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Working and published ApiNATOMY models
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Unable to get references for a connectivity model #32

Closed dbrnz closed 1 year ago

dbrnz commented 1 year ago

What is the appropriate query to use?

This would go towards resolving #30.

tgbugs commented 1 year ago

Is /dynamic/demos/apinat/modelPopulationsReferences/{model_id} not working?

dbrnz commented 1 year ago 
Couldn't access https://scicrunch.org/api/1/sparc-scigraph/dynamic/demos/apinat/modelPopulationsReferences/https://apinatomy.org/uris/models/ard-arm-cardiac
dbrnz commented 1 year ago

@tgbugs has this been resolved??

tgbugs commented 1 year ago

https://scicrunch.org/api/1/sparc-scigraph/dynamic/demos/apinat/modelPopulationsReferences/https%3A%2F%2Fapinatomy.org%2Furis%2Fmodels%2Fard-arm-cardiac

works, in python you call urllib.parse.quote(url, '') on the model_id to ensure it matches (there is no curied form of https://apinatomy/org/uris/models/ right now).

dbrnz commented 1 year ago

Thanks. I now get back the following, which doesn't show any publications. How do we get the publications (provenance) for a model? 

{'nodes': [{'id': 'ilxtr:neuron-type-aacar-2m',
   'lbl': 'neuron type aacar 2m',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 2m'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-2i',
   'lbl': 'neuron type aacar 2i',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 2i'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-9v',
   'lbl': 'neuron type aacar 9v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 9v'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-10a',
   'lbl': 'neuron type aacar 10a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 10a'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-10v',
   'lbl': 'neuron type aacar 10v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 10v'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-8v',
   'lbl': 'neuron type aacar 8v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 8v'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-1',
   'lbl': 'neuron type aacar 1',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 1'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-13',
   'lbl': 'neuron type aacar 13',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 13'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-8a',
   'lbl': 'neuron type aacar 8a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 8a'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-9a',
   'lbl': 'neuron type aacar 9a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 9a'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-11',
   'lbl': 'neuron type aacar 11',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 11'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-6',
   'lbl': 'neuron type aacar 6',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 6'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-7a',
   'lbl': 'neuron type aacar 7a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 7a'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'elements:OntologyTerm', 'lbl': None, 'meta': {'types': ['Class']}},
  {'id': 'ilxtr:neuron-type-aacar-4',
   'lbl': 'neuron type aacar 4',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 4'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-12',
   'lbl': 'neuron type aacar 12',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 12'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-5',
   'lbl': 'neuron type aacar 5',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 5'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-7v',
   'lbl': 'neuron type aacar 7v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 7v'],
    'https://apinatomy.org/uris/readable/generated': [True],
    'category': ['cell']}}],
 'edges': [{'sub': 'ilxtr:neuron-type-aacar-10v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-9v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-12',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-8a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-2m',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-4',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-8v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-7a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-11',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-2i',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-1',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-9a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-5',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-10a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-13',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-7v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-6',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}}],
 'meta': {}}
tgbugs commented 1 year ago

Ah, I think there was a schema change in the predicate used for linking references so I need to update the query.

tgbugs commented 1 year ago

The query has been updated to account for the schema change and the results are as expected. Let me know if this is working as desired on sparc-scigraph and I can deploy the query changes to sckan-scigraph. See https://github.com/SciCrunch/sparc-curation/commit/4c0d14584735d0f418e2d16f9d972b1e839d6f6d#diff-ccf692fad0a138b6f517b51f8c65539e0594bed294ff171fb749a3615aba6a68L2946

dbrnz commented 1 year ago

@tgbugs the query:

 https://scicrunch.org/api/1/sparc-scigraph/dynamic/demos/apinat/modelPopulationsReferences/https%3A%2F%2Fapinatomy.org%2Furis%2Fmodels%2Fard-arm-cardiac

returns the following, which is hardly the set of publications for the model.

{'edges': [{'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-10v'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-2i'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-9v'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-6'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-5'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-4'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-13'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-8v'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-1'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-8a'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-12'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-7v'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-9a'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-2m'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-10a'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-11'},
           {'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']},
            'obj': 'elements:OntologyTerm',
            'pred': 'type',
            'sub': 'ilxtr:neuron-type-aacar-7a'}],
 'meta': {},
 'nodes': [{'id': 'elements:OntologyTerm',
            'lbl': None,
            'meta': {'types': ['Class']}},
           {'id': 'ilxtr:neuron-type-aacar-6',
            'lbl': 'neuron type aacar 6',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 6'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-11',
            'lbl': 'neuron type aacar 11',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 11'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-2m',
            'lbl': 'neuron type aacar 2m',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 2m'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-8a',
            'lbl': 'neuron type aacar 8a',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 8a'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-8v',
            'lbl': 'neuron type aacar 8v',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 8v'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-2i',
            'lbl': 'neuron type aacar 2i',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 2i'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-10a',
            'lbl': 'neuron type aacar 10a',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar '
                                                                    '10a'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-1',
            'lbl': 'neuron type aacar 1',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 1'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-9a',
            'lbl': 'neuron type aacar 9a',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 9a'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-10v',
            'lbl': 'neuron type aacar 10v',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar '
                                                                    '10v'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-4',
            'lbl': 'neuron type aacar 4',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 4'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-13',
            'lbl': 'neuron type aacar 13',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 13'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-5',
            'lbl': 'neuron type aacar 5',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 5'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-12',
            'lbl': 'neuron type aacar 12',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 12'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-9v',
            'lbl': 'neuron type aacar 9v',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 9v'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-7a',
            'lbl': 'neuron type aacar 7a',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 7a'],
                     'types': ['Class', 'cell']}},
           {'id': 'ilxtr:neuron-type-aacar-7v',
            'lbl': 'neuron type aacar 7v',
            'meta': {'category': ['cell'],
                     'http://www.w3.org/2000/01/rdf-schema#label': ['neuron '
                                                                    'type '
                                                                    'aacar 7v'],
                     'types': ['Class', 'cell']}}]}
tgbugs commented 1 year ago

Since I pushed the most recent preview release something may have changed. Will investigate.

tgbugs commented 1 year ago

Fixed now. The new version of the pipelines left out the apinatomy:Reference triples so the final type check did not pass. This has been corrected via https://github.com/open-physiology/open-physiology-viewer/commit/9a7fa1f94fe89d2ebcf397777e2dbb28254f154d and the models have been redeployed and a new graph load pushed to sparc-scigraph.

dbrnz commented 1 year ago

I still get:

Request https://scicrunch.org/api/1/sparc-scigraph/dynamic/demos/apinat/modelPopulationsReferences/https%3A%2F%2Fapinatomy.org%2Furis%2Fmodels%2Fard-arm-cardiac

{'nodes': [{'id': 'elements:OntologyTerm',
   'lbl': None,
   'meta': {'types': ['Class']}},
  {'id': 'elements:Reference', 'lbl': None, 'meta': {'types': ['Class']}},
  {'id': 'ilxtr:neuron-type-aacar-5',
   'lbl': 'neuron type aacar 5',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 5'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-13',
   'lbl': 'neuron type aacar 13',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 13'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-9v',
   'lbl': 'neuron type aacar 9v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 9v'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-2i',
   'lbl': 'neuron type aacar 2i',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 2i'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-6',
   'lbl': 'neuron type aacar 6',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 6'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-8a',
   'lbl': 'neuron type aacar 8a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 8a'],
    'category': ['cell']}},
  {'id': 'PMID:27783854', 'lbl': None, 'meta': {'types': ['NamedIndividual']}},
  {'id': 'ilxtr:neuron-type-aacar-8v',
   'lbl': 'neuron type aacar 8v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 8v'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-7a',
   'lbl': 'neuron type aacar 7a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 7a'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-2m',
   'lbl': 'neuron type aacar 2m',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 2m'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-1',
   'lbl': 'neuron type aacar 1',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 1'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-9a',
   'lbl': 'neuron type aacar 9a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 9a'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-10a',
   'lbl': 'neuron type aacar 10a',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 10a'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-4',
   'lbl': 'neuron type aacar 4',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 4'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-12',
   'lbl': 'neuron type aacar 12',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 12'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-10v',
   'lbl': 'neuron type aacar 10v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 10v'],
    'category': ['cell']}},
  {'id': 'doi:10.1002/cphy.c150046',
   'lbl': None,
   'meta': {'types': ['NamedIndividual']}},
  {'id': 'ilxtr:neuron-type-aacar-11',
   'lbl': 'neuron type aacar 11',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 11'],
    'category': ['cell']}},
  {'id': 'ilxtr:neuron-type-aacar-7v',
   'lbl': 'neuron type aacar 7v',
   'meta': {'types': ['Class', 'cell'],
    'http://www.w3.org/2000/01/rdf-schema#label': ['neuron type aacar 7v'],
    'category': ['cell']}}],
 'edges': [{'sub': 'ilxtr:neuron-type-aacar-7v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-2i',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-1',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-13',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-12',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-9v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-5',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'doi:10.1002/cphy.c150046',
   'obj': 'elements:Reference',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-10a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-6',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-8v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-9a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-7a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-4',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-2m',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'PMID:27783854',
   'obj': 'elements:Reference',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-10v',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-11',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}},
  {'sub': 'ilxtr:neuron-type-aacar-8a',
   'obj': 'elements:OntologyTerm',
   'pred': 'type',
   'meta': {'isDefinedBy': ['https://apinatomy.org/uris/models/ard-arm-cardiac']}}],
 'meta': {}}
dbrnz commented 1 year ago

Oops, let me dig a bit deeper...

dbrnz commented 1 year ago

Is https://scicrunch.org/api/1/sparc-scigraph/dynamic/demos/apinat/modelPopulationsReferences the correct endpoint to get the publications associated with a model? It's returning the neuron populations that reference the model, which is sort-of what the name modelPopulationsReferences implies, so I wonder if you've given me the wrong query to use... :)

tgbugs commented 1 year ago

This is the correct endpoint, and if you ctrl-f for doi: and PMID: you will see that the references are in the results that you pasted.

dbrnz commented 1 year ago

Thanks @tgbugs all is now good. (It all become obvious when I queried Bolser-Lewis, which has a lot of publications (as opposed to Ardelll's two), and also I wasn't expecting to see references to the neuron populations...). Am happy to close this one!