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Metadata in JSON format

Warning

For advanced use and developers only

Metadata extraction in JSON format

All metadata extracted from the XML files can be saved in a JSON format. The format is easily interchangeable with python dictionaries can also be easily 'piped' to other bioinformatic pipelines regardless of programming language used.

Adding experimental metadata via JSON format

Additional metadata not found in the XML files can be added in a JSON format e.g. organism studied, chromatography used, contact details etc.

This allows existing bioinformatic/computational workflows, which may already have collected some additional metadata, to automatically populate additional entries in the ISA-Tab files.

Example format:

{
     "characteristics": {
             "organism": {
                     "name": "",
                     "accession": "",
                     "ref": ""
             },
             "organism_variant": {
                     "name": "",
                     "accession": "",
                     "ref": ""
             },
             "organism_part": {
                     "name": "",
                     "accession": "",
                     "ref": ""
             }
     } ....


}

See the following link for full example of JSON used for mzml2isa.

Example templates for the metadata JSON can be extracted from either mzml2isa-qt, imzml2isa-qt or nmrml2isa-qt.

Run either of the following:

python3 -m mzml2isa_qt.usermeta
python3 -m imzml2isa_qt.usermeta
python3 -m nmrml2isa_qt.usermeta

Add any metadata through the GUI and then click apply. The terminal will then spit out the JSON text.

Adding additional metadata via JSON for CLI:

For the CLI simply use the -m option and direct to the json file.

mzml2isa -i /path/to/mzml/folder -o /path/to/out_folder -s STUDYID -m metadata.json
nmrml2isa -i /path/to/mzml/folder -o /path/to/out_folder -s STUDYID -m metadata.json

Adding additional metadata via JSON for API:

For the API the usermeta paramater can be used to pass the JSON metadata as a python dictionary to the ISA_Tab class. See the following API documentation for class mzml2isa.isa.ISA_Tab and class nmrml2isa.isa.ISA_Tab

Adding additional metadata via JSON for Galaxy:

This metadata can be added manually via the dropdown options or via a prepared JSON file using the Additional user metadata in json option.

Adding additional metadata via JSON for GUI:

Not possible. This metadata is added directly via the GUI using the usermeta dialog.