# A Linked Data Application for Harmonizing Heterogeneous Biomedical Information
## 4 The Integration and Harmonization Process
### Layer 5: Drug Interactions
\begin{table}
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**Interaction Type** & **Description** \\ \hline _activator_ & A drug activates a biological response from a target, although the mechanism by which it does so may not be understood \\ \hline _agonist_ & A drug binds to a target receptor and activates the receptor to produce a biological response \\ \hline _allosteric modulator_ & Drugs exert their effects on their protein targets via a different binding site than the natural (orthosteric) ligand site \\ \hline _antagonist_ & A drug blocks or dampens agonist-mediated responses rather than provoking a biological response itself upon binding to a target receptor \\ \hline _antibody_ & An antibody drug specifically binds the target molecule \\ \hline _antisense oligonucleotide_ & A complementary RNA drug binds to an mRNA target to inhibit translation by physically obstructing the mRNA translation machinery \\ \hline _inducer_ & The drug increases the activity of its target enzyme \\ \hline _inhibitor_ & The drug binds to a target and decreases its expression or activity \\ \hline _inhibitory allosteric modulator_ & The drug will inhibit activity of its target enzyme \\ \hline _inverse agonist_ & A drug binds to the same target as an agonist but induces a pharmacological response opposite to that of the agonist \\ \hline _modulator_ & The drug regulates or changes the activity of its target, but it may not involve any direct binding to the target \\ \hline _negative modulator_ & The drug negatively regulates the amount or activity of its target, but it may not involve any direct binding to the target \\ \hline _partial agonist_ & A drug will elicit a reduced amplitude functional response at its target receptor, as compared to the response elicited by a full agonist \\ \hline _positive modulator_ & The drug increases activity of the target enzyme \\ \hline _supressor_ & The drug directly or indirectly affects its target, suppressing a physiological process \\ \hline _vaccine_ & The drugs stimulate or restore an immune response to their target \\ \hline \end{tabular}
\end{table} 
Table 6: Types of drug–gene interactions supported by layer 5. \begin{table}
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**Field** & **Description** & **Example** \\ \hline gene-name & Gene identifier (_HGNC_ taxonomy) & ITGB5 \\ entrez-id & Gene identifier (_NCBI Entrez_ taxonomy) & 3693 \\ drug-name & Name of the interacting drug & CILENGTIDE \\ drug-concept-id & Drug identifier (_ChEMBL_ taxonomy) & CHEAD429876 \\ interaction-types & Types of gene–drug interaction (controlled vocabulary, see Table 6) & inhibitor \\  & The strength of the interaction calculated by multiplying the number of sources that report the interaction with its specificity (if the gene or the drug interacts with many other drugs or genes, the interaction specificity is low, otherwise it is high) \\ \hline \end{tabular}
\end{table} 
Table 5: The main fields of the _DGldb Interactions Archive_. where gray classes and bold relationships are introduced by the scheme of this layer except for the dotted classes which are projected from the previous layers. In particular, the new class _Drug_ maps, through the _equivalent-class_ relation, the external general _Substance_ class from _ChEMBL_. The class _Gene-Drug Interaction_ maps a row of the _DGIdb Interactions Archive_ and connects the _Gene_ class with the _Drug_ class with the _interaction-has-gene_ and the _interaction-has-drug_ object properties, respectively. Additional information, connected to the _Gene-Drug Interaction_ class through the _interaction-has-type_ property, is the _Interaction Type_ that explains the way a dug or compound interacts with a gene according to a controlled vocabulary defined by _DGIdb_ as reported in Table 6. Each term is represented within the model as an individual of the _Interaction Type_ class. The meaning of each term is explained in the same table.