bridging wikipathways and metabolomics data using the chebi ontology
TRANSCRIPT
Department of Bioinformatics - BiGCaT 1
Bridging WikiPathways and metabolomics
data using the ChEBI ontology
Egon Willighagen
@egonwillighagen, 0000-0001-7542-02869 April 2015
COSMOS RDF, LOD and Semantic Omics data hackathon
Department of Bioinformatics - BiGCaT 2
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.
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 6
Crowd sourcing...
Source: http://wikipathways.org/index.php/WikiPathways:Statistics
Crowd sourcing... but funding helps...
Source: http://wikipathways.org/index.php/WikiPathways:Statistics
Department of Bioinformatics - BiGCaT 9
So, what IDs are used in WikiPathways?
Curated Collectionsubset
Department of Bioinformatics - BiGCaT 10
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 12
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 13
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
Who does it?
• http://wikipathways.org/– Maastricht Uni, Alex Pico et al. (Gladstone Institutes/SF)–… (many collaborative projects)–http://pathvisio.org/–WikiPathways-RDF → Andra Waagmeester
• http://bridgedb.org/–HMDB, ChEBI ( mapping files)→–Maastricht Uni, Carol Goble et al. (Manchester Uni)
• Anwesha Bohler–http://projects.bigcat.unimaas.nl/ReactomeConverter
• Rianne Fijten (Tox/UM)–Metabolomics data set