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- Use standard prefix notations
- Use CamelCase for the variables
- Nodes and Idividials Individuals starting with upper case
- Properties starting with lower case
- Write all SPARQL key words in capital letters ("SELECT" not "select" or "Select")
- Use BIND to assign all relevant variables a the top of the WHERE statement
- For the CQ parameters the "$" is used for the corresponding variable
- Provide at least one example in the comments for the variable BINDing
- Do not require unique labels of resources (as the queries should be able to run on many different datasets)
- Use inverse property pairs to be agnostic to their use e.g., ^idmp-sub:isActiveMoietyOf|idmp-sub:hasActiveMoiety
- Use of subproperties?
- Use of full vs. shortcut pattern: substance/ingredient role pattern vs. direct "includedIn"
Comment on Entailment Regime
If CQs require any inference then this should be explicitly noted.
Example Query
| Code Block | ||
|---|---|---|
| ||
# UC1-CQ 1: What substances have a common active moiety <M>?
prefix idmp-sub: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?Substance (SAMPLE(?SubstanceLabel) AS ?SubstanceName)
WHERE {
# Bind Variable ActiveMoiety <M>
# Example: <https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288> for GSRS Amlodipine
BIND(uc1_cq1_parameter_1 AS ?M )
# Get the Entities that have the defined active moiety
?Substance ^idmp-sub:isActiveMoietyOf|idmp-sub:hasActiveMoiety ?M .
# Make sure that we only return actual substances
?Substance a/rdfs:subClassOf* idmp-sub:Substance .
# Optionally, get the name of the substance
OPTIONAL{?Substance rdfs:label ?SubstanceLabel }
} GROUP BY ?Substance |
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