ZOOMA should match against broad/narrow/related syns

[cmungall]

Ontologies such as GO use these synonym scopes. We don't have any class with primary label 'apoptosis', but we use this as a syn for 'apoptotic process' (you may remember this @paolaroncaglia )

apoptosis finds no match in all of zooma:

$ curl -L -s 'http://www.ebi.ac.uk/spot/zooma/v2/api/services/annotate?propertyValue=apoptotis' | jq '.[] | .confidence, .semanticTags, .annotatedProperty.propertyValue'

this is found when I search for the fullname:

$ curl -L -s 'http://www.ebi.ac.uk/spot/zooma/v2/api/services/annotate?propertyValue=apoptotitic+process' | jq .
[
  {
    "uri": null,
    "annotatedProperty": {
      "uri": null,
      "propertyType": null,
      "propertyValue": "biological_process"
    },
    "_links": {
      "olslinks": [
        {
          "href": "https://www.ebi.ac.uk/ols/api/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0008150",
          "semanticTag": "http://purl.obolibrary.org/obo/GO_0008150"
        }
      ]
    },
    "semanticTags": [
      "http://purl.obolibrary.org/obo/GO_0008150"
    ],
    "replacedBy": [],
    "replaces": [],
    "derivedFrom": {
      "uri": "http://rdf.ebi.ac.uk/resource/zooma/annotation_summary/OLS",
      "annotatedProperty": {
        "uri": null,
        "propertyType": null,
        "propertyValue": "biological_process"
      },
      "_links": {
        "olslinks": [
          {
            "href": "http://purl.obolibrary.org/obo/GO_0008150",
            "semanticTag": "http://purl.obolibrary.org/obo/GO_0008150"
          }
        ]
      },
      "semanticTags": [
        "http://purl.obolibrary.org/obo/GO_0008150"
      ],
      "replacedBy": [],
      "replaces": [],
      "provenance": {
        "source": {
          "type": "ONTOLOGY",
          "name": "http://purl.obolibrary.org/obo/poro",
          "uri": "http://purl.obolibrary.org/obo/poro"
        },
        "evidence": "COMPUTED_FROM_ONTOLOGY",
        "accuracy": null,
        "generator": "http://purl.obolibrary.org/obo/poro",
        "generatedDate": null,
        "annotator": null,
        "annotationDate": null
      },
      "annotatedBiologicalEntities": []
    },
    "confidence": "GOOD",
    "provenance": {
      "source": {
        "type": "DATABASE",
        "name": "zooma",
        "uri": "www.ebi.ac.uk/spot/zooma"
      },
      "evidence": "COMPUTED_FROM_TEXT_MATCH",
      "accuracy": null,
      "generator": "ZOOMA",
      "generatedDate": 1613694799986,
      "annotator": "ZOOMA",
      "annotationDate": 1613694799986
    },
    "annotatedBiologicalEntities": []
  }
]

the result is kind of odd thoigh as it's coming from poro, an ontology of sponges which I used to maintain...

[paolaroncaglia]

Hi @cmungall ,
Yes I do remember apoptosis in GO ;-)
And I agree it'd be confusing for a user not to find any valid match when searching for "apoptosis" in Zooma.
(Note, if I search for "apoptotic process" using the web interface, the source is GO, as should be, so I'm not sure what's going on with PORO.)
I believe that the choice of not allowing Zooma to search across non-exact synonyms was deliberate, but it'd be great if that could be configurable. I'll leave it to the current developers to reply when they can.
@henrietteharmse @udp please - thank you!