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Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature

View ORCID ProfileLiviu Pirvan, View ORCID ProfileShamith A. Samarajiwa
doi: https://doi.org/10.1101/2020.04.02.022517
Liviu Pirvan
1MRC Cancer Unit, Cambridge Biomedical Campus, Box 197, University of Cambridge, Cambridge, CB2 0ZX, UK
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  • ORCID record for Liviu Pirvan
Shamith A. Samarajiwa
1MRC Cancer Unit, Cambridge Biomedical Campus, Box 197, University of Cambridge, Cambridge, CB2 0ZX, UK
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  • For correspondence: ss861@mrc-cu.cam.ac.uk
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Abstract

Motivation Pangaea is a scalable and extensible command line interface (CLI) software that integrates gene-relationship detection features to extract context-dependent structured gene-gene and gene-term relationships from the biomedical literature. It provides computational methods to identify biological relationships between a collection of genes and can be used to search and extract different types of contextual relationships amongst genes.

Results We implemented a CLI-based software for downloading PubMed articles and extracting gene relationships from abstracts using natural language processing methods. In terms of scalability, the software was designed to support the retrieval and processing of millions of articles whilst minimising memory requirements and optimising for parallel processing on multiple CPU cores. To allow extensibility, the tool permits the use of contextual custom-made models for the text processing parts, and the output is serialised as JSON objects to allow flexible post-processing workflows.

Availability The software is available online at: https://github.com/ss-lab-cancerunit/pangaea

Footnotes

  • https://github.com/ss-lab-cancerunit/pangaea

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 03, 2020.
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Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature
Liviu Pirvan, Shamith A. Samarajiwa
bioRxiv 2020.04.02.022517; doi: https://doi.org/10.1101/2020.04.02.022517
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Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature
Liviu Pirvan, Shamith A. Samarajiwa
bioRxiv 2020.04.02.022517; doi: https://doi.org/10.1101/2020.04.02.022517

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