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Empty annotation values should not be dropped #112

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matentzn opened this issue Nov 25, 2024 · 0 comments
Open

Empty annotation values should not be dropped #112

matentzn opened this issue Nov 25, 2024 · 0 comments

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@matentzn
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A (given, this is a terrible thing to do) hasExactSynonym annotation with an empty string as value (in RDF), <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym> will result in this unfortunate representation:

{
      "id" : "http://purl.obolibrary.org/obo/OBA_2050220",
      "lbl" : "vascular cell adhesion protein 1 amount",
      "type" : "CLASS",
      "meta" : {
        "definition" : {
          "val" : "The amount of a vascular cell adhesion protein 1 when measured in anatomical entity.",
          "xrefs" : [ "AUTO:patterns/patterns/entity_attribute_location" ]
        },
        "synonyms" : [ {
          "pred" : "hasExactSynonym"
        }]
      }
    }

The val key in the synonym block should be required (we need to use the linkml!).

So I would expect:

{
      "id" : "http://purl.obolibrary.org/obo/OBA_2050220",
      "lbl" : "vascular cell adhesion protein 1 amount",
      "type" : "CLASS",
      "meta" : {
        "definition" : {
          "val" : "The amount of a vascular cell adhesion protein 1 when measured in anatomical entity.",
          "xrefs" : [ "AUTO:patterns/patterns/entity_attribute_location" ]
        },
        "synonyms" : [ {
          "pred" : "hasExactSynonym",
          "val" : ""
        }]
      }
    }
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