https://wiki.openchemistry.org/index.php?title=MongoChem_PubChem_Import&feed=atom&action=historyMongoChem PubChem Import - Revision history2024-03-28T10:49:59ZRevision history for this page on the wikiMediaWiki 1.39.3https://wiki.openchemistry.org/index.php?title=MongoChem_PubChem_Import&diff=297&oldid=prevKyle.lutz: Created page with "== Importing Data == The PubChem data in the SDF format can be imported with MongoChem's SDF importer. Under the File->Import menu select SDF to bring up the import dialog. Th..."2013-04-10T17:13:34Z<p>Created page with "== Importing Data == The PubChem data in the SDF format can be imported with MongoChem's SDF importer. Under the File->Import menu select SDF to bring up the import dialog. Th..."</p>
<p><b>New page</b></p><div>== Importing Data ==<br />
The PubChem data in the SDF format can be imported with MongoChem's SDF importer. Under the File->Import menu select SDF to bring up the import dialog. Then navigate to the SDF file and click "Import". This will automatically load the data into the Mongo database.<br />
<br />
The following will be extracted from the SDF data fields and inserted into the database:<br />
<br />
* PUBCHEM_IUPAC_TRADITIONAL_NAME -> name<br />
* PUBCHEM_IUPAC_INCHI -> inchi<br />
* PUBCHEM_IUPAC_INCHIKEY -> inchikey<br />
* PUBCHEM_MOLECULAR_WEIGHT -> mass, descriptors.mass<br />
* PUBCHEM_CACTVS_TPSA -> descriptors.tpsa<br />
* PUBCHEM_XLOGP3_AA -> descriptors.xlogp3<br />
<br />
The following fields will be calculated from the molecular structure:<br />
<br />
* formula<br />
* atomCount<br />
* heavyAtomCount<br />
* vabc<br />
* mass (if PUBCHEM_MOLECULAR_WEIGHT is not present)<br />
<br />
== Sample Data ==<br />
A sample dataset containing the first 2,500 molecules in PubChem is available here: [http://github.com/OpenChemistry/avogadrodata/raw/master/data/pubchem2500.sdf.gz pubchem2500.sdf.gz].</div>Kyle.lutz