JAMI: a Java library for molecular interactions and data interoperability

M Sivade,N Del-Toro,J Heimbach,M Koch,C W Combe,J Rappsilber,J Sullivan,A Shrivastava,J De Las Rivas,Y Yehudi,S Orchard,D Alonso-López,B H M Meldal

doi:10.1186/s12859-018-2119-0

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.

Highlights

A number of different molecular interactions data download formats exist, designed to allow access to these valuable data by diverse user groups
Proteomics Standards Initiative (PSI)-Molecular Interactions (MI) XML, MITAB and MI-JSON are all capable of holding the same data, in differing degrees of detail, and are all annotated using a single shared controlled vocabulary but exist to serve different user groups
The XML format is largely used by software developers and database managers, the MITAB by biologists interested in simple binary representation and the MI-JSON for visual representation

Summary

Results

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

Conclusion

Background

Conclusions