Updating queries #19
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| prefix xsd: <http://www.w3.org/2001/XMLSchema#> | ||
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
| prefix prov: <http://www.w3.org/ns/prov#> | ||
| prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/> | ||
| prefix nidm: <http://purl.org/nidash/nidm#> | ||
| prefix fs: <https://surfer.nmr.mgh.harvard.edu/> | ||
| prefix dct: <http://purl.org/dc/terms/> | ||
| prefix dctypes: <http://purl.org/dc/dcmitype/> | ||
| prefix ilx: <http://uri.interlex.org/> | ||
|
|
||
| select distinct ?ID ?Sex ?Age | ||
| where { | ||
|
|
||
| ?tool_act a prov:Activity ; | ||
| prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
| ?as_activity prov:qualifiedAssociation [prov:agent ?agent] ; | ||
| dct:isPartOf/dct:isPartOf [dctypes:title ?study] . | ||
| ?agent ndar:src_subject_id ?ID . | ||
|
|
||
| # find sex data element uuid | ||
| {?sex_measure a nidm:PersonalDataElement ; | ||
| nidm:isAbout <http://uri.interlex.org/base/ilx_0101292> . #Biological sex | ||
| #nidm:isAbout <http://id.nlm.nih.gov/mesh/2018/M0446358> . #Genetic sex | ||
| } | ||
|
|
||
| # find age data element uuid | ||
| {?age_measure a nidm:PersonalDataElement ; | ||
| nidm:isAbout ilx:ilx_0100400 . | ||
| } | ||
|
|
||
| ?as_entity prov:wasGeneratedBy ?as_activity ; | ||
| ?sex_measure ?SexCoded ; | ||
| ?age_measure ?Age. | ||
| bind(IF((?SexCoded ="M" || ?SexCoded ="Male"^^xsd:string), "Male"^^xsd:string,"Female"^^xsd:string) as ?Sex) . | ||
| #filter (?Sex = "Male"^^xsd:string) . | ||
| } | ||
| ORDER BY ?ID |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| ## The main issue was that the measures (for left, right, and mean) were coming from different stats collections | ||
| ## (nidm:FSStatsCollection) associated with different activitities (prov:Acitivity). The previous code | ||
| ## was assuming that the measurements were coming from the same collection and activity. I also fixed other | ||
| ## minor issues for effeciency (e.g., removing unnecessary transitive subclass searches) and made the code | ||
| ## simpler to follow. - Fahim | ||
|
|
||
| prefix xsd: <http://www.w3.org/2001/XMLSchema#> | ||
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
| prefix prov: <http://www.w3.org/ns/prov#> | ||
| prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/> | ||
| prefix nidm: <http://purl.org/nidash/nidm#> | ||
| prefix fs: <https://surfer.nmr.mgh.harvard.edu/> | ||
| prefix dct: <http://purl.org/dc/terms/> | ||
| prefix dctypes: <http://purl.org/dc/dcmitype/> | ||
| prefix ilx: <http://uri.interlex.org/> | ||
|
|
||
| SELECT DISTINCT | ||
| ?ID ?Sex ?Age | ||
| ?measure_left_label ?measure_left_value | ||
| ?measure_right_label ?measure_right_value | ||
| ?measure_mean_label ?measure_mean_value | ||
|
|
||
| WHERE | ||
| { | ||
| # Gather the activity types for each type of measure associated with a given subject | ||
| ?measure_left_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
| ?measure_right_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
| ?measure_mean_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
|
|
||
| # Gather the stats collections (nidm:FSStatsCollection) generated by each acitivity type above, | ||
| # and allocate the variables for measurement types and values to be identified. | ||
| ?left_stats_collection a nidm:FSStatsCollection; | ||
| prov:wasGeneratedBy ?measure_left_activity; | ||
| ?measure_left ?measure_left_value. | ||
|
|
||
| ?right_stats_collection a nidm:FSStatsCollection; | ||
| prov:wasGeneratedBy ?measure_right_activity; | ||
| ?measure_right ?measure_right_value. | ||
|
|
||
| ?left_stats_collection a nidm:FSStatsCollection; | ||
| prov:wasGeneratedBy ?measure_mean_activity; | ||
| ?measure_mean ?measure_mean_value. | ||
|
|
||
| # Set the mesurement type identified based on the specific values for each data element | ||
| ?measure_left a fs:DataElement; | ||
| rdfs:label ?measure_left_label; | ||
| fs:measure 'ThickAvg' ; | ||
| fs:structure 'superiortemporal' ; | ||
| nidm:hasLaterality 'Left'. | ||
|
|
||
| ?measure_right a fs:DataElement; | ||
| rdfs:label ?measure_right_label; | ||
| fs:measure 'ThickAvg' ; | ||
| fs:structure 'superiortemporal' ; | ||
| nidm:hasLaterality 'Right'. | ||
|
|
||
| ?measure_mean a fs:DataElement ; | ||
| rdfs:label ?measure_mean_label; | ||
| fs:measure 'MeanThickness' ; | ||
| fs:structure 'Cortex' . | ||
|
|
||
|
|
||
| ?as_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
|
|
||
| # find sex data element uuid | ||
| {?sex_measure a nidm:PersonalDataElement ; | ||
| nidm:isAbout <http://uri.interlex.org/base/ilx_0101292> . #Biological sex | ||
| #nidm:isAbout <http://id.nlm.nih.gov/mesh/2018/M0446358> . #Genetic sex | ||
| } | ||
|
|
||
| # find age data element uuid | ||
| {?age_measure a nidm:PersonalDataElement ; | ||
| nidm:isAbout ilx:ilx_0100400 . | ||
| } | ||
|
|
||
| ?as_entity prov:wasGeneratedBy ?as_activity ; | ||
| ?sex_measure ?SexCoded ; | ||
| ?age_measure ?Age. | ||
| bind(IF((?SexCoded ="M" || ?SexCoded ="Male"^^xsd:string), "Male"^^xsd:string,"Female"^^xsd:string) as ?Sex) . | ||
| } | ||
| ORDER BY ?ID |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| prefix xsd: <http://www.w3.org/2001/XMLSchema#> | ||
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
| prefix prov: <http://www.w3.org/ns/prov#> | ||
| prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/> | ||
| prefix nidm: <http://purl.org/nidash/nidm#> | ||
| prefix fs: <https://surfer.nmr.mgh.harvard.edu/> | ||
| prefix dct: <http://purl.org/dc/terms/> | ||
| prefix dctypes: <http://purl.org/dc/dcmitype/> | ||
| prefix ilx: <http://uri.interlex.org/> | ||
|
|
||
| select distinct ?ID ?Sex ?Age ?left_hipp_vol_softwareLabel ?left_hipp_vol | ||
| ?right_hipp_vol_softwareLabel ?right_hipp_vol ?eICV_softwareLabel ?eICV | ||
| where { | ||
| # tool initialization | ||
| ?tool_act a prov:Activity ; | ||
| prov:qualifiedAssociation [prov:agent [nidm:NIDM_0000164 ?tool]] . | ||
| ?tool_act prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
|
|
||
| # Left Hippocampus Volume | ||
| ?tool_entity prov:wasGeneratedBy ?tool_act ; | ||
| ?measure_left_hipp_vol ?left_hipp_vol . | ||
| ?measure_left_hipp_vol a/rdfs:subClassOf* nidm:DataElement ; | ||
| rdfs:label ?left_hipp_vol_softwareLabel; | ||
| fs:measure 'Volume_mm3'; | ||
| fs:structure 'Left-Hippocampus'. | ||
| # Right Hippocampus Volume | ||
| ?tool_entity prov:wasGeneratedBy ?tool_act ; | ||
| ?measure_right_hipp_vol ?right_hipp_vol . | ||
| ?measure_right_hipp_vol a/rdfs:subClassOf* nidm:DataElement ; | ||
| rdfs:label ?right_hipp_vol_softwareLabel; | ||
| fs:measure 'Volume_mm3'; | ||
| fs:structure 'Right-Hippocampus'. | ||
| # estimated Intracarnial Volume | ||
| ?tool_entity prov:wasGeneratedBy ?tool_act ; | ||
| ?measure_eICV ?eICV . | ||
| ?measure_eICV a/rdfs:subClassOf* nidm:DataElement ; | ||
| rdfs:label ?eICV_softwareLabel; | ||
| fs:measure 'eTIV'; | ||
| fs:structure 'EstimatedTotalIntraCranialVol'. | ||
| ?as_activity prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||
|
|
||
| # find sex data element uuid | ||
| {?sex_measure a nidm:PersonalDataElement ; | ||
| nidm:isAbout <http://uri.interlex.org/base/ilx_0101292> . #Biological sex | ||
| #nidm:isAbout <http://id.nlm.nih.gov/mesh/2018/M0446358> . #Genetic sex | ||
| } | ||
|
|
||
| # find age data element uuid | ||
| {?age_measure a nidm:PersonalDataElement ; | ||
| nidm:isAbout ilx:ilx_0100400 . | ||
| } | ||
|
|
||
| ?as_entity prov:wasGeneratedBy ?as_activity ; | ||
| ?sex_measure ?SexCoded ; | ||
| ?age_measure ?Age. | ||
| bind(IF((?SexCoded ="M" || ?SexCoded ="Male"^^xsd:string), "Male"^^xsd:string,"Female"^^xsd:string) as ?Sex) . | ||
| #filter (?Sex = "Male"^^xsd:string) . | ||
| } | ||
|
|
||
| ORDER BY ?ID | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,29 @@ | ||||||
| # This query simply returns the brain measurements without dependencies on other | ||||||
| # demographics/assessment measures. | ||||||
|
|
||||||
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||||||
| prefix prov: <http://www.w3.org/ns/prov#> | ||||||
| prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/> | ||||||
| prefix nidm: <http://purl.org/nidash/nidm#> | ||||||
| prefix dct: <http://purl.org/dc/terms/> | ||||||
| prefix dctypes: <http://purl.org/dc/dcmitype/> | ||||||
| prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||||||
|
|
||||||
| select distinct ?ID ?tool ?softwareLabel ?federatedLabel ?laterality ?volume | ||||||
| where { | ||||||
| ?tool_act a prov:Activity ; | ||||||
| prov:qualifiedAssociation [prov:agent [nidm:NIDM_0000164 ?tool]] . | ||||||
| ?tool_act prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] . | ||||||
| ?tool_entity prov:wasGeneratedBy ?tool_act ; | ||||||
| ?measure ?volume . | ||||||
|
|
||||||
| ?measure a/rdfs:subClassOf* nidm:DataElement ; | ||||||
| rdfs:label ?softwareLabel; | ||||||
| nidm:measureOf <http://uri.interlex.org/base/ilx_0112559> ; #Volume | ||||||
| nidm:datumType <http://uri.interlex.org/base/ilx_0738276> . #Volume | ||||||
| #nidm:measureOf <http://uri.interlex.org/base/ilx_0111689> . #Thickness | ||||||
| #nidm:measureOf <http://purl.obolibrary.org/obo/PATO_0001323> . #Surface Area | ||||||
| OPTIONAL {?measure nidm:isAbout ?federatedLabel }. | ||||||
| OPTIONAL {?measure nidm:hasLaterality ?laterality }. | ||||||
| } | ||||||
| ORDER BY ?ID ?softwareLabel | ||||||
|
There was a problem hiding this comment. would it be sufficient to become consistent across runs? may be add more into the mix here, e.g.
Suggested change
? There was a problem hiding this comment. I was thinking of adding a study name to differentiate the output and aid referencing sourced tools/data, is there such a label? There was a problem hiding this comment. I dunno... I just see above that you are selecting only There was a problem hiding this comment. I ran it against the ReproLake_dev and it looks a bit cleaner with tools as the second ordering: ORDER BY ?ID ?tool ?softwareLabel |
||||||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,27 +1,17 @@ | ||
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
| prefix prov: <http://www.w3.org/ns/prov#> | ||
| prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/> | ||
| prefix nidm: <http://purl.org/nidash/nidm#> | ||
| prefix dct: <http://purl.org/dc/terms/> | ||
| prefix dctypes: <http://purl.org/dc/dcmitype/> | ||
|
|
||
| select distinct (count(?as_entity) as ?flowweighted_count) | ||
| where { | ||
| ?as_activity prov:qualifiedAssociation [prov:agent ?agent] ; | ||
| dct:isPartOf/dct:isPartOf [dctypes:title ?study] . | ||
| ?agent ndar:src_subject_id ?ID . | ||
|
|
||
| ?as_entity prov:wasGeneratedBy ?as_activity ; | ||
| nidm:hadImageContrastType nidm:FlowWeighted ; | ||
| nidm:Task ?task . | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.