Pathway information extracted from 25 years of pathway figures

Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted...

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Detalles Bibliográficos
Autores principales: Hanspers, Kristina, Riutta, Anders, Summer-Kutmon, Martina, Pico, Alexander R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Database
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649569/
https://www.ncbi.nlm.nih.gov/pubmed/33168034
http://dx.doi.org/10.1186/s13059-020-02181-2
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author Hanspers, Kristina
Riutta, Anders
Summer-Kutmon, Martina
Pico, Alexander R.
author_facet Hanspers, Kristina
Riutta, Anders
Summer-Kutmon, Martina
Pico, Alexander R.
author_sort Hanspers, Kristina
collection PubMed
description Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted 1,112,551 instances of human genes, comprising 13,464 unique NCBI genes, participating in a wide variety of biological processes. This collection represents an order of magnitude more genes than found in the text of the same papers, and thousands of genes missing from other pathway databases, thus presenting new opportunities for discovery and research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (doi:10.1186/s13059-020-02181-2).
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spelling pubmed-76495692020-11-09 Pathway information extracted from 25 years of pathway figures Hanspers, Kristina Riutta, Anders Summer-Kutmon, Martina Pico, Alexander R. Genome Biol Database Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted 1,112,551 instances of human genes, comprising 13,464 unique NCBI genes, participating in a wide variety of biological processes. This collection represents an order of magnitude more genes than found in the text of the same papers, and thousands of genes missing from other pathway databases, thus presenting new opportunities for discovery and research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (doi:10.1186/s13059-020-02181-2). BioMed Central 2020-11-09 /pmc/articles/PMC7649569/ /pubmed/33168034 http://dx.doi.org/10.1186/s13059-020-02181-2 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Database
Hanspers, Kristina
Riutta, Anders
Summer-Kutmon, Martina
Pico, Alexander R.
Pathway information extracted from 25 years of pathway figures
title Pathway information extracted from 25 years of pathway figures
title_full Pathway information extracted from 25 years of pathway figures
title_fullStr Pathway information extracted from 25 years of pathway figures
title_full_unstemmed Pathway information extracted from 25 years of pathway figures
title_short Pathway information extracted from 25 years of pathway figures
title_sort pathway information extracted from 25 years of pathway figures
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649569/
https://www.ncbi.nlm.nih.gov/pubmed/33168034
http://dx.doi.org/10.1186/s13059-020-02181-2
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