From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
Kılıç, Sefa (University of Maryland Baltimore County. Department of Biological Sciences)
Sagitova, Dinara M. (University of Maryland Baltimore County. Department of Biological Sciences)
Wolfish, Shoshannah (University of Maryland School ofMedicine)
Bely, Benoit (European Bioinformatics Institute)
Courtot, Mélanie (European Bioinformatics Institute)
Ciufo, Stacy (National Institutes of Health (Bethesda, Estats Units d'Amèrica))
Tatusova, Tatiana (National Institutes of Health (Bethesda, Estats Units d'Amèrica))
O'Donovan Claire (European Bioinformatics Institute)
Chibucos, Marcus C. (University of Maryland School of Medicine. Department of Microbiology and Immunology)
Martin, Maria J. (European Bioinformatics Institute)
Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)

Fecha:	2016
Resumen:	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.
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Publicado en:	Database, Vol. 2016 (April 2016) , art. baw055, ISSN 1758-0463

DOI: 10.1093/database/baw055
PMID: 27114493

10 p, 992.7 KB

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