Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada.
Database (Oxford). 2010 Dec 22;2010:baq026. doi: 10.1093/database/baq026. Print 2010.
Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15 471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL: http://wodaklab.org/iRefWeb.
蛋白质相互作用数据的文献整理面临着许多挑战。尽管整理者越来越多地遵循标准的数据表示方法，但不同数据库实际上从同一已发表信息中记录的数据可能存在显著差异。导致这些差异的部分原因是众所周知的，但它们对主要公共数据库共同整理的相互作用的全球影响尚未得到评估。在这里，我们量化了来自 9 个主要公共数据库共享的 15471 篇文献中整理的相互作用之间的一致性。结果表明，平均而言，两个数据库完全一致的相互作用数量占 42%，来自同一出版物的蛋白质数量占 62%。此外，所测量的差异的相当一部分可以归因于生物体或剪接异构体的不同分配、不同的生物体焦点和多蛋白复合物的替代表示。我们的研究结果强调了数据库之间不同的整理策略的影响，这对于关注由科学界生成的蛋白质相互作用数据的整理者和数据使用者来说都很重要。数据库网址：http://wodaklab.org/iRefWeb。
