Multimodality studies are a reality, with scientists commonly using several different data acquisition techniques to characterise biological systems under various experimental conditions. Yet, the deposition of such studies to public repositories remains a challenge for scientists who need familiarity with individual repositories to achieve these data publication requirements. Started during theBiohackathon 2023, theMARS project (Multi-omics Adapter for Repository Submissions) made great strides in producing a proof of concept for dispatching metadata to BioSamples, ENA and MetaboLights using the ISA-JSON format. ISA-JSON, designed for multi-omics studies, has clear specifications and is used as output format by ISA tools, DataPLANT's ARC and FAIRDOM-SEEK software.
Following this success, there is now interest in extending the service to support functional genomics data, hosted by ArrayExpress or BioStudies, EVA, EGA and e!DAL-PGP. Therefore, the objectives of this project are the following:
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Consolidate the current proof of concept and to bring it closer to a functional prototype, by further testing it and streamline it
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Extend functionalities to submit actual data files along with the metadata
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Collaborate further with repositories to support ISA-JSON format for programmatic submission via their API endpoint.
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Extend the MARS component and CLI to include additional data types and repositories, such as transcriptomics and possibly proteomics as a stretch goal.
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Develop domain specific minimal annotation profiles, building on the experience gained with Metabolights for MS and NMR based assay definitions.
To this end, we have assembled a team of subject matter experts to deliver on the task.
Bert Droesbeke, Philippe Rocca-Serra