enh: extract fiq/piq

[satra]

@jbpoline - updated query

[jbpoline]

thanks a lot - will try asap

[jbpoline]

@satra : hum, seems that this query does not give me any results ... I tried to add the ?piq ?fiq at the end of the select but (as expected) this is not the issue
does it return results for you ?

prefix GrayMatter: http://uri.interlex.org/ilx_0104768#
prefix afni: http://purl.org/nidash/afni#
prefix ants: http://stnava.github.io/ANTs/
prefix bids: http://bids.neuroimaging.io/
prefix birnlex: http://bioontology.org/projects/ontologies/birnlex/
prefix crypto: http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#
prefix dc: http://purl.org/dc/elements/1.1/
prefix dcat: http://www.w3.org/ns/dcat#
prefix dct: http://purl.org/dc/terms/
prefix dctypes: http://purl.org/dc/dcmitype/
prefix dicom: http://neurolex.org/wiki/Category:DICOM_term/
prefix foaf: http://xmlns.com/foaf/0.1/
prefix freesurfer: https://surfer.nmr.mgh.harvard.edu/
prefix fsl: http://purl.org/nidash/fsl#
prefix full4_iq: dbkeator/nidm-local-terms#2
prefix hasDatumType: http://uri.interlex.org/ilx_0738262#
prefix hasLaterality: http://uri.interlex.org/ilx_0381387#
prefix hasMeasurementType: http://uri.interlex.org/ilx_0381388#
prefix isAbout: http://uri.interlex.org/ilx_0381385#
prefix isMeasureOf: http://uri.interlex.org/ilx_0381389#
prefix measurement_datum: http://uri.interlex.org/base/ilx_0738269#
prefix ncicb: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
prefix ncit: http://ncitt.ncit.nih.gov/
prefix ndar: https://ndar.nih.gov/api/datadictionary/v2/dataelement/
prefix nfo: http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#
prefix nidm: http://purl.org/nidash/nidm#
prefix niiri: http://iri.nidash.org/
prefix nlx: http://uri.neuinfo.org/nif/nifstd/
prefix obo: http://purl.obolibrary.org/obo/
prefix onli: http://neurolog.unice.fr/ontoneurolog/v3.0/instrument.owl#
prefix owl: http://www.w3.org/2002/07/owl#
prefix pato: http://purl.obolibrary.org/obo/pato#
prefix performance_iq: dbkeator/nidm-local-terms#4
prefix prov: http://www.w3.org/ns/prov#
prefix qc_anatomical_1: dbkeator/nidm-local-terms#63
prefix qc_rest_1: dbkeator/nidm-local-terms#62
prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
prefix rdfs: http://www.w3.org/2000/01/rdf-schema#
prefix scr: http://scicrunch.org/resolver/
prefix sio: http://semanticscience.org/ontology/sio.owl#
prefix spm: http://purl.org/nidash/spm#
prefix vc: http://www.w3.org/2006/vcard/ns#
prefix verbal_iq: dbkeator/nidm-local-terms#3
prefix xml: http://www.w3.org/XML/1998/namespace
prefix xsd: http://www.w3.org/2001/XMLSchema#
prefix ilx: http://uri.interlex.org/base/ilx_

SELECT DISTINCT ?study ?ID ?Age ?Gender ?dx ?value ?tool ?structure
WHERE
{
?e a onli:assessment-instrument;
prov:wasGeneratedBy ?act;
ncicb:Age ?Age;
ncit:Diagnosis ?dx;
ndar:gender ?Gender;
full4_iq: ?fiq;
performance_iq: ?piq .

?act a onli:instrument-based-assessment;
dct:isPartOf/dct:isPartOf [ a nidm:Project;
dctypes:title ?study];
prov:wasAssociatedWith [ a prov:Person;
ndar:src_subject_id ?ID ] .

?tool_act a prov:Activity ;
prov:qualifiedAssociation [prov:wasAssociatedWith [ndar:src_subject_id ?ID]],
[prov:wasAssociatedWith [nidm:NIDM_0000164 ?tool]] .

?tool_stats prov:wasGeneratedBy ?tool_act;
?measure ?value .

?measure a measurement_datum:;
rdfs:label ?label;
isAbout: ?structure; #http://purl.obolibrary.org/obo/UBERON_0001873;
hasMeasurementType: ilx:0112559;
hasDatumType: ?datum_uri .

}

[satra]

@jbpoline - pushed a couple of changes. following the readme, i get about 58k records back.

[jbpoline]

@satra : Not sure what was happening - I had a weird port error (port was already taken by a jupyer notebook) but I changed the port so not sure that was the issue. In any case, restarted blazegraph, made sure test.ttl seemed ok and got you 58k records back ... Back on track !
thanks a lot !

[satra]

@jbpoline - see the updated query. the reason hasUnit didn't work is because it wasn't in the prefix list

[jbpoline]

@satra (also @dbkeator )
thanks - I thought I had checked that !

I am adding laterality as well I suppose it refers to right or left side of the brain ? Does this PR https://github.com/satra/simple2_NIDM_examples/pull/1/commits makes sense ?

Also: do you know if "cerebral hemisphere" is the best proxy for "total brain volume" ? it seems that in the "structure" result I have limited options (see below) but may be missing something:

{'cavum septum pellucidum': 'http://purl.obolibrary.org/obo/UBERON_0001869',
'cerebellum': 'http://purl.obolibrary.org/obo/UBERON_0002285',
'cerebellar cortex': 'http://purl.obolibrary.org/obo/UBERON_0001954',
'perivascular space': 'http://purl.obolibrary.org/obo/UBERON_0001876',
"Ammon's horn": 'http://purl.obolibrary.org/obo/UBERON_0014930',
'inferior horn of the lateral ventricle': 'http://purl.obolibrary.org/obo/UBERON_0001874',
'brainstem': 'http://purl.obolibrary.org/obo/UBERON_0001886',
'amygdala': 'http://purl.obolibrary.org/obo/UBERON_0000959',
'optic chiasma': 'http://purl.obolibrary.org/obo/UBERON_0006091',
'dorsal plus ventral thalamus': 'http://purl.obolibrary.org/obo/UBERON_0002298',
'cerebral hemisphere': 'http://purl.obolibrary.org/obo/UBERON_0009857',
'caudate nucleus': 'http://purl.obolibrary.org/obo/UBERON_0002286', 'telencephalic ventricle': 'http://purl.obolibrary.org/obo/UBERON_0002037',
'putamen': 'http://purl.obolibrary.org/obo/UBERON_0001873',
'third ventricle': 'http://purl.obolibrary.org/obo/UBERON_0006514',
'choroid plexus': 'http://purl.obolibrary.org/obo/UBERON_0002422',
'fourth ventricle': 'http://purl.obolibrary.org/obo/UBERON_0002129',
'pallidum': 'http://purl.obolibrary.org/obo/UBERON_0001897',
'nucleus accumbens': 'http://purl.obolibrary.org/obo/UBERON_0001882'}

[satra]

@jbpoline - could you please change the target of the PR to the wBrainVols branch?

the mapping file is here: https://github.com/dbkeator/segstats_jsonld/blob/master/segstats_jsonld/mapping_data/freesurfermap.json

there are several things that could constitute brain vol - i would think this may be a good starting point: http://purl.obolibrary.org/obo/UBERON_0003128

[jbpoline]

@satra : PR is now on wBrainVols - thanks for pointing this
Atm the query does not return http://purl.obolibrary.org/obo/UBERON_0003128 - looking now how I can extend it
thanks again