COCONUT: the COlleCtion of Open NatUral producTs.

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. The last version of COCONUT4MetFrag is in the file "COCONUT4MetFrag_april.csv"

To restore the dataset in MongoDB:

unzip COCONUTapril.zip
cd COCONUTapril /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:"hashed"})
db.sourceNaturalProduct.createIndex( {simpleInchiKey:1})
db.sourceNaturalProduct.createIndex( {originalInchiKey:1})
db.sourceNaturalProduct.createIndex( {originalSmiles:"hashed"})
db.sourceNaturalProduct.createIndex( {absoluteSmiles:"hashed"})
db.sourceNaturalProduct.createIndex( {idInSource:1})

db.uniqueNaturalProduct.createIndex( {inchi:"hashed"})
db.uniqueNaturalProduct.createIndex( {inchikey:1})
db.uniqueNaturalProduct.createIndex( {clean_smiles: "hashed"})
db.uniqueNaturalProduct.createIndex( {molecular_formula:1})
db.uniqueNaturalProduct.createIndex( {name:1})
db.uniqueNaturalProduct.createIndex( {coconut_id:1})
db.uniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"})
db.uniqueNaturalProduct.createIndex( {fragments:"hashed"})
db.fragment.createIndex({signature:1})
db.fragment.createIndex({signature:1, withsugar:-1})
db.sourceNaturalProduct.createIndex( {source:1})
db.sourceNaturalProduct.createIndex( {simpleInchi:"hashed"})
db.sourceNaturalProduct.createIndex( {simpleInchiKey:1})
db.sourceNaturalProduct.createIndex( {originalInchiKey:1})
db.sourceNaturalProduct.createIndex( {originalSmiles:"hashed"})
db.sourceNaturalProduct.createIndex( {absoluteSmiles:"hashed"})
db.sourceNaturalProduct.createIndex( {idInSource:1})
db.uniqueNaturalProduct.createIndex( {inchi:"hashed"})
db.uniqueNaturalProduct.createIndex( {inchikey:1})
db.uniqueNaturalProduct.createIndex( {clean_smiles: "hashed"})
db.uniqueNaturalProduct.createIndex( {molecular_formula:1})
db.uniqueNaturalProduct.createIndex( {name:1})
db.uniqueNaturalProduct.createIndex( {coconut_id:1})
db.uniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"})
db.uniqueNaturalProduct.createIndex( {fragments:"hashed"})
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.