WIP: PrefLabels added & mapping between BIDS/NIDM-E

[natachaperez]

we add a PrefLabel for each attribute in the nidm-experiment.owl file to associate with the type: http://www.w3.org/2004/02/skos/core#prefLabel "attribute name". Then I created the nidme.json file to map JSON attributes in BIDS to NIDM-experiment URLs in the model of : https://github.com/incf-nidash/nidm-specs/blob/master/nidm/nidm-results/terms/nidmr.json.

[khelm]

Hi @natachaperez The following terms are currently defined in the NIDM-E OWL file:

"ImagingInstrument": "http://uri.neuinfo.org/nif/nifstd/birnlex_2094", 
    "MagneticResonanceImagingScanner": "http://uri.neuinfo.org/nif/nifstd/birnlex_2100", 
    "MRIProtocol": "http://uri.neuinfo.org/nif/nifstd/birnlex_2177", 
    "FunctionalMRIProtocol": "http://uri.neuinfo.org/nif/nifstd/birnlex_2250", 
    "StructuralMRIProtocol": "http://uri.neuinfo.org/nif/nifstd/birnlex_2251", 
    "PositronEmissionTomographyScanner": "http://uri.neuinfo.org/nif/nifstd/ixl_0050000", 
    "SinglePhotonEmissionComputedTomographyScanner": "http://uri.neuinfo.org/nif/nifstd/ixl_0050001", 
    "MagnetoencephalographyMachine": "http://uri.neuinfo.org/nif/nifstd/ixl_0050002", 
    "ElectroencephalographyMachine": "http://uri.neuinfo.org/nif/nifstd/ixl_0050003", 
    "AnatomicalMRIProtocol": "http://uri.neuinfo.org/nif/nifstd/ixl_0050004", 
"DiffusionWeightedImagingProtocol": "http://uri.neuinfo.org/nif/nifstd/nlx_inv_20090249"

using what I believe is a more consistent naming convention, so you might want to take a look there before using these versions.

[natachaperez]

 @khelm Could you specify me the corresponding lines in the NIDM-E owl files? Cause the nidme json document above is generated by essentially using these following lines on PyNIDM/nidm/experiment/Core.py (with some changes made by myself) :

def createDefaultJSONLDcontext(self):

    from nidm.experiment.Utils import load_nidm_owl_files
    from nidm.core.Constants import namespaces

    #load current OWL files
    term_graph=load_nidm_owl_files()

    context=OrderedDict()
    context['@version'] = 1.1
    context['records'] = OrderedDict()
    context['records']['@id'] = "@graph"
    context['records']['@container'] = "@type"
    context['xsd'] = "http://www.w3.org/2001/XMLSchema#"
    context['prov'] = "http://www.w3.org/ns/prov#"
    context['agent'] = "http://www.w3.org/ns/prov#agent"
    context['entity'] = "http://www.w3.org/ns/prov#entity"
    context['activity'] = "http://www.w3.org/ns/prov#activity" 
    context['hadPlan'] = "http://www.w3.org/ns/prov#hadPlan"
    context['hadRole'] = "http://www.w3.org/ns/prov#hadRole"
    context['wasAttributedTo'] = "http://www.w3.org/ns/prov#wasAttributedTo"
    context['association'] = "http://www.w3.org/ns/prov#association"
    context['usage'] = "http://www.w3.org/ns/prov#usage"
    context['generation'] = "http://www.w3.org/ns/prov#generation"
    context['startedAtTime'] = OrderedDict()
    context['startedAtTime']['@id'] = "http://www.w3.org/ns/prov#startedAtTime"
    context['startedAtTime']['@type'] = "http://www.w3.org/2001/XMLSchema#dateTime"
    context['endedAtTime'] = OrderedDict()
    context['endedAtTime']['@id'] = "http://www.w3.org/ns/prov#endedAtTime"
    context['endedAtTime']['@type'] = "http://www.w3.org/2001/XMLSchema#dateTime"

    #load Constants.namespaces
    #context.update(Constants.namespaces)

    """context.update ({
        "xsd": {"@type": "@id","@id":"http://www.w3.org/2001/XMLSchema#"},
        "prov": {"@type": "@id","@id":"http://www.w3.org/ns/prov#"},
        "agent": { "@type": "@id", "@id": "prov:agent" },
        "entity": { "@type": "@id", "@id": "prov:entity" },
        "activity": { "@type": "@id", "@id": "prov:activity" },
        "hadPlan": { "@type": "@id", "@id": "prov:hadPlan" },
        "hadRole": { "@type": "@id", "@id": "prov:hadRole" },
        "wasAttributedTo": { "@type": "@id", "@id": "prov:wasAttributedTo" },
        "association": { "@type": "@id", "@id": "prov:qualifiedAssociation" },
        "usage": { "@type": "@id", "@id": "prov:qualifiedUsage" },
        "generation": { "@type": "@id", "@id": "prov:qualifiedGeneration" },
        "startedAtTime": { "@type": "xsd:dateTime", "@id": "prov:startedAtTime" },
        "endedAtTime": { "@type": "xsd:dateTime", "@id": "prov:endedAtTime" },
    })"""

    #add namespaces from Constants.namespaces
    for key,value in namespaces.items():
        #context['@context'][key] = value
        context[key] = value

    #add terms from Constants.nidm_experiment_terms
    for term in Constants.nidm_experiment_terms:
        #context['@context'][term.localpart] = term.uri
        context[term.localpart] = term.uri

    #add prefix's from current document...this accounts for new terms
    context.update ( self.prefix_to_context() )

    #WIP
    #link toward nidm-experiment owl file and 
    owls = '/udd/nperez/softs/nidm-specs/nidm/nidm-experiment/terms/nidm-experiment.owl'

    owl_imports = glob.glob(os.path.join(os.path.dirname(owls),os.pardir, os.pardir, "imports", '*.ttl'))

    # OwlReader to read and extract informations in owl file 
    owl = OwlReader(owls, import_owl_files=owl_imports)

    #cycle through OWL graph and add terms
    # For anything that has a label

    #for s, o in sorted(term_graph.subject_objects(Constants.RDFS['label'])):
    #    json_key = str(o)
    #    if '_' in json_key:
    #        json_key = str(o).split('_')[1]
    #    context['@context'][json_key] = OrderedDict()

    #    if s in term_graph.ranges:
    #        context['@context'][json_key]['@id'] = str(s)
    #        context['@context'][json_key]['@type'] = next(iter(term_graph.ranges[s]))
    #    else:
    #        context['@context'][json_key] = str(s)

    for s, o in sorted(owl.graph.subject_objects(Constants.SKOS['prefLabel'])):
        json_key = str(o)
        context[json_key] = OrderedDict()
        if s in owl.ranges:
            ranges = next(iter(owl.ranges[s]))
            if 'http://www.w3.org/2001/XMLSchema#int' in ranges or 'http://www.w3.org/2001/XMLSchema#double' in ranges or 'http://www.w3.org/2001/XMLSchema#integer' in ranges or  'http://www.w3.org/2001/XMLSchema#positiveInteger' in ranges:
                context[json_key]['@id'] = str(s)
                context[json_key]['@type'] = ranges
            else:
                context[json_key] = str(s)
        else:
            context[json_key] = str(s)

    return context

and I use the nidm-e owl file to do so.