Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
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DOI：
10.1186/s12859-018-2118-1
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发表时间：
2018-04-11
影响因子：
3
通讯作者：
Orchard S
中科院分区：
文献类型：
--
作者：
Sivade Dumousseau M;Alonso-López D;Ammari M;Bradley G;Campbell NH;Ceol A;Cesareni G;Combe C;De Las Rivas J;Del-Toro N;Heimbach J;Hermjakob H;Jurisica I;Koch M;Licata L;Lovering RC;Lynn DJ;Meldal BHM;Micklem G;Panni S;Porras P;Ricard-Blum S;Roechert B;Salwinski L;Shrivastava A;Sullivan J;Thierry-Mieg N;Yehudi Y;Van Roey K;Orchard S
系统生物学家研究相互作用数据，以在分子水平上理解整个细胞系统及其环境的行为。为了有效地实现这一目标，研究人员必须以标准的数据格式获得高质量的交互数据集，并有一套工具来分析这些数据并从中形成实验可验证的假设。PSI-MI XML标准交换格式最初于2004年发布，并于2007年进行了扩展，以便能够下载和交换分子相互作用数据。PSI-XML2.5被设计用来描述实验数据，到目前为止已经满足了这一基本要求。然而，出现了新的用例，这种格式不能适当地适应。这些包括从多个出版物中提取的数据，如变构/合作相互作用和蛋白质复合物，动态相互作用以及将动力学和亲和数据与特定突变变化联系起来的需求。经过广泛的社区咨询，HUPO-PSI的分子交互工作组扩展了现有的、使用良好的分子交互数据XML交换格式，以满足新的用例，并能够捕获新的数据类型。PSI-MI XML3.0扩展了该格式的功能，超出了简单的实验数据，并附带更新了服务于该格式的工具套件。该格式已由关键数据生产者实施，如国际分子交换（IMEx）联盟的蛋白质相互作用数据库和复杂门户。PSI-MI XML3.0是由组成PSI-MI工作组的数据生产者、数据用户、工具开发人员和数据库提供者开发的。该小组现在积极支持PSI-MI XML2.5作为实验数据的主要交换格式，PSI-MI XML3.0（另外处理更复杂的数据类型），以及更简单的、以制表符分隔的MITAB2.5、2.6和2.7，用于快速解析和下载。本文的在线版本（10.1186/s12859-018-2118-1）包含补充材料，授权用户可以使用。
Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download. The online version of this article (10.1186/s12859-018-2118-1) contains supplementary material, which is available to authorized users.
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