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 To restore the dataset in MongoDB: <pre><code class="language-bash">unzip COCONUTv2.zip cd COCONUTv1/COCONUT/ mongorestore --db=COCONUT --noIndexRestore . </code></pre> It is generally useful to avoid restoring indexes, as they can interfere with the local installation. Here are the commands to rebuild indexes: <pre><code class="language-json">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}) </code></pre> <br> <strong>This version of COCONUT is beta and will be curated further, but can already be used as it is.</strong>