Skip to content

16.md

Latest commit

 

History

History
40 lines (28 loc) · 3.93 KB

16.md

File metadata and controls

40 lines (28 loc) · 3.93 KB

Project 16: MiCoReCa (Microbiome Community Resource Catalogue): Towards Centralized Curation and Integration

The rapid growth of microbiome research has led to the development of numerous bioinformatics tools and databases, but information about them remains fragmented across disparate, often outdated cataloging efforts, hindering resource discovery and utilization. To address this critical gap, the ELIXIR Microbiome Community proposes the development of MiCoReCa (Microbiome Community Resource Catalogue), a comprehensive, dynamic, open-access catalogue of microbiome-related bioinformatics resources (tools, workflows, training, standards, and databases).

Leveraging our community's expertise, this initiative will utilize standardized ontologies like EDAM and cross-reference established platforms like bio.tools and WorkflowHub to create a centralized, findable inventory. A key feature is the community-driven process for identifying and curating missing ontological terms and metadata, ensuring MiCoReCa's accuracy and relevance in collaboration with partner platforms. Furthermore, the catalogue will integrate links to training materials from TeSS to support appropriate tool usage, and connect with OpenEBench for benchmarking capabilities.

This project will not only provide a vital resource for the microbiome field, enhancing research efficiency and reproducibility, but will also establish a sustainable, adaptable infrastructure potentially applicable to other ELIXIR Communities. This effort represents a significant contribution by the ELIXIR Microbiome Community to streamline microbiome bioinformatics.

Objectives

  • Extract and expose Microbiome resources from ELIXIR Ecosystem and Bioconda

    • Identify keywords to filter microbiome resources on RSEc-Atlas, WorkflowHub, TeSS, and Bioconda
    • Coordination with Research Software Ecosystem to have microbiome community in the RSEc-Atlas
    • Extract resources and and filter for microbiome resource by scrapping
      • RSEc-Atlas and BioConda for tools,
      • WorkflowHub for workflows,
      • TeSS for training resources
    • Identify missing microbiome tools in bio.tools using Bioconda and WorkflowHub
    • Create a page exposing all microbiome resources as a catalog

  • Expand, curate, and improve annotation of Microbiome resources

    • Improve tool annotations on bio.tools (EDAM, etc)
    • Add missing microbiome tools in bio.tools found in Bioconda and WorkflowHub
    • Discuss Topics, Format, Operation, and Data in EDAM for Microbiome analysis

  • Document the process to be reusable by other communities

Organization

To coordinate, 1 daily stand-up will be run to coordinate. We also created:

Lead(s)

Nikolaos Strepis, Bérénice Batut, Vivek Ashokan