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    WP1 RI nominated resources 1: OmicsDI on the EOSC cloud infrastructure and provision for local satellite


    The Omics Discovery Index (OmicsDI), an ELIXIR Interoperability Resource, provides a discovery portal for omics datasets from genomics, transcriptomics, proteomics, metabolomics, and systems biology models, increasing the FAIRness of public omics datasets.

    It indexes the metadata of > 2,000,000 datasets from 20 partner repositories on four continents. Partner repositories provide their metadata in a push model and create a file in a defined and documented XML format which is then validated, harmonised, and indexed (based on Lucene) through the OmicsDI workflows. OmcisDI allows the user to browse by species, disease, tissue, database, omics type, and even more and to obtain multi-faceted search results for these categories. 

    OmicsDI provides prototype multi-dimensional usage metrics for its datasets based on the access within OmicsDI, downloads, dataset re-use, and references to dataset identifiers. We have developed a public API allowing external sites to include a simple visualisation of OmicsDI-based impact metrics for their datasets, supporting an assessment of the actual impact of FAIR datasets. 

    In systems biology, a number of independent public repositories provide mathematical models of biological systems to the community, but no central discovery support is provided. To address this problem, we have developed ModelXchange, a cloud-ready satellite instance of OmicsDI that is specialised for systems biology, and collaborated with four major community resources, the Physiome Model Repository, Cell Collective, BioModels, and FAIRDOMHub to create a central discovery portal for systems biology models across all four resources. This specialisation of multi-omics infrastructure has a significant community impact, turning it into a valuable tool for the specific omics field. In addition, it represents a “simplified case study” that addresses the EOSC challenge to provide general infrastructures that are useful for specific domains but does not require too much adaptation overhead.


    Yasset Perez Riverol, Juan Antonio Vizcaino, Rahuman Sheriff, Tung Nguyen, Henning Hermjakob, EMBL-EBI, UK

    Phil Gribbon, ITMP, Germany

    Wolfgang Müller, HITS gGmbH, Germany

    Tomas Helikar, University of Nebraska, USA

    David Nickerson, University of Auckland, New Zealand


    RIs involved


    • ModelXchange – Global Coordination of FAIR Systems Biology Resources (in preparation)