ Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 København Ø, Denmark, ; CMBI, Raboudumc, Geert Grootplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
¹² Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
¹³ Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
¹⁴ National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560 065, India.
¹⁵ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
¹⁶ Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK.
¹⁷ Spedding Research Solutions, 6 Rue Ampere, 78110 Le Vesinet, France and.
¹⁸ Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, Box 1031, 17121 Solna, Sweden.
¹⁹ CMBI, Raboudumc, Geert Grootplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.

Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology*
Congresses as Topic
Databases, Nucleic Acid*
Databases, Protein*
Humans
Molecular Sequence Annotation*
Proteins* / chemistry
Proteins* / genetics

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding