search

VirtualFlyBrain / VFB2

Virtual Fly Brain Documentation Site
https://virtualflybrain.org
MIT License
2 stars 4 forks source link

Gross type list is missing elements #326

Open dosumis opened 2 years ago

dosumis commented 2 years ago

e.g. some neurons in this list have the 'cholinergic' tag. Others are 'sensory neuron', but neither appear in list

image
dosumis commented 2 years ago

Tags are in JSON

image
Robbie1977 commented 2 years ago 
<id>: 14412
curie: VFB:0010123s
has_exact_synonym: {"annotations":{},"value":"skid:2615448"},{"annotations":{},"value":"Uniglomerular mALT VM5d adPN 2615449 FML XZ"}
iri: http://virtualflybrain.org/reports/VFB_0010123s
label: Uniglomerular mALT VM5d adPN#L3 (FAFB:2615448)
label_rdfs: Uniglomerular mALT VM5d adPN#L3 (FAFB:2615448)
qsl: Uniglomerular_mALT_VM5d_adPN3L3_4FAFB526154484
short_form: VFB_0010123s
sl: Uniglomerular_mALT_VM5d_adPN3L3_4FAFB526154484
uniqueFacets: Adult,Cholinergic
<id>: 118480
comment: For image, see FlyBase:FBrf0211729.
curie: FBbt:00100385
database_cross_reference: VFB:FBbt_00100385
definition: {"annotations":{"database_cross_reference":["FlyBase:FBrf0211729","FlyBase:FBrf0246460"]},"value":"Adult uniglomerular antennal lobe projection neuron from the ad neuroblast (ALad1) lineage with dendrites that mainly innervate antennal lobe glomerulus VM5d. Neurons of this class are derived from the 15th larval division of the neuroblast ALad1 (FBbt:00067346) (Yu et al., 2010). There are around four of these per hemisphere, they fasciculate with the medial antennal lobe tract and they are cholinergic (Bates et al., 2020)."}
description: Adult uniglomerular antennal lobe projection neuron from the ad neuroblast (ALad1) lineage with dendrites that mainly innervate antennal lobe glomerulus VM5d. Neurons of this class are derived from the 15th larval division of the neuroblast ALad1 (FBbt:00067346) (Yu et al., 2010). There are around four of these per hemisphere, they fasciculate with the medial antennal lobe tract and they are cholinergic (Bates et al., 2020).
has_exact_synonym: {"annotations":{},"value":"VM5d_adPN"},{"annotations":{},"value":"VM5d adPN"}
has_obo_namespace: fly_anatomy.ontology
id: FBbt:00100385
iri: http://purl.obolibrary.org/obo/FBbt_00100385
label: adult antennal lobe projection neuron VM5d adPN
label_rdfs: adult antennal lobe projection neuron VM5d adPN
qsl: adult_antennal_lobe_projection_neuron_VM5d_adPN
short_form: FBbt_00100385
sl: adult_antennal_lobe_projection_neuron_VM5d_adPN
symbol: VM5d_adPN
uniqueFacets: Adult,Cholinergic

So Cholinergic tag exists in the unique facets but seems to be filtered out so I'll debug the UK bundle

Robbie1977 commented 2 years ago

Query for OWL Class ID list to VFB JSON results rows:

MATCH (primary:Class) WHERE primary.short_form in ['FBbt_00100385'] WITH primary CALL apoc.cypher.run('WITH primary OPTIONAL MATCH (primary)<- [:has_source|SUBCLASSOF|INSTANCEOF*]-(i:Individual)<-[:depicts]- (channel:Individual)-[irw:in_register_with] ->(template:Individual)-[:depicts]-> (template_anat:Individual) RETURN template, channel, template_anat, i, irw limit 5', {primary:primary}) yield value with value.template as template, value.channel as channel,value.template_anat as template_anat, value.i as i, value.irw as irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE COLLECT({ anatomy: { short_form: i.short_form, label: coalesce(i.label,''), iri: i.iri, types: labels(i), symbol: coalesce(i.symbol[0], '')} , channel_image: { channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), unique_facets: apoc.coll.sort(coalesce(channel.uniqueFacets,[])), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), unique_facets: apoc.coll.sort(coalesce(technique.uniqueFacets,[])), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), unique_facets: apoc.coll.sort(coalesce(template.uniqueFacets,[])), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }} }) END AS anatomy_channel_image ,primary RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets,[])), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'bac066c' AS version, 'anatomy_query' AS query, anatomy_channel_image

returns

[
  {
    "term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/FBbt_00100385",
"symbol": "VM5d_adPN",
"types": [
          "Entity",
          "Adult",
          "Anatomy",
          "Cell",
          "Cholinergic",
          "Class",
          "Nervous_system",
          "Neuron"
        ],
"short_form": "FBbt_00100385",
"unique_facets": [
          "Adult",
          "Cholinergic"
        ],
"label": "adult antennal lobe projection neuron VM5d adPN"
      },
"description": [
        "Adult uniglomerular antennal lobe projection neuron from the ad neuroblast (ALad1) lineage with dendrites that mainly innervate antennal lobe glomerulus VM5d. Neurons of this class are derived from the 15th larval division of the neuroblast ALad1 (FBbt:00067346) (Yu et al., 2010). There are around four of these per hemisphere, they fasciculate with the medial antennal lobe tract and they are cholinergic (Bates et al., 2020)."
      ],
"comment": [
        "For image, see FlyBase:FBrf0211729."
      ]
    },
    "version": "bac066c",
    "query": "anatomy_query",
    "anatomy_channel_image": [
      {
        "channel_image": {
"channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_jrchk7id",
"types": [
              "Entity",
              "Individual"
            ],
"short_form": "VFBc_jrchk7id",
"unique_facets": [],
"label": "VM5d_adPN_R - 1006258344_c"
          },
"image": {
"template_channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_00101567",
"types": [
                "Entity",
                "Individual",
                "Template"
              ],
"short_form": "VFBc_00101567",
"unique_facets": [],
"label": "JRC2018Unisex_c"
            },
"index": [],
"template_anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_00101567",
"types": [
                "Entity",
                "Adult",
                "Anatomy",
                "Individual",
                "Nervous_system",
                "Template",
                "has_image"
              ],
"label": "JRC2018Unisex",
"short_form": "VFB_00101567"
            },
"image_folder": "http://www.virtualflybrain.org/data/VFB/i/jrch/k7id/VFB_00101567/"
          },
"imaging_technique": {
"symbol": "FIB-SEM",
"iri": "http://purl.obolibrary.org/obo/FBbi_00050000",
"types": [
              "Entity",
              "Class"
            ],
"short_form": "FBbi_00050000",
"unique_facets": [],
"label": "focussed ion beam scanning electron microscopy (FIB-SEM)"
          }
        },
        "anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_jrchk7id",
"types": [
            "Entity",
            "Adult",
            "Anatomy",
            "Cell",
            "Cholinergic",
            "Individual",
            "Nervous_system",
            "Neuron",
            "has_image",
            "has_neuron_connectivity",
            "has_region_connectivity",
            "FlyEM_HB",
            "NBLAST",
            "neuronbridge"
          ],
"label": "VM5d_adPN_R (FlyEM-HB:1006258344)",
"short_form": "VFB_jrchk7id"
        }
      },
      {
        "channel_image": {
"channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_jrchk7id",
"types": [
              "Entity",
              "Individual"
            ],
"short_form": "VFBc_jrchk7id",
"unique_facets": [],
"label": "VM5d_adPN_R - 1006258344_c"
          },
"image": {
"template_channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_00101384",
"types": [
                "Entity",
                "Individual",
                "Template"
              ],
"short_form": "VFBc_00101384",
"unique_facets": [],
"label": "JRC_FlyEM_Hemibrain_c"
            },
"index": [],
"template_anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_00101384",
"types": [
                "Entity",
                "Adult",
                "Anatomy",
                "Individual",
                "Nervous_system",
                "Template",
                "has_image"
              ],
"label": "JRC_FlyEM_Hemibrain",
"short_form": "VFB_00101384"
            },
"image_folder": "http://www.virtualflybrain.org/data/VFB/i/jrch/k7id/VFB_00101384/"
          },
"imaging_technique": {
"symbol": "FIB-SEM",
"iri": "http://purl.obolibrary.org/obo/FBbi_00050000",
"types": [
              "Entity",
              "Class"
            ],
"short_form": "FBbi_00050000",
"unique_facets": [],
"label": "focussed ion beam scanning electron microscopy (FIB-SEM)"
          }
        },
        "anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_jrchk7id",
"types": [
            "Entity",
            "Adult",
            "Anatomy",
            "Cell",
            "Cholinergic",
            "Individual",
            "Nervous_system",
            "Neuron",
            "has_image",
            "has_neuron_connectivity",
            "has_region_connectivity",
            "FlyEM_HB",
            "NBLAST",
            "neuronbridge"
          ],
"label": "VM5d_adPN_R (FlyEM-HB:1006258344)",
"short_form": "VFB_jrchk7id"
        }
      },
      {
        "channel_image": {
"channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_jrchk7if",
"types": [
              "Entity",
              "Individual"
            ],
"short_form": "VFBc_jrchk7if",
"unique_facets": [],
"label": "VM5d_adPN_R - 1914823414_c"
          },
"image": {
"template_channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_00101384",
"types": [
                "Entity",
                "Individual",
                "Template"
              ],
"short_form": "VFBc_00101384",
"unique_facets": [],
"label": "JRC_FlyEM_Hemibrain_c"
            },
"index": [],
"template_anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_00101384",
"types": [
                "Entity",
                "Adult",
                "Anatomy",
                "Individual",
                "Nervous_system",
                "Template",
                "has_image"
              ],
"label": "JRC_FlyEM_Hemibrain",
"short_form": "VFB_00101384"
            },
"image_folder": "http://www.virtualflybrain.org/data/VFB/i/jrch/k7if/VFB_00101384/"
          },
"imaging_technique": {
"symbol": "FIB-SEM",
"iri": "http://purl.obolibrary.org/obo/FBbi_00050000",
"types": [
              "Entity",
              "Class"
            ],
"short_form": "FBbi_00050000",
"unique_facets": [],
"label": "focussed ion beam scanning electron microscopy (FIB-SEM)"
          }
        },
        "anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_jrchk7if",
"types": [
            "Entity",
            "Adult",
            "Anatomy",
            "Cell",
            "Cholinergic",
            "Individual",
            "Nervous_system",
            "Neuron",
            "has_image",
            "has_neuron_connectivity",
            "has_region_connectivity",
            "FlyEM_HB",
            "NBLAST",
            "neuronbridge"
          ],
"label": "VM5d_adPN_R (FlyEM-HB:1914823414)",
"short_form": "VFB_jrchk7if"
        }
      },
      {
        "channel_image": {
"channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_jrchk7if",
"types": [
              "Entity",
              "Individual"
            ],
"short_form": "VFBc_jrchk7if",
"unique_facets": [],
"label": "VM5d_adPN_R - 1914823414_c"
          },
"image": {
"template_channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_00101567",
"types": [
                "Entity",
                "Individual",
                "Template"
              ],
"short_form": "VFBc_00101567",
"unique_facets": [],
"label": "JRC2018Unisex_c"
            },
"index": [],
"template_anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_00101567",
"types": [
                "Entity",
                "Adult",
                "Anatomy",
                "Individual",
                "Nervous_system",
                "Template",
                "has_image"
              ],
"label": "JRC2018Unisex",
"short_form": "VFB_00101567"
            },
"image_folder": "http://www.virtualflybrain.org/data/VFB/i/jrch/k7if/VFB_00101567/"
          },
"imaging_technique": {
"symbol": "FIB-SEM",
"iri": "http://purl.obolibrary.org/obo/FBbi_00050000",
"types": [
              "Entity",
              "Class"
            ],
"short_form": "FBbi_00050000",
"unique_facets": [],
"label": "focussed ion beam scanning electron microscopy (FIB-SEM)"
          }
        },
        "anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_jrchk7if",
"types": [
            "Entity",
            "Adult",
            "Anatomy",
            "Cell",
            "Cholinergic",
            "Individual",
            "Nervous_system",
            "Neuron",
            "has_image",
            "has_neuron_connectivity",
            "has_region_connectivity",
            "FlyEM_HB",
            "NBLAST",
            "neuronbridge"
          ],
"label": "VM5d_adPN_R (FlyEM-HB:1914823414)",
"short_form": "VFB_jrchk7if"
        }
      },
      {
        "channel_image": {
"channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_00101241",
"types": [
              "Entity",
              "Individual"
            ],
"short_form": "VFBc_00101241",
"unique_facets": [],
"label": "PN glomerulus VM5d 35448 AA_c"
          },
"image": {
"template_channel": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFBc_00101567",
"types": [
                "Entity",
                "Individual",
                "Template"
              ],
"short_form": "VFBc_00101567",
"unique_facets": [],
"label": "JRC2018Unisex_c"
            },
"index": [],
"template_anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_00101567",
"types": [
                "Entity",
                "Adult",
                "Anatomy",
                "Individual",
                "Nervous_system",
                "Template",
                "has_image"
              ],
"label": "JRC2018Unisex",
"short_form": "VFB_00101567"
            },
"image_folder": "http://www.virtualflybrain.org/data/VFB/i/0010/1241/VFB_00101567/"
          },
"imaging_technique": {
"symbol": "TEM",
"iri": "http://purl.obolibrary.org/obo/FBbi_00000258",
"types": [
              "Entity",
              "Class"
            ],
"short_form": "FBbi_00000258",
"unique_facets": [],
"label": "transmission electron microscopy (TEM)"
          }
        },
        "anatomy": {
"symbol": "",
"iri": "http://virtualflybrain.org/reports/VFB_00101241",
"types": [
            "Entity",
            "Adult",
            "Anatomy",
            "Cell",
            "Cholinergic",
            "Individual",
            "Nervous_system",
            "Neuron",
            "has_image",
            "has_neuron_connectivity",
            "FAFB",
            "NBLAST"
          ],
"label": "Uniglomerular mALT VM5d adPN#R2 (FAFB:35447)",
"short_form": "VFB_00101241"
        }
      }
    ]
  }
]
Robbie1977 commented 2 years ago

I left the filters as was to avoid breaking anything or adding any new labels but looks like there was too much hard-wired (to the type rather than uniqueFacets) filtering. As these are no longer required I have stripped out the filtering.

dosumis commented 2 years ago

What filters were these?

Robbie1977 commented 2 years ago

Previously we had to have a manually curated filter otherwise we'd show all labels the query simply returned labels(n) e.g.

            "Entity",
            "Adult",
            "Anatomy",
            "Cell",
            "Cholinergic",
            "Individual",
            "Nervous_system",
            "Neuron",
            "has_image",
            "has_neuron_connectivity",
            "FAFB",
            "NBLAST"