git clone git@github.com:omixlab/Mabel.git
cd Mabel
To run searches, make sure these environment variables are set (see example_env)
CELERY_BROKER_URL=XXXXXXXXXXXXXXXXX
CELERY_RESULT_BACKEND=XXXXXXXXXXXXX
SQLALCHEMY_DATABASE_URI=XXXXXXXXXXX
FLASK_SECRET_KEY=XXXXXXXXXXXXXXXXXX
make build
make run
Create your account, then log in to the application. In your profile, set the Elsevier (Scopus, Elsevier) and PubMed tokens. These can be requested at NCBI NCBI and Elsevier Developer Portal Elsevier Developer Portal. Elsevier requests are limited; if you need more than 10,000 requests, you can email their development team.
After all tokens are set, you can perform requests in the Articles Extractor (Basic or Advanced).
If you enable the optional feature Biological Entities, entities can be extracted using two different methodologies:
- SciSpacy + BioSyn (for normalization)
- PubTator (works only with articles that have PMIDs)
If you want to use other models, you can add a dictionary in TSV format to train the normalizer.