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

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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

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CAPC automation

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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