Paper Info
Title
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Abstract
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.
Year
DOI
Venue
2016
10.1093/database/baw055
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Field
DocType
Volume
Data mining,Identifier,Computer science,UniProt,Datasets as Topic,Ontology (information science),Analysis tools,RefSeq,World Wide Web,Annotation,Bioinformatics,Database,Transcriptional Regulatory Elements
Journal
2016
ISSN
Citations 
PageRank 
1758-0463
0
0.34
References 
Authors
18
11
Name
Order
Citations
PageRank
Sefa Kiliç1121.33
Dinara M Sagitova2120.99
Shoshannah Wolfish300.34
Benoit Bely4515.25
Mélanie Courtot538836.72
S Ciufo6658.13
Tatiana Tatusova72701651.69
Claire O'Donovan82584329.29
Marcus C. Chibucos9154.02
Maria Jesus Martin102793365.41
Ivan Erill11416.84