ELIXIR Service Bundle supporting multi-omics genotype-phenotype associations in non-Human species (BIOTEC-07-2020)

As the ESFRI Research Infrastructure for life science data, ELIXIR Nodes provide a range of services that can be used by researchers and consortia applying to the Horizon 2020 topic ‘Multi-omics for genotype-phenotype associations’.

For instance, ELIXIR offers multiple services that support the integration and understanding of different ‘omics datasets. ELIXIR maintains that making data FAIR (Findable, Accessible, Interoperable, Reusable) is a critical prerequisite for any project of this type and thus always recommends deposition and archiving of existing ‘omics data sets in one of our selected Deposition Databases. These support a wide range of data types and are free to use.

For multi-omics type studies, archives of particular interest may include: ENA (for deposition of nucleotide sequences), ArrayExpress (for Transcriptomics data) MetaboLights (for metabolomics data), Biostudies (for unstructured experimental data) and EVA (for variant data archival and accessioning). For deposition of large, complex or non-normalised data sets it is recommended/good practice to establish a data coordination centre that includes resource owners.

To access and/or download deposited datasets (for the purposes of multi-omics data integration and analysis), ELIXIR recommends accessing the ELIXIR Core Data Resources. These are entirely open and free to use. Beyond the Core Data Resources, ELIXIR also provides a wide range of Node services and resources that may be of use in this topic, including MGnify (for meta-genomics data processing and archival), Marine Metagenomics Portal (for marine data) and GnpIS (for Plant data) and many others.

ELIXIR recognises that the combination of disparate data sets can be technically challenging and have developed a range of services to support this effort. For instance we have identified the ELIXIR Recommended Interoperability Resources - key interoperability resources for Life Sciences. The resources are relevant for project data annotation and integration efforts and better use of ontologies in the phenotype descriptions. Services include OLS, FAIRsharing, ISA Framework, BridgeDB, Plant Phenotyping Experiment Ontology.

Whilst all the services listed above are free to use, it is recommended that applicants to BIOTEC-07-2020 engage the ELIXIR Hub, and potentially include key partners in any application, as we have multiple experts who have experience in building tool sets that support the sustainable data validation and integration of ‘omics data across diverse areas of non-human data.

Analysis of multi-’omics data is still a developing field, even once the challenges of data access are overcome. For large studies, compute capacity may become limiting and ELIXIR recommends engaging with the ELIXIR Hub for advice on available Clouds and other Compute resources which may be required. To access these compute resources, it is almost certain funds will need to be allocated to the relevant ELIXIR Institute as part of the proposal. In addition, ELIXIR has deep expertise in the field of workflows, for instance through our Galaxy community. Therefore, if applicants have requirements around data analysis, data reproducibility or data quality it is recommended they engage with the ELIXIR Hub.

Training for all of the resources highlighted above may be required and can be found through the ELIXIR training portal, TeSS. If an applicant identifies the need for more extensive training within the project, for instance through the generation of new training materials, then this might require dedicated funding to be included in the application and it is suggested that the applicant engages with the ELIXIR Hub, in the first instance.

Finally, ELIXIR has extensive contacts with the European Life Science commercial community built up through our SME events, held across several major cities over the past few years. We have made contact with over 400 companies and the ELIXIR Hub is a good route to explore making links into the commercial sector in order to identify interesting Use Cases.

If the relevant expertise can’t be found as described above, applicants could consider searching our broader registries e.g. BioTools or FAIRsharing, or contacting a relevant ELIXIR Head of Node (Leads for our Member states), as tabulated below: