Bridging WikiPathways and metabolomics data using the ChEBI ontology

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My presentation about how ChEBI can be used in combination with WikiPathways: 1. adding semantics to pathway diagrams, 2. identifier mapping databases for BridgeDb, 3. use in mapping experimental data onto pathways.

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Bridging WikiPathways and metabolomics data using the ChEBI ontology

  1. 1. Department of Bioinformatics - BiGCaT 1 Bridging WikiPathways and metabolomics data using the ChEBI ontology Egon Willighagen (@egonwillighagen) 25 March 2013, ChEBI 3rd User Workshop
  2. 2. Department of Bioinformatics - BiGCaT 2 Where do the metabolites go?
  3. 3. Department of Bioinformatics - BiGCaT 3 Unexplored territory
  4. 4. Department of Bioinformatics - BiGCaT 4 Systems biology: a map of life Kelder, Thomas, et al. "WikiPathways: building research communities on biological pathways." Nucleic acids research 40.D1 (2012): D1301-D1307.
  5. 5. Department of Bioinformatics - BiGCaT 5 Pathways for the People (CC-BY)
  6. 6. Department of Bioinformatics - BiGCaT 6 Crowd sourcing... Source: http://wikipathways.org/index.php/WikiPathways:Statistics
  7. 7. Department of Bioinformatics - BiGCaT 7 Other sourcing... • Stable Projects (9) – NetPath, SBGN, BiGCaT (us), ... • Active Projects (15) – Open PHACTS, Reactome, NCBI (=BioModels), Aglilent, ...
  8. 8. Department of Bioinformatics - BiGCaT 8 Reactome Slide: Anwesha Bohler
  9. 9. Department of Bioinformatics - BiGCaT 9 Bridging: identifiers
  10. 10. Department of Bioinformatics - BiGCaT 10 So, what IDs are used in WikiPathways? Curated Collection subset
  11. 11. Department of Bioinformatics - BiGCaT 11 PathVisio: pathway enrichment (etc) Van Iersel, M.P., et al. "Presenting and exploring biological pathways with PathVisio." BMC bioinformatics 9.1 (2008): 399. http://pathvisio.org/ Martina Kutmon→
  12. 12. Department of Bioinformatics - BiGCaT 12 BridgeDb Van Iersel, M.P., et al. "The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services." BMC Bioinformatics 11.1 (2010): 5. New tools ● Open PHACTS' IMS ● Bioclipse ● R
  13. 13. Department of Bioinformatics - BiGCaT 13 BridgeDb Metabolite ID Mapping database ● HMDB ● ChEBI
  14. 14. Department of Bioinformatics - BiGCaT 14 BridgeDb: scientific lenses • Gene – gene-protein – gene-probe • Metabolite – Tautomers – Compound class – Charge (acid/ate) Brenninkmeijer, CYA, et al. "Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision." Proceedings of 2nd International Workshop on Linked Science. 2012.
  15. 15. Department of Bioinformatics - BiGCaT 15 A random metabolomics data set CAS numbers: 1843 CAS numbers (unique): 1733 CAS numbers with mappings: 718 (41%) CAS numbers matches: 55 (3%) Pathways found: 66 Matches via CAS: 9 Matches via mapping: 24 Matches via ChEBI super class: 33 Matches via ChEBI charged species: 0 Matches via ChEBI tautomers: 0 CAS: 544-63-8 (myristic acid) Ce:28875 Ce:15904 (long-chain fatty acid)→ → → [WP368 Mitochondrial LC-Fatty Acid Beta-Oxidation, WP357 Fatty Acid Biosynthesis]
  16. 16. Department of Bioinformatics - BiGCaT 16 SPARQLs SELECT ?super WHERE { <http://purl.obolibrary.org/obo/CHEBI_$id> rdfs:subClassOf+ ?super . } SELECT ?super WHERE { <http://purl.obolibrary.org/obo/CHEBI_$id> rdfs:subClassOf [ a owl:Restriction ; owl:onProperty obo:is_conjugate_acid_of ; owl:someValuesFrom ?super ] }
  17. 17. Department of Bioinformatics - BiGCaT 17 Computer Assisted Pathway Curation
  18. 18. Department of Bioinformatics - BiGCaT 18 CAPC automation
  19. 19. Department of Bioinformatics - BiGCaT 19 Conclusion: ChEBI needs • Charge states for all metabolites • Compound classes • (tautomers?) • Consistent ChEBI:IDs • How to detect “replaced” ChEBI IDs? • What are “secondary” IDs?
  20. 20. Department of Bioinformatics - BiGCaT 20 Who does it? • http://wikipathways.org/ – Maastricht Uni, Alex Pico (Gladstone Institutes/SF) – … (many collaborative projects) – http://pathvisio.org/ • http://bridgedb.org/ – HMDB, ChEBI ( mapping files)→ – Maastricht Uni, Carol Goble (Manchester Uni) • Anwesha Bohler – http://projects.bigcat.unimaas.nl/ReactomeConverter • Rianne Fijten (Tox/UM) – Metabolomics data set

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