ChEMBL Terminologies

Molecule Tutorials - Herong's Tutorial Examples

∟ChEMBL Database - European Molecular Biology Laboratory

∟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>