From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/.
Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
Sefa
S
Kılıç
Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
Dinara M
DM
Sagitova
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Shoshannah
S
Wolfish
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Benoit
B
Bely
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Mélanie
M
Courtot
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Rockville Pike, Bethesda, MD, 20894, USA.
Stacy
S
Ciufo
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Rockville Pike, Bethesda, MD, 20894, USA.
Tatiana
T
Tatusova
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Claire
C
O'Donovan
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Marcus C
MC
Chibucos
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Maria J
MJ
Martin
Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA erill@umbc.edu.
Ivan
I
Erill
D003628:Database Management Systems; D030541:Databases, Genetic; D066264:Datasets as Topic; D014584:User-Computer Interface