GFOPontology

Update ontology

GFOP

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.

microbeMASST

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.

Example: Yersiniabactin

Classyfire

Download the classyfire ontology in json format. Run the classyfire_to_json_ontology.py script to generate the correct format for the tree.

Build ontology 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

Mass Spectrometry Searches using MASST

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236533/ https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp

Pipeline

edit bundle_to_html.py, line 83 to soup.body.append(new_script)

source /usr/local/pythonenvs/gfop_env/bin/activate
pip install pandas==1.5.3

cd src/
python microbe_masst_results.py -h
usage: microbe_masst_results.py [-h] [--metadata_file METADATA_FILE]
                                [--masst_file MASST_FILE] [--out_tsv_file OUT_TSV_FILE]

Merge MASST results with microbeMASST metadata

options:
  -h, --help            show this help message and exit
  --metadata_file METADATA_FILE
                        microbe masst metadata
  --masst_file MASST_FILE
                        a tab separated file with additional data that is added to
                        metadata file
  --out_tsv_file OUT_TSV_FILE
                        output file in .tsv format

python microbe_masst_results.py \
> --masst_file ../examples/yersiniabactin.tsv
     ncbi  matched_size
0     562             9
1   blank            15
2  316435            40
3  749550             1
4  749535             1
5  749527             1
6       2             2

cat dist/microbe_masst_counts.tsv
ncbi    matched_size
562     9
blank   15
316435  40
749550  1
749535  1
749527  1
2       2

python build_tree.py -h
usage: build_tree.py [-h] [--in_html IN_HTML] [--ontology ONTOLOGY] [--in_data IN_DATA]
                     [--out_html OUT_HTML] [--compress COMPRESS] [--out_tree OUT_TREE]
                     [--format FORMAT] [--node_key NODE_KEY] [--data_key DATA_KEY]

Create tree data by merging extra data into an ontology. Then create a distributable html file that
internalizes all scripts, data, etc.

options:
  -h, --help           show this help message and exit
  --in_html IN_HTML    The input html file
  --ontology ONTOLOGY  the json ontology file with children
  --in_data IN_DATA    a tab separated file with additional data that is added to the ontology
  --out_html OUT_HTML  output html file
  --compress COMPRESS  Compress output file (needs minify_html)
  --out_tree OUT_TREE  output file
  --format FORMAT      Format the json output False or True
  --node_key NODE_KEY  the field in the ontology to be compare to the field in the data file
  --data_key DATA_KEY  the field in the data file to be compared to the field in the ontology

This last script should create dist/oneindex.html to view ontology.

Update ontology​

GFOP​

microbeMASST​

Classyfire​

Build ontology tree​

Mass Spectrometry Searches using MASST​

Pipeline​