ELIXIR recognises 4 UK services as essential for biological data preservation

In December 2023, ELIXIR announced the addition of four ELIXIR-UK services as Core Data Resources (CDRs): HGNC, LIPID MAPS®, PomBase and VEuPathDB

These four resources have been identified as crucial for life sciences as part of the latest edition of the ELIXIR CDR selection process in 2023.

The title gives recognition to the work of the members of the UK Node that has culminated in recognising the resources of fundamental importance to the broader life sciences community and the long-term preservation of biological data.

Granting CDR status to these ELIXIR-UK resources presents an opportunity for enhanced sustainability and funding, addressing the challenge of securing long-term support for scientific resources. These resources now join the select group of ELIXIR Core Data Resources, providing a framework for policymakers and funders to formulate sustainable strategies within the life sciences landscape.

The meticulous selection process is based on qualitative and quantitative indicators across five key categories:

  • Scientific focus and quality of science
  • Community served by the resource
  • Quality of service
  • Legal and funding infrastructure, and governance
  • Impact and translational stories

This recognition underscores the UK Node’s commitment to promoting excellence and fostering the infrastructure vital for future advancements in life sciences.

HGNC 

The HUGO Gene Nomenclature Committee (HGNC) is the only worldwide authority that assigns standardised nomenclature to human genes and is one of the longest-running life science standardisation projects. The HGNC database (www.genenames.org) currently contains over 43,000 approved gene symbols; each named gene has a Symbol Report that contains data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. HGNC’s gene nomenclature guidelines are discussed in PMID:32747822

The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HGNC, to approve gene nomenclature in vertebrate species without an existing dedicated nomenclature committee. The VGNC aims to harmonize gene nomenclature across selected vertebrate species (currently chimpanzee, macaque, dog, cat, cattle, pig and horse)  in line with human gene nomenclature, with orthologs assigned the same nomenclature where possible (PMID: 37173739). 

The HGNC project has also been recognised as a Global Core Biodata Resource since 2022.

LIPID MAPS

LIPID MAPS is a multi-institutional, global online resource hosting tools, databases and educational resources for lipid research.  The LIPID MAPS Nomenclature and Classification System for lipids was established in 2003 and is used worldwide.  The resource is primarily based at Cardiff University and Babraham Institute, Cambridge with co-investigators at University of California, San Diego, University of Edinburgh and Swansea University.

LIPID MAPS databases catalogue lipids at varying levels of characterisation, and numerous software tools and educational resources are provided to support their usage.  Our recent improvements include richer metadata with literature provenance, taxonomic data, and improved interoperability to facilitate FAIR compliance. In collaboration with WikiPathways and expert biochemists, LIPID MAPS curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. 

PomBase

PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation, and access to large-scale data sets. PomBase is also a major contributor to the GO consortium and is a member of the RNACentral consortium.

With the active involvement of members from University College London and the University of Cambridge as part of the UK Node, PomBase actively engages authors to participate in community curation to build Findable, Accessible, Interoperable and Reusable (FAIR)-shared biological knowledge from small-scale publications (PMID:32353878)

VEuPathDB

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB.org) provides a single point of access to diverse genomic and other large-scale datasets related to eukaryotic pathogens and invertebrate disease vectors. Organisms supported by this resource include (but are not limited to) the US-based NIAID list of emerging and re-emerging infectious diseases.


For further information and access to these resources, please visit ELIXIR’s CDR webpage or ELIXIR-UK services page.

To visit the official announcement from ELIXIR Europe, visit their news release

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