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):133. doi: 10.1186/s12859-018-2119-0.
A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types.
A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats.
Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.
目前存在许多不同的分子相互作用数据下载格式，旨在允许不同用户群体访问这些有价值的数据。这些格式包括由 HUPO-PSI 的分子相互作用工作组开发的 PSI-XML 和 MITAB 标准交换格式，以及其他资源生成的特定于用途的其他下载。目前的责任在于用户确保软件能够读取/写入每个格式的所有必要版本。随着数据提供者努力满足越来越复杂的用户需求和数据类型，这个问题可能会增加。
EMBL-EBI 和剑桥大学之间的合作产生了 JAMI，这是一个统一标准分子相互作用数据格式的单一库，如 PSI-MI XML 和 PSI-MITAB。JAMI 是一个免费的开源库，它使开发分子相互作用计算工具和管道成为可能，而无需生成不同版本的软件来读取不同版本的数据格式。
基于 JAMI 框架开发的软件和工具能够集成和支持 PSI-MI XML 和 PSI-MITAB。使用 JAMI 可以避免为了达到所需的输出格式而在格式之间链式转换的要求，并防止由于代码变得更加模块化而导致代码和单元测试重复。JAMI 的模型接口从底层格式抽象出来，将每个数据格式的复杂性和要求隐藏起来，供使用 JAMI 作为库的开发人员使用。
