The goal of this repository is to find medical text concepts from a document and map them to a specific level of hierachy in the snomed ontology.
Please follow intallation instructions in the following link:
scispacy = 0.5.1
medspacy = 0.2.0.0
pymedtermino2 => Owlready2 = 0.37
Download UMLS and Snomed CT Files from the UMLS website.
You need to apply for permission to download the files. Follows this https://owlready2.readthedocs.io/en/latest/pymedtermino2.html.
Please run concept_distribution.ipynb to find relations between parent concepts and child concepts.
Note that sometimes the processed pym.sqlite file will be locked. Current work around is to copy the file and replace the original file and run the notebook again as shown in remove_sql_lock.sh.
To find concept id from the interactive interface. See https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes. Note that this interface uses old version of the snomed ontology.
With the following text sentence: Alterations in the hypocretin receptor 2 and preprohypocretin genes produce narcolepsy in some animals. , this repo can find medical concepts from the sentence and map them to the snomed ontology.
