Evidence map›Paper›PMID 26284514›Full record

ArticleDatabase : the journal of biological databases and curation2015

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 and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Facilities that make the PDB data collection more powerful.Protein science : a publication of the Protein Society · 2020
    Article
  4. Biocuration in the structure-function linkage database: the anatomy of a superfamily.Database : the journal of biological databases and curation · 2017
    Article
  5. Article
  6. Review
  7. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Patricia C BabbittDepartment of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
Pantelis G BagosDepartment of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, Lamia, 35100, Greece.
Amos BairochSIB-Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
Alex BatemanEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Arnaud ChatonnetINRA, UMR866 Dynamique Musculaire et Métabolisme, F-34000 Montpellier, France.
Mark Jinan ChenRazavi 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.
David J CraikQueensland Bioscience Precinct, 306 Carmody Rd, Building 80, The University of Queensland, Australia.
Robert D FinnEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
David GloriamDepartment of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 København Ø, Denmark.
Daniel H HaftNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Bernard HenrissatArchitecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France, ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Gemma L HollidayDepartment of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
Vignir IsbergDepartment 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.
Quentin KaasQueensland Bioscience Precinct, 306 Carmody Rd, Building 80, The University of Queensland, Australia.
David LandsmanNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Nicolas LenfantINRA, UMR866 Dynamique Musculaire et Métabolisme, F-34000 Montpellier, France.
Gerard ManningRazavi 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.
Nozomi NaganoBiotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Narayanaswamy SrinivasanMolecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
Claire O'DonovanEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Kim D PruittNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Ramanathan SowdhaminiNational Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560 065, India.
Neil D RawlingsEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Milton H SaierDepartment of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
Joanna L SharmanCentre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK.
Michael SpeddingSpedding Research Solutions, 6 Rue Ampere, 78110 Le Vesinet, France and.
Konstantinos D TsirigosDepartment of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, Box 1031, 17121 Solna, Sweden.
Ake VastermarkDepartment of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
Gerrit VriendCMBI, Raboudumc, Geert Grootplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.

Funding

TransportPDB: Center for the X-ray Structure Determination of Human TransportersU54GM094610 · NIGMS · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI SAIER, MILTON H. · 2010 to 2014
$12.2M
Resource for Biocomputing Visualization and InformaticsP41GM103311 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2012 to 2017
$8.2M
Laying the Foundation of Genomic EnzymologyR01GM060595 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BABBITT, PATRICIA CLEMENT · 2000 to 2018
$5.4M
The Transporter Classification Database (TCDB)R01GM077402 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SAIER, MILTON H. · 2006 to 2021
$4.7M
Structural And Functional Analysis Of Protein Sequence FamiliesZIALM000071 · NLM · NATIONAL LIBRARY OF MEDICINE · PI LANDSMAN, DAVID · 2009 to 2025
$3.7M
European Research Council 639125NIGMS NIH HHS GM077402NIGMS NIH HHS GM094610NIGMS NIH HHS P41 GM103311NIGMS NIH HHS P41GM103311NIGMS NIH HHS R01 GM060595NIGMS NIH HHS R01 GM077402NIGMS NIH HHS R01 GM60595NIGMS NIH HHS U54 GM094610Wellcome Trust 099156/Z/12/Z
6 · The paper itself

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.

Indexed as

Computational BiologyDatabases, Nucleic AcidDatabases, ProteinMolecular Sequence AnnotationProteinsCongresses as TopicHumansProteins

Identifiers

PMID26284514
PMCPMC4499208

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.