help.md

title
Help

Video Tour

Take a video tour of the PFOCR website!

<iframe width="560" height="315" src="https://www.youtube.com/embed/8XRS_dTX-eM?si=ufH5i7Ah7Dc8sMx9" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

TogoTV. Feb 13 2024, YouTube: https://youtu.be/8XRS_dTX-eM, DOI: https://doi.org/10.7875/togotv.2024.004.

Navigate

Search

The collection of pathway figures can be searched by gene symbol, title and other keywords, either directly in the Search field at the top of each page or on the front page. For example, search for your favorite pathway by a word from the title (i.e. "Statin"), or your favorite gene either by symbol (i.e. "BRCA1").

• Go to dedicated Search page.
• Alternatively, check out PFOCRummage to search human figures by gene set enrichment, PMC query and keywords.

Browse

The Pathway Figure OCR content can be browsed by cross-references to other databases:

• Pathway Figures translated to WikiPathways: View a subset of figures that have been manually translated into WikiPathways models.
• Pathway Figures deposited at NDEx: View the subset of pathway figures below that have been coverted to the Cytoscape CX format and deposited at NDEx.

Or by parsing JSON files containing all pathway figure information:

• All figure information
• Figure information by organism

Download

Download GMT: Gene Matrix Transposed

• The latest GMT for all pathway figures can be found at https://data.wikipathways.org/pfocr/current. Archives of prior releases can be found in sibling directories.

Downloading and Accessing Individual Pathways

• The permanent link to a specific pathway has the pattern https://pfocr.wikipathways.org/figures/{figid}.html. This link is also accessible from the options drop-down under the figure from the pathway figure page.
• View the figure at PMC directly from the options drop-down under the figure from the pathway figure page.
• To read the associated paper at PMC, access the options drop-down under the figure from the pathway figure page.
• If the figure has been translated to a WikiPathways model, you can open it directly at WikiPathways from the pathway figure page by accessing the options drop-down under the figure.
• Open a network representation of the list of genes at NDEx from each pathway figure page by accessing the options drop-down under the figure.
• Download individual pathway figures in JPG format from each pathway figure page by accessing the options drop-down under the figure.
• Download the list of annotated genes in the GPML (Graphical Pathway Markup Language) format from each pathway figure page by accessing the options drop-down under the figure. These starter GPMLs are meant to facilitate the curation of WikiPathways models by providing curators with already annotated nodes.

Analyze

Pathway gene sets can be used for analysis in multiple tools:

• The Enrichr tool includes the Pathway Figure OCR gene sets as one of its libraries for enrichment analysis.
• Use PFOCRummage to search by gene set enrichment, PMC or keywords.
• Use the NDEx Integrated Query for quick enrichment analysis.
• Run IEA locally for interactive enrichment analyses.
• Use WebGestalt for more advanced enrichment analysis options.
• Use our GMT file as a custom data source in the g:Profiler tool for enrichment analysis.
• Parse the JSON of all figure information
• Parse the JSON of figure information by organism