COCONUT: the COlleCtion of Open NatUral producTs.

<p>COCONUT is a&nbsp;COlleCtion of Open NatUral producTs.</p> <p>&nbsp;</p> <p>The database is now available at&nbsp;<a href="https://coconut.naturalproducts.net/">coconut.naturalproducts.net</a>, where the latest updates will appear before being available here.</p> <p>To assemble COCONUT, data from 55&nbsp;open access collections and databases of natural products was retrieved and curated.</p> <p>This archive contains two files:</p> <ul> <li>The MongoDB dump, the most complete version of the dataset, with extensive molecular annotations</li> <li>The COCONUT4MetFrag file, used for <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a>. The last version of COCONUT4MetFrag is in the file &quot;COCONUT4MetFrag_april.csv&quot;</li> <li>The COCONUT.sdf file containing all unique NP molecules with selected metadata</li> </ul> <p>To restore the dataset in MongoDB:</p> <pre><code class="language-bash">unzip COCONUT_2021_03.zip cd COCONUT_2021_03/COCONUT_2021_03/ mongorestore --db=COCONUT --noIndexRestore . </code></pre> <p>It is generally useful to avoid restoring indexes, as they can interfere with the local installation. Here are the commands to rebuild indexes:</p> <pre><code class="language-json">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}) </code></pre> <p><br> <strong>This version of COCONUT is beta and will be curated further, but can already be used as it is.</strong></p>