Abstractor
Abstraction generator: Generate AskOmics abstraction from a distant SPARQL endpoint or a RDF file
Installation
With pip
Create and activate a python virtual environment
# Create a python virtual environment
python3 -m venv venv
# Activate python virtual env
source venv/bin/activateInstall
pip install abstractorWith git
First, clone the git repo
# clone
git clone https://github.com/askomics/abstractor.git
# cd
cd abstractorThen, create and activate a python virtual environment
# Create a python virtual environment
python3 -m venv venv
# Activate python virtual env
source venv/bin/activateInstall
python setup.py installUse
# Get help
abstractor -hUsage
General usage
Use abstractor --help to get all available options.
With a SPARQL endpoint
abstractor -s <endpoint_url> -o <output_file>Example with NeXtProt:
abstractor -s https://sparql.nextprot.org -o nextprot_abstraction.ttlExample with Uniprot, using OWL:
abstractor -s https://sparql.nextprot.org -o nextprot_abstraction.ttl -m owlWith Askomics SPARQL endpoint
abstractor --askomics-internal-namespace http://askomics.org/internal/ -s https://bbip.askomics.org/virtuoso/sparql -o askomics_bbip.ttl -m askomicsWith a RDF file
abstractor -s <path> -t <type> -o <output_file>Example with a file data.rdf. Input and output file in xml format.
abstractor -s ~/me/data.xml -t xml -o data_abstraction.xml -f xmlObtained TTL file can be used with AskOmics
