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OCR results from 65k pathway figures published between 1995 and 2019

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posted on 05.06.2020, 20:30 by Alexander Pico, Anders Riutta, Kristina Hanspers, Martina Kutmon
In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. First, we trained a machine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Then, we performed OCR to extract recognized human gene symbols from the images. Altogether, we identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts.

This supplementary file contains the tidy results from optical character recognition (OCR) on 65k pathway figures published between 1995 and 2019. Columns include:

1. figid - Unique figure identifier: concatenation of PMCID and figure filename
2. pmcid - PubMed Central Identifier
3. word - Character string extracted by OCR and eventually matched to human HGNC lexicon
4. symbol - Transformed word that matched lexicon
5. source - Source of lexicon that matched symbol
6. hgnc_symbol - Official human gene symbol
7. entrez - Official NCBI Gene identifier


The WikiPathways Project: At the Intersection of Big Data and Researcher Knowledge

National Institute of General Medical Sciences

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  • GM - National Institute of General Medical Sciences (NIGMS)

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I confirm there is no human identifiable information in this dataset.