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RF simple2 query for more exhaustively defined sorting, tuned up formatting of .sparql, new produced output #18

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RF simple2 query for more exhaustively defined sorting, tuned up formatting of .sparql, new produced output #18

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6bbb849
simple2 query: define ilxb for http://uri.interlex.org/base/
yarikoptic Feb 11, 2024
93a9545
simple2 query: delete trailing whitespace and excessive empty lines
yarikoptic Feb 11, 2024
59efc2e
simple2 query: make result sorted not only by study but then ?ID ?sof…
yarikoptic Feb 11, 2024
8c9dc43
simple2 query: remove excessive indentation and empty lines
yarikoptic Feb 11, 2024
add998d
[DATALAD RUNCMD] Regenerate simple2_query_output.csv using current ve…
yarikoptic Feb 11, 2024
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110 changes: 52 additions & 58 deletions queries/simple2_query.sparql
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ prefix nidm: <http://purl.org/nidash/nidm#>
prefix onli: <http://neurolog.unice.fr/ontoneurolog/v3.0/instrument.owl#>
prefix freesurfer: <https://surfer.nmr.mgh.harvard.edu/>
prefix dx: <http://ncitt.ncit.nih.gov/Diagnosis>
prefix ants: <http://stnava.github.io/ANTs/>
prefix ants: <http://stnava.github.io/ANTs/>
prefix dct: <http://purl.org/dc/terms/>
prefix dctypes: <http://purl.org/dc/dcmitype/>
prefix ncicb: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
Expand All @@ -15,66 +15,60 @@ prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix uberon: <http://purl.obolibrary.org/obo/UBERON_>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix ilx: <http://uri.interlex.org/>
prefix ilxb: <http://uri.interlex.org/base/>

select distinct ?study ?ID ?Age ?dx ?Gender ?FIQ ?PIQ ?VIQ ?tool ?softwareLabel ?federatedLabel ?laterality ?volume
where {
?measure a/rdfs:subClassOf nidm:DataElement;
rdfs:label ?softwareLabel;
nidm:measureOf <http://uri.interlex.org/base/ilx_0112559> ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738276> .
OPTIONAL {?measure nidm:isAbout ?federatedLabel }.
OPTIONAL {?measure nidm:hasLaterality ?laterality }.
?measure a/rdfs:subClassOf nidm:DataElement;
rdfs:label ?softwareLabel;
nidm:measureOf ilxb:ilx_0112559 ;
nidm:datumType ilxb:ilx_0738276 .
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more indentation would help with readability here

OPTIONAL {?measure nidm:isAbout ?federatedLabel }.
OPTIONAL {?measure nidm:hasLaterality ?laterality }.

?tool_entity a prov:Entity;
?measure ?volume .
?tool_entity a prov:Entity;
?measure ?volume .

?tool_act a prov:Activity ;
prov:qualifiedAssociation [prov:agent [nidm:NIDM_0000164 ?tool]] ;
prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] .
?tool_entity prov:wasGeneratedBy ?tool_act .

?as_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] .


# find age data element uuid
{?age_measure a nidm:PersonalDataElement ;
nidm:isAbout ilx:ilx_0100400 .

}
# find sex data element uuid
{?sex_measure a nidm:PersonalDataElement ;
nidm:isAbout <http://uri.interlex.org/base/ilx_0101292> .
}
# find diagnosis data element uuid
{?DX_measure a nidm:PersonalDataElement ;
nidm:isAbout ncit:Diagnosis .

}
# find fiq data element uuid
{?FIQ_measure a nidm:PersonalDataElement ;
nidm:isAbout <http://uri.interlex.org/base/ilx_0739365> .
}
# find piq data element uuid
{?PIQ_measure a nidm:PersonalDataElement ;
nidm:isAbout <http://uri.interlex.org/base/ilx_0739363> .
}
# find viq data element uuid
{?VIQ_measure a nidm:PersonalDataElement ;
nidm:isAbout <http://uri.interlex.org/base/ilx_0739359> .
}

?as_entity prov:wasGeneratedBy ?as_activity ;
?age_measure ?Age;
?sex_measure ?GenderCoded ;
?FIQ_measure ?FIQ ;
?PIQ_measure ?PIQ ;
?VIQ_measure ?VIQ ;
?DX_measure ?dx .

bind(IF((?GenderCoded ="1" || ?GenderCoded ="Male"^^xsd:string), "Male"^^xsd:string,"Female"^^xsd:string) as ?Gender) .




} order by ?study
?tool_act a prov:Activity ;
prov:qualifiedAssociation [prov:agent [nidm:NIDM_0000164 ?tool]] ;
prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] .
?tool_entity prov:wasGeneratedBy ?tool_act .

?as_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] .

# find age data element uuid
{?age_measure a nidm:PersonalDataElement ;
nidm:isAbout ilx:ilx_0100400 .
}
# find sex data element uuid
{?sex_measure a nidm:PersonalDataElement ;
nidm:isAbout ilxb:ilx_0101292 .
}
# find diagnosis data element uuid
{?DX_measure a nidm:PersonalDataElement ;
nidm:isAbout ncit:Diagnosis .
}
# find fiq data element uuid
{?FIQ_measure a nidm:PersonalDataElement ;
nidm:isAbout ilxb:ilx_0739365 .
}
# find piq data element uuid
{?PIQ_measure a nidm:PersonalDataElement ;
nidm:isAbout ilxb:ilx_0739363 .
}
# find viq data element uuid
{?VIQ_measure a nidm:PersonalDataElement ;
nidm:isAbout ilxb:ilx_0739359 .
}

?as_entity prov:wasGeneratedBy ?as_activity ;
?age_measure ?Age;
?sex_measure ?GenderCoded ;
?FIQ_measure ?FIQ ;
?PIQ_measure ?PIQ ;
?VIQ_measure ?VIQ ;
?DX_measure ?dx .

bind(IF((?GenderCoded ="1" || ?GenderCoded ="Male"^^xsd:string), "Male"^^xsd:string,"Female"^^xsd:string) as ?Gender) .

} order by ?study ?ID ?softwareLabel ?laterality ?softwareLabel ?volume
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