RF

Integration of glycan-related data into the GlyCosmos Portal

Poster presentation — ASBMB 2023  •  Ran Fukazawa (GaLSIC, Soka University)

Abstract

Source: ASBMB poster abstract and slides. See references below.

My contributions (high level)

  • Curated and mapped glycan-related disease records from the Alliance of Genome Resources into the GlyCosmos RDF data model.
  • Converted MatrixDB protein–GAG interaction records into RDF triples using the Human Disease Ontology and MatrixDB identifiers.
  • Integrated the converted data into GlyCosmos and added browse/search UI hooks under Pathways / Interactions / Diseases / Organisms.
  • Authored SPARQL queries and helped verify results by cross-referencing KEGG, FlyGlycoDB and GGDB.
View poster slide

Technical notes

RDF store: Virtuoso / Apache Jena Fuseki
Query language: SPARQL
Ontologies: Disease Ontology, OBO RO
Sources: AGR, MatrixDB, KEGG, GGDB

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References

  1. Yamada I, et al. The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences. Nature Methods (2020).
  2. Alliance of Genome Resources & MatrixDB sources (integrated for this work). See uploaded materials.