OntoContext ====== To annotate biomedical texts using three ontologies and gene names recovering using the geniatagger:
||Anatomical Ontology (UBERON) for anatomical localisation
This package is coded using python 2.7 It need: || ||the Concept databases can be downloaded from here (https://github.com/walidbedhiafi/OntoContext1/blob/master/OntoContext/Concepts.sqlite)
This package is tested under Linux Python 2.7 and is available from the PyPI. To install via pip :
pip install ontocontext
import OntoContext from OntoContext.annot import annotation from OntoContext.crisscross import crisscross annotation('path_to_texts_folder', 'table_name_to_store_annotations', 'path_to_the_genia_tagger') print crisscross('table_name_to_store_annotations')
OntoContext is distributed under a MIT License.