Supplementary Materials for Article: PECO ontology for food safety domain applied in systems automating systematic literature reviews

Dataset (dataset.zip) contains the following folders:

input data and results - it consists of 30 folders that correspond to 30 SLRs questions. Each subfolder has: 1) file 'question.txt' containing the question; 2) file 'results.json' which lists all annotations obtained by the dictionary annotator; 3) files - 'chebi_PECOpaths.csv', 'foodon_PECOpaths.csv', 'mesh_PECOpaths.csv', 'nci_PECOpaths.csv', 'refsa_PECOpaths.csv', 'snomed_PECOpaths.csv' - they enumerate all full and shortened paths generated by the Python scripts.

python_scripts - it contains 6 Python scripts dedicated to 6 ontologies whose concepts are inclcluded in PECO ontology.

tables - it contains data necessary to run the Python scripts dedicated to 5 ontologies: ChEBI, FoodOn, MeSH, NCI Thesaurus and DFC-EFSA.

Each python script (in folder python_scripts) has constants at the beginning defining the paths to the individual input files. Relative paths have been set, so there is no need to modify them. It is possible to run each script without having to change the folder structure. It is also necessary to install the required packages to run it