European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007, Salamanca, Spain.
BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.
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.
系统生物学家研究相互作用数据，以便在分子水平上了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，研究人员拥有高质量的相互作用数据集是至关重要的，这些数据集应采用标准数据格式，并配备一套工具，以便分析这些数据并从中形成可通过实验验证的假设。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，以实现分子相互作用数据的下载和交换。PSI-XML2.5 的设计目的是描述实验数据，迄今为止，它已经满足了这一基本要求。然而，新的用例出现了，格式无法正确容纳。这些用例包括从不止一篇文献中提取的数据，例如变构/协同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力数据与特定突变变化联系起来的需求。
HUPO-PSI 的分子相互作用工作组根据广泛的社区咨询，扩展了现有的、广泛使用的分子相互作用数据 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 扩展了格式的功能，超越了简单的实验数据，同时对服务于该格式的工具套件进行了相应更新。该格式已由关键数据生成者实施，例如蛋白质相互作用数据库的国际分子交换 (IMEx) 联盟和复合物门户。
PSI-MI XML3.0 是由构成 PSI-MI 工作组的数据生成者、数据使用者、工具开发人员和数据库提供商开发的。该工作组现在积极支持 PSI-MI XML2.5 作为实验数据的主要交换格式、PSI-MI XML3.0 作为处理更复杂数据类型的格式，以及更简单的、以制表符分隔的 MITAB2.5、2.6 和 2.7 格式，用于快速解析和下载。
