VirtualFlyBrain / pipeline

A repository for amalgamating pipeline issue tickets and general VFB pipeline doc
https://hub.docker.com/repository/docker/virtualflybrain/pipeline
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Two extraneous Anatomy Individual nodes being created during production DB loading #41

Closed Robbie1977 closed 6 years ago

Robbie1977 commented 6 years ago

http://pdb-firstload.virtualflybrain.org/browser/

MATCH (n:Individual) where n.label starts with 'VFB_' return n

"data": [
        {
          "row": [
            {
              "iri": "http://www.virtualflybrain.org/owl/VFB_00002270",
              "ontology_name": "vfb",
              "has_children": false,
              "ontology_prefix": "VFB",
              "short_form": "VFB_00002270",
              "ontology_iri": "http://purl.obolibrary.org/obo/fbbt/vfb/vfb.owl",
              "label": "VFB_00002270",
              "is_defining_ontology": false,
              "is_root": true,
              "obo_id": "VFB:00002270",
              "olsId": "vfb:http://www.virtualflybrain.org/owl/VFB_00002270",
              "is_obsolete": false
            }
          ],
          "graph": {
            "nodes": [
              {
                "id": "55095",
                "labels": [
                  "Individual",
                  "VFB",
                  "_Individual",
                  "Neuron",
                  "Anatomy",
                  "Cell"
                ],
                "properties": {
                  "iri": "http://www.virtualflybrain.org/owl/VFB_00002270",
                  "ontology_name": "vfb",
                  "has_children": false,
                  "ontology_prefix": "VFB",
                  "short_form": "VFB_00002270",
                  "ontology_iri": "http://purl.obolibrary.org/obo/fbbt/vfb/vfb.owl",
                  "label": "VFB_00002270",
                  "is_defining_ontology": false,
                  "is_root": true,
                  "obo_id": "VFB:00002270",
                  "olsId": "vfb:http://www.virtualflybrain.org/owl/VFB_00002270",
                  "is_obsolete": false
                }
              }
            ],
            "relationships": []
          }
        },
        {
          "row": [
            {
              "iri": "http://www.virtualflybrain.org/owl/VFB_00014660",
              "ontology_name": "vfb",
              "has_children": false,
              "ontology_prefix": "VFB",
              "short_form": "VFB_00014660",
              "ontology_iri": "http://purl.obolibrary.org/obo/fbbt/vfb/vfb.owl",
              "label": "VFB_00014660",
              "is_defining_ontology": false,
              "is_root": true,
              "obo_id": "VFB:00014660",
              "olsId": "vfb:http://www.virtualflybrain.org/owl/VFB_00014660",
              "is_obsolete": false
            }
          ],
          "graph": {
            "nodes": [
              {
                "id": "59325",
                "labels": [
                  "Individual",
                  "VFB",
                  "_Individual",
                  "Neuron",
                  "Anatomy",
                  "Cell"
                ],
                "properties": {
                  "iri": "http://www.virtualflybrain.org/owl/VFB_00014660",
                  "ontology_name": "vfb",
                  "has_children": false,
                  "ontology_prefix": "VFB",
                  "short_form": "VFB_00014660",
                  "ontology_iri": "http://purl.obolibrary.org/obo/fbbt/vfb/vfb.owl",
                  "label": "VFB_00014660",
                  "is_defining_ontology": false,
                  "is_root": true,
                  "obo_id": "VFB:00014660",
                  "olsId": "vfb:http://www.virtualflybrain.org/owl/VFB_00014660",
                  "is_obsolete": false
                }
              }
            ],
            "relationships": []
          }
        }
      ]

The correct (full data with standard IRI) nodes are also created and this seems to be the only ones created.

Have tried recreating OWL from latest KB and using that for loading but issue still there.

The IRI shouldn't have 'www.' plus '/owl/' rather than '/reports/'

Resource node also created along with additional INSTANCEOF edge.

matentzn commented 6 years ago

I must admit, I have not even the beginning of an idea where that bug is routed. @dosumis ?

dosumis commented 6 years ago

Legacy mapping file merged during the VFB.owl build process. Fixing now.

dosumis commented 6 years ago

Fixed in https://github.com/VirtualFlyBrain/VFB_owl/commit/2b81d5423e62ad5186fd2247eaa96452b9c78cea#diff-81b41c7333caeae0ed620fe949646e57