QTL TableMiner++ (QTM)

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

• Oracle/OpenJDK8
• Apache Maven 3.x
• SQLite 3.x
• Apache Solr 6.x with cores based on domain-specific vocabularies and ontologies (Solr cores):
  • Gene Ontology (GO)
  • Plant Trait Ontology (TO)
  • Phenotypic quality ontology (PATO)
  • Solanaceae Phenotype Ontology (SPTO)
  • STATistics Ontology (STATO)
  • Chemical Entities of Biological Interest (ChEBI)
• access to full-text articles (in XML) from Europe PMC

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