In case of an update to the GFOP ontology, replace the data/GFOP.owl file (download from webprotege as RDF/XML) and run the gfop_to_json.py script. This will create a json tree of the ontology.
Download MASST results as .tsv file for all data file matches. Run the microbe_masst_results.py script to extract a file with all the matches to specific IDs in the metadata table. The build_tree.py script is then adding these results onto the tree ontology.
Download the classyfire ontology in json format. Run the classyfire_to_json_ontology.py script to generate the correct format for the tree.
Run the build_tree.py script to create a single html file that contains the javascript tree, data, and html page. This will:
- Input: Ontology (json), extra data (tsv), html page with dependencies
- Output: Merged tree data (json), self-contained html page (single file)
- Merges extra data (e.g., MASST results) from a tsv-file (tab-separated) into an ontology tree (optional)
- Uses base html file to internalize the tree data and all dependencies
- Find the resulting tree data file and html file in the dist folder. Default: dist/oneindex.html