Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process.Database URL: http://www.tfcheckpoint.org.
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway.
Sushil
S
Tripathi
Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway.
Steven
S
Vercruysse
Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway.
Konika
K
Chawla
Department of Computational Biology and Bioinformatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA.
Karen R
KR
Christie
Department of Computational Biology and Bioinformatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA.
Judith A
JA
Blake
Centre for Cardiovascular Genetics, Institute of Cardiovascular Science University College, London WC1E 6JF, UK.
Rachael P
RP
Huntley
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Sandra
S
Orchard
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Henning
H
Hermjakob
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway Department of Medical Laboratory Technology, Norwegian University of Science and Technology (NTNU) 7491 Trondheim, Norway.
Liv
L
Thommesen
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway astrid.lagreid@ntnu.no martin.kuiper@ntnu.no.
Astrid
A
Lægreid
Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway astrid.lagreid@ntnu.no martin.kuiper@ntnu.no.
Martin
M
Kuiper
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004268:DNA-Binding Proteins / Q000235:genetics*; D066289:Data Curation / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D008322:Mammals; D051379:Mice; D051381:Rats; D014157:Transcription Factors / Q000235:genetics*
D004268:DNA-Binding Proteins; D014157:Transcription Factors