The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data
The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data
复制标题
DOI：
10.1038/nbt926
复制
发表时间：
2004-02-01
影响因子：
46.9
通讯作者：
Apweiler, R
中科院分区：
文献类型：
--
作者：
Hermjakob, H;Montecchi-Palazzi, L;Apweiler, R
蛋白质组学的一个主要目标是完整描述细胞生理学背后的蛋白质相互作用网络。大量的小规模以及近期的大规模实验有助于拓展我们对相互作用网络性质的理解。然而，目前跨实验的必要数据整合因公开可用的蛋白质相互作用数据的碎片化而受阻，这些数据以不同格式存在于数据库、作者网站，有时仅存在于印刷出版物中。在此，我们提出一个用于蛋白质相互作用数据表示和交换的社区标准数据模型。该数据模型是由蛋白质组学标准倡议（PSI）的成员联合开发的，PSI是人类蛋白质组组织（HUPO）的一个工作组，并且得到了主要的蛋白质相互作用数据提供者的支持，特别是生物分子相互作用网络数据库（BIND）、Cellzome（德国海德堡）、相互作用蛋白质数据库（DIP）、达纳法伯癌症研究所（美国马萨诸塞州波士顿）、人类蛋白质参考数据库（HPRD）、Hybrigenics（法国巴黎）、欧洲生物信息学研究所（EMBL - EBI，英国欣克斯顿）的IntAct、分子相互作用（MINT，意大利罗马）数据库、蛋白质 - 蛋白质相互作用数据库（PPID，英国爱丁堡）以及相互作用基因/蛋白质检索搜索工具（STRING，EMBL，德国海德堡）。
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).