From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
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DOI：
10.1093/database/baw055
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发表时间：
2016-04-25
影响因子：
5.8
通讯作者：
Erill, Ivan
中科院分区：
文献类型：
--
作者：
Kilic, Sefa;Sagitova, Dinara M.;Erill, Ivan
特定领域的数据库是生物医学界的重要资源，利用专家知识来管理已发表的文献，并提供参考数据和知识的访问。然而，这些数据库的范围有限，在其基础设施、知名度、资金和对更广泛的科学界的有用性方面构成了重大挑战。CollectTF是一个面向社区的数据库，记录了细菌结构域中实验验证的转录因子（TF）结合位点。在其寻求成为一个社区资源的注释转录调控元件在细菌基因组中，CollecTF旨在摆脱传统的数据库范式的领域特定的数据库。通过采用完善的本体、标识符和协作，CollectTF已逐渐成为注释和向主要生物序列资源（RefSeq、UniProtKB和基因本体联盟）提交关于转录调控元件的信息的门户。数据库概念的这一根本性变化利用了贡献社区的特定领域知识来提供高质量的注释，同时利用稳定的信息中心的可用性来促进长期访问并提供数据的高可见性。作为提交门户，CollectTF通过直接注释RefSeq基因组记录、在UniProtKB条目中定义基于TF的调控网络以及向Gene Ontology提交功能注释来生成TF结合位点信息。作为一个数据库，CollecTF提供了增强的搜索和浏览，有针对性的数据导出，结合基序分析工具以及与基序发现和搜索平台的集成。这一创新方法将使CollectTF能够将其有限的资源集中用于生成高质量的信息和提供专门的数据访问。
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.