Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
ChEMBL Data Resource - activity
Provides a tutorial example on what are ChEMBL 'activity' data resources and how to access them with REST API.
"activity" is a primary data resource type provided by ChEMBL API. It represents a single biological test result data of a single chemical compound against a single biological target.
1. Get a list of all activities. Note that there are 17,276,334 "Activity" records as of January 2021.
herong$ curl https://www.ebi.ac.uk/chembl/api/data/activity <response> <activities> <activity> <activity_comment/> <activity_id>31863</activity_id> ... </activity> <activity> ... </activity> ... <activities> <page_meta> <limit>20</limit> <next>/chembl/api/data/activity?limit=20&offset=20</next> <offset/> <previous/> <total_count>17276334</total_count> </page_meta> </response>
2. Get the activity of a given id.
herong$ curl https://www.ebi.ac.uk/chembl/api/data/activity/31863 <activity> <activity_comment/> <activity_id>31863</activity_id> <activity_properties/> <assay_chembl_id>CHEMBL663853</assay_chembl_id> <assay_description>Inhibitory concentration ...</assay_description> <assay_type>B</assay_type> <assay_variant_accession/> <assay_variant_mutation/> <bao_endpoint>BAO_0000190</bao_endpoint> <bao_format>BAO_0000357</bao_format> <bao_label>single protein format</bao_label> <canonical_smiles>c1ccc(-c2nc3c(-c4nc5ccccc5o4)...</canonical_smiles> <data_validity_comment/> <data_validity_description/> <document_chembl_id>CHEMBL1137930</document_chembl_id> <document_journal>Bioorg. Med. Chem. Lett.</document_journal> <document_year>2004</document_year> <ligand_efficiency/> <molecule_chembl_id>CHEMBL113081</molecule_chembl_id> <molecule_pref_name/> <parent_molecule_chembl_id>CHEMBL113081</parent_molecule_chembl_id> <pchembl_value/> <potential_duplicate/> <qudt_units>http://www.openphacts.org/units/Nanomolar</qudt_units> <record_id>206172</record_id> <relation>></relation> <src_id>1</src_id> <standard_flag>True</standard_flag> <standard_relation>></standard_relation> <standard_text_value/> <standard_type>IC50</standard_type> <standard_units>nM</standard_units> <standard_upper_value/> <standard_value>100000.0</standard_value> <target_chembl_id>CHEMBL1806</target_chembl_id> <target_organism>Homo sapiens</target_organism> <target_pref_name>DNA topoisomerase II alpha</target_pref_name> <target_tax_id>9606</target_tax_id> <text_value/> <toid/> <type>IC50</type> <units>uM</units> <uo_units>UO_0000065</uo_units> <upper_value/> <value>100.0</value> </activity>
Foreign keys to other resources:
<molecule_chembl_id>CHEMBL113081</molecule_chembl_id> The molecule stracuture of the compoound <target_chembl_id>CHEMBL1806</target_chembl_id> The biological testing target <assay_chembl_id>CHEMBL663853</assay_chembl_id> The assay describine how the test was done <document_chembl_id>CHEMBL1137930</document_chembl_id> The document where the test was published
Table of Contents
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
►ChEMBL Database - European Molecular Biology Laboratory
Call ChEMBL Data Web Service Directly
ChEMBL Data Resource - molecule
►ChEMBL Data Resource - activity
ChEMBL Data Resource - document
ChEMBL Data Resource - chembl_id_lookup
chembl_webresource_client - Python Client
chembl_webresource_client - Usage Examples
chembl_webresource_client - RetryError Exception
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)