PubChem BioAssays

PubChem BioAssay contains small-molecule and RNAi screening data along with associated annotation information from contributing organizations.  BioAssay contains a collection of bioactivity and toxicity data that has greatly supported research in fields such as medicinal chemistry, drug discovery, pharmaceutical genomics and informatics research.  As a primary archive, the provenance of all records belongs to the submitter.  

 

Each test result provided points to an entry in the PubChem Substance database using a unique identifier for that molecule's record.  If the tested substance has a known structure, it is displayed.  Each test result must provide an expert opinion on the overall activity of the substance in this experiment, which is typically "active" or "inactive".  This simple designation gives a lot of power to the end-user to filter test results across bioassays and even across organizations to find related molecules with interesting activity.

 

To access a PubChem BioAssay record by its numeric identifier (AID), e.g.https://pubchem.ncbi.nlm.nih.gov/bioassay/1. Or search in PubChem with some query (e.g. assay description, compound name, and protein/gene target) and select the BioAssays tab. Bioactivity data together with chemical structures (in SMILES format) are available for download, e.g.https://pubchem.ncbi.nlm.nih.gov/bioassay/2244#section=Data-Table, which might facilitate the studies of structure-activity analysis.

 

User can also upload a list of AIDs or provide keywords in the PubChem Search to find a list of bioassay hits (if any), where user can take further actions, e.g. downloading data in various formats (CSV, XML, JSON, etc.)

 

For bulk bioassay download, we highly recommend to use the PubChem FTP site (https://ftp.ncbi.nlm.nih.gov/pubchem).

 

Our programmatic services (e.g. PUG-REST) can also be used to access PubChem BioAssay data. Examples:

Description URL
Assay Description https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/450/description/XML
Assay Targets https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/490,1000/targets/ProteinGI,ProteinName,GeneID,GeneSymbol/XML
Assay Summary https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/summary/XML (by AID, assay summary)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/concise/CSV (by AID, concise bioactivity data)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sid/104234342/assaysummary/XML (by SIDs output in XML format)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/1000,1001/assaysummary/CSV (by CIDs, output in CSV format)
Assay Data Table https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/CSV (full data table)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/CSV?sid=26736081,26736082,26736083 (data table filtered by given SIDs)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/CSV?cid=16750016,16749998 (data table filtered by given CIDs)
Assay Doese-Response https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/504526/doseresponse/XML (all data)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/504526/doseresponse/CSV?sid=104169547,109967232 (data for given SIDs)
Assay Tested Substances/Compounds https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/sids/XML (all substances)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/sids/XML?sids_type=active (only active substances)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/sids/XML?sids_type=inactive (only inactive substances)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/504526/sids/JSON?sids_type=doseresponse (only substances with dose-response data)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/cids/XML (compounds for all substances)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1000/cids/XML?cids_type=active (compounds for active substances)
Search https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/target/accession/P00533/aids/JSON (by protein target accession)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/target/genesymbol/USP2/aids/TXT (by gene target symbol)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/activity/EC50/aids/TXT (by activity type EC50)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/type/doseresponse/aids/JSON (all assays with dose-response data)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/sourceall/NCATS/aids/XML (all assays for given depositor/source)

 

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