MetaNetX index/query scripts

• index.py index MetaNetX compounds, compartments, and reactions data including the xref data, tested with MetaNetX Aug 2019 release, version 3.2

• query.py query MetaNetX compounds, compartments, and reactions

• ../../tests/test_metanetx_queries.py

MetaNetX downloads

http://www.metanetx.org/mnxdoc/mnxref.html

# Download MetaNetX csv files
mkdir -p data/metanetx
wget -nc -P data/metanetx -r ftp://ftp.vital-it.ch/databases/metanetx/MNXref/latest/\
  --no-directories

Example command lines

Index with Elasticsearch or MongoDB:

# Index with Elasticsearch, requires about 10-15m
 ./nosqlbiosets/metanetx/index.py --metanetxdatafolder ./data/metanetx\
        --db Elasticsearch;
# Index with MongoDB, requires ~10m
 ./nosqlbiosets/metanetx/index.py --metanetxdatafolder ./data/metanetx\
        --index biosets --db MongoDB;

Elasticsearch query to get distribution of reactions among source/reference libraries:

curl -XGET "http://localhost:9200/metanetx_reaction/_search?pretty=true"\
 -H 'Content-Type: application/json' -d'
{
  "size": 0,
  "aggs": {
    "libs": {
      "terms": {
        "field": "xrefs.lib.keyword",
        "size": 10
      }
    }
  }
}'

Notes

MetaNetX scripts here use the words ‘metabolite’ and ‘compound’ with the same meaning:

A compound in chemistry is a combination of atoms from at least two different elements. Compounds do not contain mixtures of elements. They form through a chemical binding process and are in stable ratios.

Metabolites are the intermediates and products of metabolism.

The term metabolite is usually restricted to small molecules. A small molecule is a low molecular weight (< 900 daltons) organic compound.