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Updating queries #19

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d9a2b14
updating nidm files to include collection
dbkeator Jul 24, 2023
03c24d0
updating freesurfer CDEs file to support FS 7.X where some region nam…
dbkeator Sep 28, 2023
02356b8
updating instructions for blazegraph for m1 chip support
dbkeator Jan 12, 2024
7f7186f
Updating queries
seanhatton Jun 3, 2024
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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

1. start blazegraph

`docker run --name blazegraph --rm -d -p 8889:8080 lyrasis/blazegraph:2.1.5`
`docker run --name blazegraph --rm -d -p 8889:8080 islandora/blazegraph:3.1.1`

2. to upload all the turtle files, from the root of this repo do:

Expand Down Expand Up @@ -85,4 +85,4 @@ sparql.setQuery(query)
sparql.setReturnFormat(JSON)
results = sparql.query().convert()
print(len(results['results']['bindings']))
```
```
212 changes: 211 additions & 1 deletion cde/fs_cde.ttl
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Original file line number Diff line number Diff line change
Expand Up @@ -1864,7 +1864,7 @@ fs:fs_000137 a fs:DataElement ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738264> ;
nidm:hasUnit "mm" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0000956> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0111689> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Mean Thickness (mm)" ;
fs:fsunit "mm" ;
fs:isAbout_label "cerebral cortex" ;
Expand Down Expand Up @@ -47962,5 +47962,215 @@ fs:fs_003579 a fs:DataElement ;
fs:structure_id 255 ;
fs:unit "MR" .

fs:fs_003580 a fs:DataElement ;
rdfs:label "Left-Thalamus NVoxels" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0102597> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "voxel" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0112559> ;
fs:description "Left-Thalamus Number of Voxels (unitless)" ;
fs:fsunit "unitless" ;
fs:key_source "Table" ;
fs:measure "NVoxels" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "unitless" .

fs:fs_003581 a fs:DataElement ;
rdfs:label "Left-Thalamus Volume_mm3 (mm^3)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738276> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "mm^3" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0112559> ;
fs:description "Left-Thalamus Volume (mm^3)" ;
fs:fsunit "mm^3" ;
fs:key_source "Table" ;
fs:measure "Volume_mm3" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "mm^3" .

fs:fs_003582 a fs:DataElement ;
rdfs:label "Left-Thalamus normMean (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738264> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Left-Thalamus Intensity normMean (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normMean" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "MR" .

fs:fs_003583 a fs:DataElement ;
rdfs:label "Left-Thalamus normStdDev (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738265> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Left-Thalamus Itensity normStdDev (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normStdDev" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "MR" .

fs:fs_003584 a fs:DataElement ;
rdfs:label "Left-Thalamus normMin (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738266> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Left-Thalamus Intensity normMin (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normMin" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "MR" .

fs:fs_003585 a fs:DataElement ;
rdfs:label "Left-Thalamus normMax (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738267> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Left-Thalamus Intensity normMax (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normMax" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "MR" .

fs:fs_003586 a fs:DataElement ;
rdfs:label "Left-Thalamus normRange (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738268> ;
nidm:hasLaterality "Left" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Left-Thalamus Intensity normRange (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normRange" ;
fs:structure "Left-Thalamus" ;
fs:structure_id 10 ;
fs:unit "MR" .

fs:fs_003587 a fs:DataElement ;
rdfs:label "Right-Thalamus NVoxels" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0102597> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "voxel" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0112559> ;
fs:description "Right-Thalamus Number of Voxels (unitless)" ;
fs:fsunit "unitless" ;
fs:key_source "Table" ;
fs:measure "NVoxels" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "unitless" .

fs:fs_003588 a fs:DataElement ;
rdfs:label "Right-Thalamus Volume_mm3 (mm^3)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738276> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "mm^3" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0112559> ;
fs:description "Right-Thalamus Volume (mm^3)" ;
fs:fsunit "mm^3" ;
fs:key_source "Table" ;
fs:measure "Volume_mm3" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "mm^3" .

fs:fs_003589 a fs:DataElement ;
rdfs:label "Right-Thalamus normMean (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738264> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Right-Thalamus Intensity normMean (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normMean" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "MR" .

fs:fs_003590 a fs:DataElement ;
rdfs:label "Right-Thalamus normStdDev (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738265> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Right-Thalamus Itensity normStdDev (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normStdDev" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "MR" .

fs:fs_003591 a fs:DataElement ;
rdfs:label "Right-Thalamus normMin (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738266> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Right-Thalamus Intensity normMin (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normMin" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "MR" .

fs:fs_003592 a fs:DataElement ;
rdfs:label "Right-Thalamus normMax (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738267> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Right-Thalamus Intensity normMax (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normMax" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "MR" .

fs:fs_003593 a fs:DataElement ;
rdfs:label "Right-Thalamus normRange (MR)" ;
nidm:datumType <http://uri.interlex.org/base/ilx_0738268> ;
nidm:hasLaterality "Right" ;
nidm:hasUnit "https://surfer.nmr.mgh.harvard.edu/MR" ;
nidm:isAbout <http://purl.obolibrary.org/obo/UBERON_0001897> ;
nidm:measureOf <http://uri.interlex.org/base/ilx_0738276> ;
fs:description "Right-Thalamus Intensity normRange (MR)" ;
fs:fsunit "MR" ;
fs:key_source "Table" ;
fs:measure "normRange" ;
fs:structure "Right-Thalamus" ;
fs:structure_id 49 ;
fs:unit "MR" .

fs:DataElement rdfs:subClassOf nidm:DataElement .

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