QTLTableMiner++ tool for mining tables in scientific articles
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QTM
README.md
articles.txt
db_schema.sql
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README.md

QTL TableMiner++ (QTM)

Build Status DOI

Description

A significant amount of experimental information about Quantitative Trait Locus (QTL) studies are described in (heterogenous) tables of scientific articles. Briefly, a QTL is a genomic region that correlates with a trait of interest (phenotype). QTM is a command-line tool to retrieve and semantically annotate results obtained from QTL mapping experiments. It takes full-text articles from the Europe PMC repository as input and outputs the extracted QTLs into a relational database (SQLite) and text file (CSV).

Requirements

Installation

git clone https://github.com/PBR/QTM.git
cd QTM
mvn install
solr/install_solr.sh

Example use

  • input: articles.txt with PMCIDs (one per line)
  • output: qtl.csv and qtl.db (see the database model or Entity-Relationship diagram here)

./QTM articles.txt

./QTM -h

...
USAGE
=====
  QTM [-v|-h]
  QTM [-o FILE_PREFIX] FILE

ARGUMENTS
=========
  FILE				List of full-text articles from Europe PMC.
				Enter one PMCID per line.

OPTIONS
=======
  -o, --output FILE_PREFIX	Output files in SQLite/CSV formats.
				(default: qtl.{db,csv})
  -v, --version			Print software version.
  -h, --help			Print this help message.

Note: The example I/O files are provided in the data directory. In case you don't have Internet access or the Europe PMC API does not work, please copy the articles (.xml) from this directory to the root of this repository.