DOI: 10.5061/dryad.vmcvdncs0
title: CORD-19 Software Mentions

description: In an effort to automate the process of identifying and analyzing the use
 of software in biomedical research, we have developed a SciBERT-based
 machine learning model to extract mentions of software from scientific
 articles. The input to this model is the full text from a scientific
 article and the output is a list of mentioned software within
 it.  We applied this model to the CORD-19 full-text articles and
 stored the output in this dataset, which includes metadata of over 77,000
 COVID-19 and coronavirus-related papers and a list of software tools
 mentioned in each.
description: We have developed a machine learning model to extract mentions of
 software from scientific articles. The SoftCite dataset was used to train and evaluate the model. This model has been applied to the CORD-19 collection of full-text coronavirus-related research papers. This dataset comprises the output of this model and each scientific article's relevant metadata. <br> <br> Data are derived from the CORD-19 dataset provided by AllenAI, release version <strong>2021-02-08</strong> (changelog cord-19_2021-02-08.tar.gz 7.4GB c5446fea 29f69de2) downloaded from AWS on 08-Feb-2021. 
description: <strong>Notes:</strong> 
 Not all papers in the CORD-19 dataset mention software. We only
 include here the subset of articles for which there was full-text and
 which also had at least one detected software mention
 Software names have not been normalized, nor have they been
 resolved to any external dictionary.  e.g. the list of software mentions
 includes “excel”, “microsoft excel”, “ms excel”, and “office excel”.
    Dataset contains DOIs for each mentioning paper
 where available (96% of papers). External identifiers (such as PubMed
 Central IDs, PubMed PMIDs, and arXiv IDs) for the remainder of papers can
 often be imputed from the paper URLs, e.g. the arXiv ID for the paper with
 the URL "https://arxiv.org/pdf/2011.09270v1.pdf" is
 "2011.09270"   In some cases, mentions of
 software are incorrectly separated into multiple tokens, e.g.
 ['scikit', 'learn'] 
 <strong>Schema:</strong> 
 
 <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Column</b> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Type</b> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Description</b> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">paper_id</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">string</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">ID of paper from CORD-19 dataset. 40-character sha1 of the PDF</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">doi</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">string</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Digital Object Identifier of the article, from CORD-19</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">title</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">string</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Title of the article, from CORD-19</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">source_x</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">array</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Provenance of the article from CORD-19 dataset, e.g. arXiv, bioRxiv, Elsevier, Medline, PMC, WHO, Wiley </b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">license</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">string</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">License of the article, from CORD-19</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">publish_time </b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">date (mm/dd/yyyy) </b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Publication date of the article, from CORD-19</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">journal</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">string</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Journal short name, from CORD-19 (e.g. PLoS Compu Biol)</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">url</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">array</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">URL(s) of article, from CORD-19</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">software</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">array</b></pre> <pre dir="ltr"> <b id="docs-internal-guid-798d7ec2-7fff-a995-d0d3-50ff5ede4861">Software mentions extracted from article full-text</b></pre>