# PubChemRDF Case 1: What protein targets does donepezil (CHEBI_53289) inhibit with an IC50 less than 10 µM?
SELECT DISTINCT ?protein
FROM pubchem:protein
FROM pubchem:measuregroup
FROM pubchem:endpoint
FROM pubchem:substance
WHERE
{
?sub rdf:type obo:CHEBI_53289;
obo:RO_0000056 ?mg.
?mg obo:RO_0000057 ?protein;
obo:OBI_0000299 ?ep.
?protein rdf:type sio:SIO_010043.
?ep rdf:type bao:BAO_0000190;
obo:IAO_0000136 ?sub;
sio:SIO_000300|sio:SIO_000738 ?value.
filter (?value < 10)
}
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The database uses the data coming from the PubChemRDF project that provides RDF formatted information available in the PubChem archive. It mainly comprises information from the PubChem Compound, Substance, and Bioassay databases.
The PubChemRDF data includes many semantic relationships, for which existing ontologies are employed, whenever it is possible. Parts of these ontologies (e.g., class hierarchies, resource labels) are loaded into the database as well. Summarization of the used ontologies and relationship predicates are summarized in the PubChemRDF documentation.
Detail information can be found in the following documents:The user interface of the application is divided into three parts. The left part contains a query editor that allows users to write SPARQL queries. The query result is visualized as a table in the central part of the application. And finally, the right part of the application is used to visualize details about the selected resource.
The query editor is based on the third-party CodeMirror component. It highlights SPARQL syntax, and supports auto-completion of predicates used in the PubChemRDF data. Namespace prefixes used by the PubChemRDF project are predefined in used SPARQL engine, so they do not have to be explicitly defined in a query.
The users can write a whole SPARQL query from the beginning or they can load a predefined query which can be further modified. If the query is stored in a file, then the Open button allows the users to load the query into the editor. Another possibility is to select one of the predefined examples queries by clicking on the Examples button. These examples are adopted from PubChemRDF use cases. And finally, the third option is to use a wizard to generate a query.
A prepared query can be submitted to the SPARQL engine for evaluation by clicking on the Run button. Alternatively, the query can be saved into the file for later use.
The wizard allows the users to generate queries that search for compounds, bioassays, participants (proteins or genes) or their combinations. If the compound search and the bioassay search are both enabled, then the generated query searches only for the compounds that were tested in the searched bioassays. Similarly, if the bioassay search and the participant search are both enabled, then the query searches only for bioassays having the given participants.
The following search criteria can be set:Finally, the wizard allows specifying which kinds of searched entities should be included in the final result. It is also possible to specify the requested ordering of the result.
Please note that queries generated by the wizard are not submitted automatically and have to be also submitted by clicking on the Run button.
The result of a submitted query is shown as the table in the central part of the application interface. Each variable used in the select clause of the query is represented by one column. Individual solution mapping forming single results are represented by rows. Only the first thousand solution mappings (i.e., rows) are shown. Other solutions can be showed by using the pagination navigation buttons located at the bottom of the result table. The showed solutions can be filtered by the filter box on the top of the result table. The filtration criteria can be restricted only to contents of a selected variable.
If the value to which a variable is bound is an IRI identifying a resource of a supported type, then the appropriate item template is used to visualize the appropriate table cell. Otherwise, the value itself is used as the cell content. The visualisation typically contains the label of the resource, that is separately searched for the given resource in the database.
The Details tab located at the right part of the application is used to visualize details about the selected resource. The IRI of the resource can be entered directly by the address bar, or the resource can be selected from the result table. If details about the supported resource are requested, the application uses the appropriate page template to generate details about the resource.
The Properties tab can be used to display all relations between selected resource and other resources or values. It uses the given resource as a subject and shows all predicates (properties) and objects (values) for which triples subject-predicate-object are stored in the database.
The web application is intended to be used only as a user interface. If it is required to use the database from other programs, for example as part as federated queries, the SPARQL endpoint https://idsm.elixir-czech.cz/sparql/endpoint/idsm should be used.
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