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Dataset Open Access

COCONUT: the COlleCtion of Open NatUral producTs.

Maria Sorokina; Christoph Steinbeck

COCONUT is a COlleCtion of Open NatUral producTs.

To assemble COCONUT, data from 50 open access collections and databases of natural products was retrieved and curated.

This archive contains two files:

  • The MongoDB dump, the most complete version of the dataset, with extensive molecular annotations
  • The COCONUT4MetFrag file, used for MetFrag

To restore the dataset in MongoDB:

unzip COCONUTv1.zip
cd COCONUTv1/COCONUT/
mongorestore --db=COCONUT --noIndexRestore .

It is generally useful to avoid restoring indexes, as they can interfere with the local installation. Here are the commands to rebuild indexes:

mongo
use COCONUT

db.sourceNaturalProduct.createIndex( {source:1})
db.sourceNaturalProduct.createIndex( {simpleInchi:1})
db.sourceNaturalProduct.createIndex( {simpleInchiKey:1})
db.uniqueNaturalProduct.createIndex( {inchi:1})
db.uniqueNaturalProduct.createIndex( {inchikey:1})
db.uniqueNaturalProduct.createIndex( {smiles:1})
db.uniqueNaturalProduct.createIndex( {clean_smiles:1})
db.uniqueNaturalProduct.createIndex( {molecular_formula:1})
db.uniqueNaturalProduct.createIndex( {name:1})
db.fragment.createIndex({signature:1})
db.fragment.createIndex({signature:1, withsugar:-1})


This version of COCONUT is beta and will be curated further, but can already be used as it is.

Files (1.4 GB)
Name Size
COCONUT4MetFrag.csv
md5:d7736795d57e0404c20c9a3ca2b400e8
120.2 MB Download
COCONUTv1.zip
md5:5490171dfddf98f7fefb1d8c49a66ce2
1.2 GB Download
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