Published November 19, 2019
| Version 2
Dataset
Open
COCONUT: the COlleCtion of Open NatUral producTs.
Description
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 COCONUTv2.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.