Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary
Keywords
Repository
QTLTableMiner++ tool for mining tables in scientific articles
Basic Info
- Host: GitHub
- Owner: PBR
- License: apache-2.0
- Language: Java
- Default Branch: master
- Homepage: https://www.research-software.nl/software/qtl-tableminer
- Size: 369 MB
Statistics
- Stars: 4
- Watchers: 3
- Forks: 6
- Open Issues: 5
- Releases: 2
Topics
Metadata Files
README.md
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.txtandconfig.propertiesfiles - output:
qtl.csvandqtl.dbfiles
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.
```bash
cp data/*.xml .
./QTM articles.txt ```
Owner
- Name: Wageningen UR Plant Breeding
- Login: PBR
- Kind: organization
- Location: Wageningen
- Website: http://www.plantbreeding.wur.nl
- Repositories: 30
- Profile: https://github.com/PBR
Wageningen UR Plant Breeding
GitHub Events
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Dependencies
- com.google.code.gson:gson 2.6.2
- com.googlecode.json-simple:json-simple 1.1.1
- commons-lang:commons-lang 2.6
- net.sf.jwordnet:jwnl 1.4_rc3
- net.sourceforge.argparse4j:argparse4j 0.8.1
- net.sourceforge.jexcelapi:jxl 2.6.12
- org.apache.directory.studio:org.apache.commons.io 2.4
- org.apache.httpcomponents:httpclient 4.5.9
- org.apache.jena:jena-arq 2.9.2
- org.apache.jena:jena-core 3.1.0
- org.apache.solr:solr-solrj 6.2.1
- org.xerial:sqlite-jdbc 3.8.11.2