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From data repositories to submission portals: rethinking the role of
domain-specific databases in CollecTF
#MMPMID27114493
K?l?ç S
; Sagitova DM
; Wolfish S
; Bely B
; Courtot M
; Ciufo S
; Tatusova T
; O'Donovan C
; Chibucos MC
; Martin MJ
; Erill I
Database (Oxford)
2016[]; 2016
(?): ? PMID27114493
show ga
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/.
free
free
free
