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/activate

Install

pip install abstractor

With git

First, clone the git repo

# clone
git clone https://github.com/askomics/abstractor.git
# cd
cd abstractor

Then, create and activate a python virtual environment

# Create a python virtual environment
python3 -m venv venv
# Activate python virtual env
source venv/bin/activate

Install

python setup.py install

Use

# Get help
abstractor -h

Usage

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.ttl

Example with Uniprot, using OWL:

abstractor -s https://sparql.nextprot.org -o nextprot_abstraction.ttl -m owl

With Askomics SPARQL endpoint

abstractor --askomics-internal-namespace http://askomics.org/internal/ -s https://bbip.askomics.org/virtuoso/sparql -o askomics_bbip.ttl -m askomics

With 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 xml

Obtained TTL file can be used with AskOmics