About PFOCRummage

Biochemistry, molecular biology, pharmacology, and cell biology research papers commonly contain pathway diagrams. These diagrams capture the relationships between genes, cells, diseases, metabolites, drugs, cellular comportments, and other relevant terms. The Pathway Figure Optical Character Recognition (PFOCR) is a open science initiative which extracts gene sets from published articles in PubMed Central (PMC). So far, PFOCR extracted loading from pathway diagrams contained in loading. PFOCRummage serves these gene set for enrichment analysis, free text, and term search. Users of PFOCRummage can submit their own gene sets to find matching gene sets ranked by their overlap with the query gene set.

This database is updated monthly to use the latest human release of PFOCR.

This site is programmatically accessible via a GraphQL API.

This site is based on the Rummagene framework developed by the Ma'ayan Lab