JAMI: a Java library for molecular interactions and data interoperability

Abstract

BackgroundA 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.ResultsA 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.ConclusionSoftware 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.

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

“…Annotations to Complex Portal identifiers are exported to and available through GO annotation files (GPAD, GPI) and can be searched and viewed via the web application QuickGO (https://www.ebi.ac.uk/QuickGO/search/CPX-591). The InterMine open source data warehouse system (19) has developed a pipeline to import protein complexes into the InterMine environment using the recently published JAMI library (20) to read and translate the data into interaction objects and export a MI-JSON file to the ComplexViewer. YeastMine and HumanMine are already making relevant data sets publicly available.…”

Integration of macromolecular complex data into theSaccharomycesGenome Database

“…We added macromolecular complex data to YeastMine (yeastmine.yeastgenome.org), our data warehouse, in 2015, using the JAMI (Java Molecular Interaction framework) library to read molecular interaction data in PSI-MI XML3.0 format and translate these into interaction objects (11). We then created pre-generated queries and a list of all curated molecular complexes (yeastmine.yeastgenome.org/yeastmine/bagDetails.do?scope=all&bagName=All+Curated+MolecularComplexes) to allow SGD users to search for and explore the information associated with macromolecular complexes.…”