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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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Department of Bioinformatics - BiGCaT 1
Bridging WikiPathways and metabolomics
data using the ChEBI ontology
Egon Willighagen (@egonwillighagen)25 March 2013, ChEBI 3rd User Workshop
Department of Bioinformatics - BiGCaT 2
Where do the metabolites go?
Department of Bioinformatics - BiGCaT 3
Unexplored territory
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.
Department of Bioinformatics - BiGCaT 5
Pathways for the People (CC-BY)
Department of Bioinformatics - BiGCaT 6
Crowd sourcing...
Source: http://wikipathways.org/index.php/WikiPathways:Statistics
Department of Bioinformatics - BiGCaT 7
Other sourcing...
• Stable Projects (9)– NetPath, SBGN,
BiGCaT (us), ...
• Active Projects (15)– Open PHACTS,
Reactome, NCBI (=BioModels), Aglilent, ...
Department of Bioinformatics - BiGCaT 8
Reactome
Slide: Anwesha Bohler
Department of Bioinformatics - BiGCaT 9
Bridging: identifiers
Department of Bioinformatics - BiGCaT 10
So, what IDs are used in WikiPathways?
Curated Collection subset
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→
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
Department of Bioinformatics - BiGCaT 13
BridgeDb
Metabolite ID Mapping database● HMDB● ChEBI
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.
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]
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
]
}
Department of Bioinformatics - BiGCaT 17
Computer Assisted Pathway Curation
Department of Bioinformatics - BiGCaT 18
CAPC automation
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?
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