neoplasmer (ALPHA RELEASE)
Matches names of cancers and cancer-related conditions to ontology classes
Usage (via Docker)
Currently the recommended way to do this is on the command line via the neoplasmer.sh bash script:
./neoplasmer.sh tests/data/vicc_input.txt
You do not need to install anything other than Docker. The shell script is standalone.
The input file is a newline delimited list of terms. See tests/data/ for examples.
The first execution will take a minute or two; some warning messages
may be printed, these can be ignored. Two directories will be created: RDF-Cache and .cache
Subsequent executions will be much faster
You can see example results in scratch/vicc-results.tsv
Python client
First, start a service:
./neoplasmer.sh --port 9055
Then install python libs:
pip3 install -r requirements.txt
Run the test client:
python3 bin/neoplasmer-client.py 'lung cancer' 'brain glioma'