Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
ChEMBL Terminologies
This section provides a tutorial example to install chembl_webresource_client, the Official Python client for accessing ChEMBL API.
Here is a list terminologies used in ChEMBL database:
Activity - A single test result of a chemical compound against a biological target.
<activity> <activity_id>31865 </activity_id> <activity_properties/> <assay_chembl_id>CHEMBL693237 </assay_chembl_id> <assay_description>In vivo concentration required against ... </assay_description> <molecule_chembl_id>CHEMBL324340 </molecule_chembl_id> <target_chembl_id>CHEMBL3879801 </target_chembl_id> <target_pref_name>NON-PROTEIN TARGET </target_pref_name> <type>IC50 </type> <units>uM </units> <uo_units>UO_0000065 </uo_units> <value>50.0 </value> </activity>
Assay - A test system to evaluate the effects of a chemical compounds at the biochemical level or cell level.
<assay> <assay_cell_type>143B </assay_cell_type> <assay_chembl_id>CHEMBL615125 </assay_chembl_id> <assay_organism>Homo sapiens </assay_organism> <assay_type_description>Functional </assay_type_description> <bao_format>BAO_0000219 </bao_format> <bao_label>cell-based format </bao_label> <cell_chembl_id>CHEMBL3307382 </cell_chembl_id> <confidence_description>Target assigned is non-molecular </confidence_description> <confidence_score>1 </confidence_score> <description>Inhibitory activity against tumor osteosarcoma cell line 143B after 72 hr continuous exposure to compound </description> <document_chembl_id>CHEMBL1133252 </document_chembl_id> <relationship_description>Non-molecular target assigned </relationship_description> <relationship_type>N </relationship_type> <target_chembl_id>CHEMBL614508 </target_chembl_id> </assay>
Cell - A basic structural, functional, and biological unit of all known organisms. A cell is the smallest unit of life. A cell may have millions of proteins.
Binding Site - A place on a protein's surface that binds a ligand or a drug.
Document - A piece of information collected from a source.
Drug - A medicine or other substance which has a physiological effect when ingested or otherwise introduced into the body.
Ligand - A small molecule that is able to bind to proteins by weak interactions such as ionic bonds, hydrogen bonds, Van der Waals interactions, and hydrophobic effects. In some cases, a ligand also serves as a signal triggering molecule. A ligand can be a substrate inhibitor, activator or a neurotransmitter.
Molecule - A Molecule is a group of two or more atoms that form the smallest identifiable unit of a pure substance. For example:
<molecule> <cross_references> <molecule> <xref_id>aspirin </xref_id> <xref_name>aspirin </xref_name> <xref_src>DailyMed </xref_src> </molecule> ... </cross_references> <dosed_ingredient>True </dosed_ingredient> <first_approval>1950 </first_approval> <inorganic_flag/> <max_phase>4 </max_phase> <molecule_chembl_id>CHEMBL25 </molecule_chembl_id> <molecule_properties> <alogp>1.31 </alogp> <aromatic_rings>1 </aromatic_rings> <cx_logd>-2.16 </cx_logd> <cx_logp>1.24 </cx_logp> <cx_most_apka>3.41 </cx_most_apka> <cx_most_bpka/> <full_molformula>C9H8O4 </full_molformula> <full_mwt>180.16 </full_mwt> ... </molecule_properties> <molecule_structures> <canonical_smiles>CC(=O)Oc1ccccc1C(=O)O </canonical_smiles> ... </molecule_structures> <molecule_synonyms> <synonym> <molecule_synonym>8-Hour Bayer </molecule_synonym> <syn_type>TRADE_NAME </syn_type> <synonyms>8-HOUR BAYER </synonyms> </synonym> ... </molecule_synonyms> <molecule_type>Small molecule </molecule_type> ... </molecule>
Organism - A living thing that has an organized structure that can react to stimuli, reproduce, grow, adapt, and maintain homeostasis. An organism could be a single cell.
Protein - A biological polymers composed of amino acids. Amino acids, linked together by peptide bonds, form a polypeptide chain. One or more polypeptide chains twisted into a 3-D shape form a protein. A protein may have millions of proteins.
Source - A place where the data was collected. For example:
<source> <src_description>Novartis Malaria Screening</src_description> <src_id>3</src_id> <src_short_name>NOVARTIS</src_short_name> </source
Target - A target is a protein, cell, tissue or organism that a chemical compound tries to interact, either boosting or inhibiting its function. For example,
<target> <cross_references> <target> <xref_id>P00533 </xref_id> <xref_name/> <xref_src>canSAR-Target </xref_src> </target> ... </cross_references> <organism>Homo sapiens </organism> <pref_name>Epidermal growth factor receptor erbB1 </pref_name> <species_group_flag/> <target_chembl_id>CHEMBL203 </target_chembl_id> <target_components> <target_component> <accession>P00533 </accession> <component_description>Epidermal growth factor receptor </component_description> <component_id>147 </component_id> <component_type>PROTEIN </component_type> <relationship>SINGLE PROTEIN </relationship> <target_component_synonyms> <target_component_synonym> <component_synonym>EGFR </component_synonym> <syn_type>GENE_SYMBOL </syn_type> </target_component_synonym> ... </target_component_synonyms> ... </target_component> </target_components> <target_type>SINGLE PROTEIN </target_type> <tax_id>9606 </tax_id> </target>
Tissue - A set of similar cells and their extracellular matrix from the same origin that together carry out a specific function. For example:
<tissue> <bto_id/> <caloha_id/> <efo_id/> <pref_name>Lamina propria</pref_name> <tissue_chembl_id>CHEMBL3987795</tissue_chembl_id> <uberon_id>UBERON:0000030</uberon_id> </tissue>
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)