Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.
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DOI：
10.1093/database/bas026
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发表时间：
2012
期刊：
影响因子：
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通讯作者：
Lu Z
中科院分区：
文献类型：
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作者：
Névéol A;Wilbur WJ;Lu Z
高通量实验和生物信息学技术正在产生爆炸式的数据量，对于需要访问、分析和处理现有数据的生物学家和研究人员来说，这些数据量正变得难以追踪。许多可用的数据都存储在专门的数据库中，如基因表达综合数据库（GEO）的微阵列或蛋白质数据库（PDB）的蛋白质结构和坐标。数据集也由其作者在文献数据库（如MEDLINE和PubMed Central）中存档的出版物中进行描述。目前，生物数据库与文献之间的链接管理主要依赖于手工劳动，这使得它成为一项耗时且艰巨的任务。本文分析了GEO、PDB和MEDLINE之间的链接管理现状。我们发现，根据所涉及的来源和数据库，链接管理是异构的，并且来源之间的重叠很低，PDB和GEO的重叠<50%。此外，我们还表明，文本挖掘工具可以自动提供有价值的证据，帮助策展人扩大他们审查的文章和数据库条目的范围。因此，我们提出了建议，以提高策划链接的覆盖范围，以及在保持高质量策划的同时，从不同数据库获得的信息的一致性。数据库url: http://www.ncbi.nlm.nih.gov/PubMed、http://www.ncbi.nlm.nih.gov/geo/、http://www.rcsb.org/pdb/
High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/