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65k pathway figures published between 1995 and 2019

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posted on 05.06.2020 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 identification of 65k pathway figures published between 1995 and 2019. Columns include:

1. figid - Unique figure identifier: concatentation of PMCID and figure filename (see 11 and 12)
2. number - Figure number in parent paper
3. reftext - Citation for parent paper
4. year - Publication year of parent paper
5. pathway_score - Pathway likelihood score from machine learning
6. pmc_ranked_result_index - Ranking from original PubMed Central query result
7. figtitle - Figure title in parent paper
8. papertitle - Title of parent paper
9. caption - Figure caption in parent paper
10. figlink - URL to figure
11. pmcid - PubMed Central Identifier
12. filename - Figure filename
13. source_f - Local file path (ignore)
14. type.man - Manual classification of pathway (p), composite (c) or other (o)
15. automl_index - Stored index from sorting by pathway_score (see 5)

Funding

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

National Institute of General Medical Sciences

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History

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

Is this associated with a publication?

Yes

DOI(s) of associated publication(s):

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

Yes

Licence

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Licence

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