How we assist knowledge collection

Chris Evelo Dept of – BiGCaT Maastricht University

Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Serving the monks Paper: WikiPathways: Pathway Editing for the People. Alexander R. Pico, Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Bruce R. Conklin, Chris Evelo. PLoS Biology 2008: 6: 7. e184 Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009

Commentaries: Big data: Wikiomics. Mitch Waldrop. Nature 455, 22-25 (2008) We the curators. Allison Doerr. Nature Methods 5, 754 - 755 (2008) WikiPathways

• Public resource for biological pathways • Wiki: – Anyone can contribute and curate

• More up-to-date representation of biological

Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 knowledge What are biological pathways? Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 How are Pathways used?

• Example: RNA interference in C. elegans Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009

The nematode C. elegans Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Connect to Genome Databases Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Data Visualization Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 On to the real thing… Fasten seat belts! Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009

Photo by Timo Arnall Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Search: “ One carbon” Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Click Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Editing

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Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Registration by e-mail address All edits logged Draw the and interactions

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Click & drag Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Draw the proteins and interactions

Click Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Draw the proteins and interactions

Click & drag Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Draw the proteins and interactions Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Draw the proteins and interactions Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Draw the proteins and interactions Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Draw the proteins and interactions Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Annotate the proteins

Double click Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Annotate the proteins Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Add reference to literature

Click Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Save the pathway

Click save Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Updated pathway page Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Download Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 “ Wiki’ s work because it is easier to undo damage than to create it. Imagine what cities would look like if it was easier to clean graffiti than to create it” – Clay Shirkey Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Revision history

Select two versions

Click Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Diff tool Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 September 2008 Growth More users, , pathways,

February 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009

April 2009 Contributions – new pathways

February 2008 November 2007

June 2007

January 2008 Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Contributions – small edits Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Species • We can add any species that is in ENSEMBL • Or anything where you create an ENSEMBL like DB • Just ask! Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Metabolomics

Visualization and statistics fully supported

HMDB

Chebi Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 NuGOwiki Automatic content generation

GO: ontology visualization • Automatic pathway (table) generator for any GO level • Ask for tool or pathways

• Go statistics in GenMAPP, Go_Elite, R (through webservice) Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Automatic content generation

KEGG • Automatic pathway converter • Ask for tool or pathways

• We need two versions: – Original

Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 – Community updated Automatic content generation

BioPAX • Part of BioPAX already implemented • Full converter in development using Paxtools • Can also be used for (round trip) Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Assisted content generation

Suggestions from: • HMDB • KEGG • BIND • Text mining (Phasar) Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Portals Need one? Webservice

Web service Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Request Response Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 What for?

• Build web applications

• Extend existing applications

• Include in workflows / analysis pipelines Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Available services

• Download – All pathway information in various formats – Pathway metadata – Colored pathway images – Gene lists • Find – By keyword searches

Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 – By gene / / small molecule identifier – Interactions by gene / protein Available services

• Update – Notify community by curation tags – Update pathway content – Create new pathways

• Write access upon request Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Search engine Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Visualizing gene expression

Integrates data from ArrayExpress Atlas with WikiPathways pathways Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 plugin Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Search and open pathways from WikiPathways directly in Cytoscape. Taverna workflows Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009

Include pathway information in Taverna workflows. http://www.myexperiment.org/packs/40 R Example

• SSOAP http://www.omegahat.org/SSOAP/ Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 R- example: GSEA

• Get all pathways as gene lists • Download a GEO dataset (on papillary renal cell carcinoma) • Perform Parametric Gene Set Enrichment Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Enrichment analysis Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Nature Precedings : doi:10.1038/npre.2009.3115.1 : Posted 21 Apr 2009 • WikiPathways web service: – Programmatic interface to WikiPathways data – Language-independent – Latest pathway information

• Powerful tool when combined with other web services and libraries

Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 http://www.wikipathways.org/webservice Credit system Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 www..org

Gladstone Institutes (San Francisco) Alexander Pico Kristina Hanspers Bruce Conklin

Department of Bioinformatics (Maastricht) Thomas Kelder Martijn van Iersel

Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009 Chris Evelo Enjoy! Nature Precedings : doi:10.1038/npre.2009.3115.1 Posted 21 Apr 2009