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Need information about Pathway Commons? Here's where you'll find tools, tutorials, and other helpful resources.

Overview

Detailed and comprehensive pathway information is a key element for understanding human genetic variation and disease and will enable genomic medicine to move towards diagnosis and therapy in a patient-specific context. Large data initiatives at the NIH and in the wider health care community can leverage the vast biological knowledge captured in pathway resources to better organize and analyze their data.

Pathway Commons is a convenient single point of access for all publicly accessible pathway information. In close coordination with database teams and NHGRI staff, we aim to provide for the efficient exchange of pathway data; aggregation and integration into a shared public information store; distribution in a value-added form as aggregated data sets and as context-tailored data feeds; and availability to the end-user in the context of domain-specific portals, such as genetics, genomics, personalized medicine, model organism and bioinformatics web portals, exploiting advanced internet web service technology.

Pathway Commons was originally developed at the Memorial Sloan Kettering Cancer Center and the University of Toronto. The Pathway Commons team is a collaboration between the Bader lab at the University of Toronto, the Sander lab at the Dana-Farber Cancer Institute and Harvard Medical School, and the Demir lab at Oregon Health & Science University.

People

If you have any questions, suggestions or if you wish to contribute Outreach materials, please don't hesitate to contact the @PathwayCommons/outreach team.

Gary Bader
- Principal Investigator - @gbader
Augustin Luna
- Postdoctoral Research Fellow - @cannin
Jeffrey Wong
- Outreach Manager - @jvwong

Training

Tutorials

This section contains teaching materials that we've collected which will help kick start you on your way to familiarizing yourself with Pathway Commons.

BioPAX
- Level: Intermediate-Advanced
  - Workshop: Biological Pathway Exchange (BioPAX) Ontology and Pathway Commons Database
    - International Conference on Biomedical Ontology - Lisbon, Portugal; July 27-30, 2015
    - Organizers
      - Augustin Luna, Memorial Sloan Kettering Cancer Center - @cannin
      - Emek Kemir, Memorial Sloan Kettering Cancer Center - @emekdemir
PaxtoolsR
- Level: Introductory
  - Workshop: Introduction to Pathway Commons using PaxtoolsR
    - Exploring Cancer Pharmacogenomics - University of São Paulo, Brazil; January
    - Organizer
      - Augustin Luna, Research Fellow, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute - @cannin
Guide
- Level: Introductory
  - Workflows, primers, case studies and presentations focusing on pathways and pathway analysis of experimental data

Developer Resources

cPath2 API: OpenAPI/Swagger UI for Pathway Commons web services
cPath2 client: A JavaScript client (NPM) for Pathway Commons web services
biopax-validator service: BioPAX Validator webservice info
SIF graph API: Sifgraph webservice API docs
factoid-converters API: still an experimental, internal use app

Brand

Pathway Commons brand materials to help you include PC on your website or publication.

Logos

Download all our logos or select individual formats/images.

To include one of the logos on your web page, you can simply link to one of the resources in the images/brand directory. For example, to include the PC logo with background:

  <img src="http://pathwaycommons.github.io/about/images/brand/pc_logo_background.png" />

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PathwayCommons/about

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