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Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
Bridging WikiPathways and metabolomics data using the ChEBI ontology
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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 …

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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  • 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. Department of Bioinformatics - BiGCaT 2 Where do the metabolites go?
  • 3. Department of Bioinformatics - BiGCaT 3 Unexplored territory
  • 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. Department of Bioinformatics - BiGCaT 5 Pathways for the People (CC-BY)
  • 6. Department of Bioinformatics - BiGCaT 6 Crowd sourcing... Source: http://wikipathways.org/index.php/WikiPathways:Statistics
  • 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. Department of Bioinformatics - BiGCaT 8 Reactome Slide: Anwesha Bohler
  • 9. Department of Bioinformatics - BiGCaT 9 Bridging: identifiers
  • 10. Department of Bioinformatics - BiGCaT 10 So, what IDs are used in WikiPathways? Curated Collection subset
  • 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. 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. Department of Bioinformatics - BiGCaT 13 BridgeDb Metabolite ID Mapping database ● HMDB ● ChEBI
  • 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. 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. 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. Department of Bioinformatics - BiGCaT 17 Computer Assisted Pathway Curation
  • 18. Department of Bioinformatics - BiGCaT 18 CAPC automation
  • 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. 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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