Datasets for Potential of Robotic Lab Methods Usage in Biomedical Papers

Published: 28 September 2017| Version 3 | DOI: 10.17632/gy7bfzcgyd.3
Contributors:
Paul Groth,
Jessica Cox

Description

This is a collection of data used for the article "Indicators for the use of Robotic Labs in Basic Biomedical Research". The primary result files are: -metamapMethods.csv -sodaMethods.csv These were generated by running descriptive statistics of annotating the papers listed in articles_piis_dois.csv with the Medical Subject Headings 2015 vocabulary.

Files

Steps to reproduce

See AutomatedMethodIndexingWithMESHLower.ipynb, MethodIndexingWithMESHMetaMap.ipynb, and NERcompViz.ipynb for more details. In general: 1) Retrieve the XML content of the articles listed in articles_piis_dois.csv. This can be done using get_articles_xml.py 2) Annotate the articles using MESH 2015.nt as a dictionary. You can use an off the shelf dictionary based annotator for this task or https://github.com/elsevierlabs-os/soda . Apply this only to the paragraph content. We also used the MetaMap annotator 3) The resulting annotations can be joined with mesh2015-investigativetechniques.csv and cloudlab_mesh_final.csv to perform the various analytics that appear in the associated article.