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

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

ChEMBL Database - European Molecular Biology Laboratory

 What Is ChEMBL

 ChEMBL Speical Web Portals

 Download ChEMBL Database

 ChEMBL FTP Repository

 ChEMBL Web Services API

 Call ChEMBL Data Web Service Directly

 ChEMBL Data Resource - molecule

 ChEMBL Data Resource - activity

 ChEMBL Data Resource - assay

 ChEMBL Data Resource - document

 ChEMBL Data Resource - target

 ChEMBL Data Resource - chembl_id_lookup

 ChEMBL Related Tools

 chembl_webresource_client - Python Client

 chembl_webresource_client - Usage Examples

 chembl_webresource_client - RetryError Exception

ChEMBL Terminologies

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB