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QTL TableMiner++ (QTM)

Build Status DOI Published in BMC Bioinformatics

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 QTLs in a relational database (SQLite, see the ER diagram) and a text file (CSV).

Requirements

Installation

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

Usage

./QTM -h
usage: QTM [-h] [-v] [-o OUTPUT] [-c CONFIG] [-V VERBOSE] FILE

Software to extract QTL data from full-text articles.

positional arguments:
  FILE                   input list of articles (PMCIDs, one per line)

named arguments:
  -h, --help             show this help message and exit
  -v, --version          show version and exit
  -o OUTPUT, --output OUTPUT
                         filename prefix for output in SQLite (.db) and text (.csv) files (default: qtl)
  -c CONFIG, --config CONFIG
                         config file (default: config.properties)
  -V VERBOSE, --verbose VERBOSE
                         verbosity console output: 0-7 for OFF, FATAL,  ERROR,  WARN,  INFO,  DEBUG, TRACE or ALL (default: 4 [INFO])

Example data

  • input: articles.txt and config.properties files
  • output: qtl.csv and qtl.db files

Note: If you don't have access to Internet or Europe PMC, you can still run QTM on XML files stored in the data directory.

# cp data/*.xml .
./QTM articles.txt