ExtractThesaurusANSM

Scripts to extract and structure the content of the "thesaurus of drug interactions" published, in a PDF format, by the French Agency for the Safety of Health Products (ANSM) at this address: https://ansm.sante.fr/documents/reference/thesaurus-des-interactions-medicamenteuses-1

Data

The ANSM interaction working group publishes guidelines once or twice a year. All the files are in the thesauri folder.

Extraction details

You need to download tika-app-1.11.jar:

wget https://archive.apache.org/dist/tika/tika-app-1.11.jar

Automatic extraction

bash extract.sh --help
bash extract.sh -p -t

The program creates a TXT folder and a JSON folder in each thesaurus folder.

Step by step

First, PDF files are transformed into txt files with Apache Tika.
For example:

java -jar tika-app-1.11.jar -h ./thesauri/2019_09/PDF/index_des_substances_09_2019.pdf > ./index_des_substances_09_2019.txt
java -jar tika-app-1.11.jar -t ./thesauri/2019_09/PDF/Thesaurus_09_2019.pdf > 
./Thesaurus_09_2019.txt

The message "ERROR FlateFilter: stop reading corrupt stream due to a DataFormatException" can be ignored, the content is correctly extracted.

Next txt files are transformed to JSON files. For example:

python extractSubstanceDrugClasses.py -f ./index_substances092019.txt
python extractInteraction.py -f ./thesauri/2019_09/TXT/Thesaurus_09_2019.txt

The error message "SeverityLevelerror while extraction PDDI between X and Y" means that the programs has failed to structure the mechanism of action and the severity level of X and Y. To fix this issue, we need to structure it manually and add it to "./python/Interactions/pddis_manually_extracted.json"

Tests

Run all the tests with this command:

python -m unittest discover ./

See Also

Detect Potential Drug Drug Interactions: https://github.com/scossin/pddiansm

Citation

@mastersthesis{cossin:dumas-01442668,
  TITLE = {{Interactions m{\'e}dicamenteuses : donn{\'e}es li{\'e}es et applications}},
  AUTHOR = {Cossin, S{\'e}bastien},
  URL = {https://dumas.ccsd.cnrs.fr/dumas-01442668},
  PAGES = {80},
  YEAR = {2016},
  MONTH = Nov,
  KEYWORDS = {Interaction m{\'e}dicamenteuse ;  Web S{\'e}mantique ;  Interop{\'e}rabilit{\'e} ;  Pharmacovigilance },
  PDF = {https://dumas.ccsd.cnrs.fr/dumas-01442668/file/Med_spe_2016_Cossin.pdf},
  HAL_ID = {dumas-01442668},
  HAL_VERSION = {v1},
}

Cossin S. Interactions médicamenteuses : données liées et applications. 30 nov 2016.