PMC clinical trial disentangled tables data set

Published: 19 May 2017 | Version 1 | DOI: 10.17632/wk53twxddf.1

Description of this data

The database is created by processing 6558 clinical trial articles from PubMed Central public sample 2014. The articles are obtained by matching PMC and Medline documents. The documents that were selected contained in publication type word "Clinical" in Medline.

The documents were processed using TableDisentangler tool, that is able to create the majority of the database. Then documents were annotated using UMLS/MetaMap and script that is a part of TableDisentangler tool for communication with MetaMap. Three case studies were performed for information extraction from these data:

  • Extraction of patients' age
  • Extraction of gender distribution
  • Extraction of FEV1 measures (this has been performed for COPD studies only)

Information extraction case studies were performed using TabInOut tool for generating table information extraction rules.

Database schema can be seen on the following link:

Files included in the dataset:

  • - This file contains raw xml clinical documents from PMC
  • - Contains database with processed data using TableDisentangler and TabInOut

Experiment data files

Related links

This data is associated with the following publication:

Disentangling the Structure of Tables in Scientific Literature

Published in: Natural Language Processing and Information Systems

Latest version

  • Version 1


    Published: 2017-05-19

    DOI: 10.17632/wk53twxddf.1

    Cite this dataset

    Milosevic, Nikola (2017), “PMC clinical trial disentangled tables data set”, Mendeley Data, v1


Views: 163
Downloads: 25


The University of Manchester


Data Mining, Clinical Trials, Descriptive Tables, Data Processing, Text Mining


CC BY 4.0 Learn more

The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.

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You can share, copy and modify this dataset so long as you give appropriate credit, provide a link to the CC BY license, and indicate if changes were made, but you may not do so in a way that suggests the rights holder has endorsed you or your use of the dataset. Note that further permission may be required for any content within the dataset that is identified as belonging to a third party.