Workflows

Download Entries from PubChem (1)

• Download

Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results. Adding support for downloading this XML file and writing it to filesystem is planned.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

download (2)

• Download

Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

PubChem substructure search (2)

• Download

Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

smiles-identity-idlist (2)

• Download

Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

smiles-identity-idlist (1)

• Download

Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

file-similarity-entrez-url (2)

• Download

Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li