Json’s Metabolite Services (JMS)

A Python library for

• mapping identifiers between genome scale metabolic models and metabolite databases
• reusable data structures for peaks, compounds and indexed data stores
• efficient mass and empirical compound search functions

As the name suggests, JSON or similar Python dictionaries are used widely in this library. The definition of these data structures was a result of patterning our scientific work, and we encourage reuse and community contributions. A few examples:

// A LC-MS peak:
{
    'id_number': 555,
    'mz': 133.0970, 
    'rtime': 654, 
    'height': 14388.0, 
    'left_base': 648, 
    'right_base': 662, 
}

// A compound (i.e. metabolite):
{
    'primary_id': HMDB0000195,
    'primary_db': 'HMDB',
    'name': 'Inosine',
    "neutral_formula": C10H12N4O5,
    "neutral_formula_mass": 268.08077, 
    'SMILES': 'OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(O)N=CN=C12', 
    'inchikey': 'UGQMRVRMYYASKQ-KQYNXXCUSA-N',
    'LogP': -2.10,
    'other_ids': {'PubChem': '6021',
                  'KEGG': 'C00294',
                  'ChEBI': '17596',
                  'MetaNetX': 'MNXM1103335',
                  },
}

// An empirical compound:
{
    "neutral_formula_mass": 268.08077, 
    "neutral_formula": C10H12N4O5,
    "alternative_formulas": [],
    "interim_id": C10H12N4O5_268.08077,
    "identity": [
            {'compounds': ['HMDB0000195'], 'names': ['Inosine'], 
                    'score': 0.6, 'probability': null},
            {'compounds': ['HMDB0000195', 'HMDB0000481'], 'names': ['Inosine', 'Allopurinol riboside'], 
                    'score': 0.1, 'probability': null},
            {'compounds': ['HMDB0000481'], 'names': ['Allopurinol riboside'], 
                    'score': 0.1, 'probability': null},
            {'compounds': ['HMDB0003040''], 'names': ['Arabinosylhypoxanthine'], 
                    'score': 0.05, 'probability': null},
            ],
    "MS1_pseudo_Spectra": [
            {'feature_id': 'FT1705', 'mz': 269.0878, 'rtime': 99.90, 
                    'isotope': 'M0', 'modification': '+H', 'charged_formula': '', 'ion_relation': 'M+H[1+]'},
            {'feature_id': 'FT1876', 'mz': 291.0697, 'rtime': 99.53, 
                    'isotope': 'M0', 'modification': '+Na', 'charged_formula': '', 'ion_relation': 'M+Na[1+]'},
            {'feature_id': 'FT1721', 'mz': 270.0912, 'rtime': 99.91, 
                    'isotope': '13C', 'modification': '+H', 'charged_formula': '', 'ion_relation': 'M(C13)+H[1+]'},
            {'feature_id': 'FT1993', 'mz': 307.0436, 'rtime': 99.79, 
                    'isotope': 'M0', 'modification': '+K', 'charged_formula': '', 'ion_relation': 'M+K[1+]'},
            ],
    "MS2_Spectra": [
            'AZ0000711', 'AZ0002101'
            ],
    "Database_referred": ["Azimuth", "HMDB", "MONA"],
}

These examples show a core set of attributes. Users can extend to include other attributes that meet their own project needs. With consistent core concepts, some simple mapping dictionaries will produce interoperability between projects.

In empirical compound, MS1_pseudo_Spectra are for adduction ions (A-ions); the biological_ion is usually different (B-ions).

Install

pip install jms-metabolite-services

How to use

See notebooks under docs/ for demonstration.

Run test:

# decompress the HMDB4 data if needed
➜  JMS✗ xz -d jms/data/compounds/list_compounds_HMDB4.json.xz 
# run test from top dir
➜  JMS✗ python3 -m jms.test 

Example code of annotating a feature table against HMDB as in test.py:

import json
from jms.dbStructures import annotate_peaks_against_kcds
from jms.io import read_table_to_peaks

list_compounds = json.load(open('jms/data/compounds/list_compounds_HMDB4.json'))
mydata = read_table_to_peaks('testdata/full_Feature_table.tsv', '\t')

annotate_peaks_against_kcds(mydata, list_compounds, 
                                export_file_name_prefix='jms_annotated_',
                                mode='pos',  mz_tolerance_ppm=5)

Links

Source code: https://github.com/shuzhao-li/JMS

Package Repository: https://pypi.org/project/jms-metabolite-services/

Related projects:

metDataModel: data models for metabolomics

mass2chem: common utilities in interpreting mass spectrometry data, annotation

khipu: a Python library for generalized, low-level annotation of MS metabolomics

Asari: trackable and scalable LC-MS data preprocessing

mummichog: metabolomics pathway/network analysis

Dev notes

The PyPi package excludes subdirectories in /data.

The App Engine web tool will be in a different repository.

Citation

To come.