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Type: Data Repository + Virtual Research Environment (VRE)

Gene Expression Enrichment with the TopAnat tool

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Lead Institution

About

TopAnat is an anatomical expression enrichment tool that associates genes with the anatomical structures (e.g., brain) by their expression levels. TopAnat is a domain-specific data analysis tool in Life Sciences that could be integrated into a VRE such as Galaxy.
TopAnat relies on the Bgee database. Bgee integrates and curates multiple transcriptomics datasets produced with different technologies by researchers, including single-cell and bulk RNA-Seq. Bgee focuses on metazoans, and currently integrates 52 animal species.
The Bgee infrastructure is recognised as a Global Core Biodata Resource, i.e. a resource that is “of fundamental importance to the wider biological and life sciences community”. At the European level, it is recognised as an ELIXIR Recommended Interoperability Resource, that is, a resource “that facilitates the FAIR-supporting activities in scientific research”.

Project objective: Enable AI-based data discovery and access including EOSC pairing data and software

  • Our contribution: TopAnat tool can be available as one of the tools to be paired with other data sources (i.e., input data). Moreover, Bgee datasets can be available too for pairing with other software tools.

Project objective: Accelerate research with automated orchestration and deployment of data analysis

  • Our contribution: TopAnat tool can be used to execute a domain-specific data analysis for gene expression enrichment, if the expected input data format is provided.

Project objective: Increase FAIRness in EOSC by integrating FAIR and data quality assessment tools in the research lifecycle

  •  Our contribution: the FAIR assessment tools can be evaluated and applied to TopAnat results and Bgee datasets overall.

Project objective: Facilitate the uptake of research FAIRification and reproducibility services 

  • Our contribution: we will provide our experience in making data analysis reproducible. 

 

  • The Bgee data and the TopAnat tool will be available and discoverable within the EOSC Matchmaker.

  • Integration of the TopAnat tool with the EOSC Data Player. For example, TopAnat can be integrated into a VRE such as Galaxy for deployment and data orchestration. This may include gene ID mappers and the interoperability with other tools (i.e., data input or output) to perform an analysis workflow on the researcher’s data. 

  • FAIRness assessment and reproducibility toolset and policies applied and evaluated with the TopAnat output data and Bgee datasets. 

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