Hi all, I guess there are probably several ways of doing this. I'm looking to get access to every Pubchem CID. All compounds are published for download, but the files are quite large in size and there are many of them; also, I don't need a good proportion of the data in those files.
Any idea how to get hold of every single CID in PubChem as a list?
Once I have a list of all valid CIDs, I can use pubchempy (python Pubchem API) to retrieve each SMILE and then use RDKit to generate a Fingerprint of my choosing.
I will then generate a molecular structure fingerprint for N case compounds (around 200 of them; I have the CIDs for these case compounds), then perform several similarity matches between each of the N case compounds and each fingerprint from the CIDs I managed to gain access to.
Why don't you ask the people at PubChem directly?
General Help Desk:
Programmatic Access Questions:
Submission Questions:
I guess "Programmatic Access Questions" would be the ones to ask
Annemarie Honegger - in case someone knows, it's nice to have that information in the public domain/searchable.
I have no control over that - There is a option of bulk download over ftp
see: https://pubchemdocs.ncbi.nlm.nih.gov/downloads
Bulk Download
PubChem data are available for bulk download on the PubChem FTP site (ftp://ftp.ncbi.nlm.nih.gov/pubchem).
In addition, one may download a subset of PubChem records using the following services:
- PubChem Structure Download service (https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi) This service allows one to download a list of compound or substance records in PubChem. A list of CIDs or SIDs for records to download may be provided directly into the web page form or uploaded from a local file (one SID/CID per line with no heading). Alternatively, they may be provided by using Entrez history, which stores a list of CIDs or SIDs returned from a previous Entrez search. The records can be exported in several formats, including SDF, PNG, SMILES, InChI, XML, and either text or binary ASN.1. The files may be optionally compressed in standard gzip (.gz) or bzip2 (.bz2) formats. Downloads through the structure download tool are limited to a maximum of 500,000 records per request, with an exception of image downloads, which are limited to 50,000 per request.
- PubChem Assay Download service (https://pubchem.ncbi.nlm.nih.gov/assay/assaydownload.cgi) This tool is used to download bioassay description and test results for a list of assay records. It is also possible to download results for a specific subset of substances tested in the input assays. The input assay list and optional substance list may be provided into the web page form or uploaded from a local file. The supported output formats are ASN.1, XML, JSON, and CSV. This service returns requested assay records in separate files, compressed into a single "zip" file. Up to 1,000 bioassay records can be downloaded at a time.
Programmatic Download
PubChem data may be downloaded programmatically using various programmatic access routes including E-Utilities, Power User Gateway (PUG), PUG-SOAP, PUG-REST, PUG-View, and PubChemRDF REST interface. For more details, refer to PubChem programmatic access overview.
but I understood that you are asking for something that goes beyond to what is documented on the site.
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