NodeNorm ES won't return NCBITaxon:2 alongside "MESH:C029371",

[gaurav]

This query to the POST interface returns null for "NCBITaxon:2":

{
  "curies": ["MESH:C029371", "NCBITaxon:2"],
  "conflate": true,
  "description": false,
  "drug_chemical_conflate": false
}

But replacing that MESH identifier with another identifier returns "NCBITaxon:2" correctly:

{
  "curies": ["MESH:D008795", "NCBITaxon:2"],
  "conflate": true,
  "description": false,
  "drug_chemical_conflate": false
}

Reported by @uhbrar

[ctrl-schaff]

This a CURIE duplication issue. When we search our index with these two CURIE's we get the following:

{
  "query": {
    "bool": {
      "filter": [
        {
          "terms": {
            "identifiers.i": [
              "MESH:C029371",
              "NCBITaxon:2"
            ]
          }
        }
      ]
    }
  }
}

{
  "took": 11,
  "timed_out": false,
  "_shards": { 
    "total": 10,
    "successful": 10,
    "skipped": 0,
    "failed": 0
  },
  "hits": { ]
    "total": { 
      "value": 3,
      "relation": "eq"
    },
    "max_score": 0,
    "hits": [ 
      {
        "_index": "nodenorm_20251106_lv86fxt0",
        "_id": "UMLS:C0063134",
        "_score": 0,
        "_source": { 
          "type": "biolink:Protein",
          "ic": 0,
          "identifiers": [
            { 
              "i": "UMLS:C0063134",
              "l": "hydroxyethyloxamic acid",
              "d": [ ],
              "t": [ ],
              "c": { 
                "gp": null,
                "dc": null
              }
            },
            {  
              "i": "MESH:C029371",
              "l": "hydroxyethyloxamic acid",
              "d": [ ],
              "t": [ ],
              "c": {  
                "gp": null,
                "dc": null
              }
            }
          ],
          "preferred_name": "hydroxyethyloxamic acid",
          "taxa": [ ]
        }
      },
      {  
        "_index": "nodenorm_20251106_lv86fxt0",
        "_id": "PUBCHEM.COMPOUND:165301",
        "_score": 0,
        "_source": { 
          "type": "biolink:SmallMolecule",
          "ic": 0,
          "identifiers": [ 
            { 
              "i": "PUBCHEM.COMPOUND:165301",
              "l": "Hydroxyethyloxamic acid",
              "d": [ ],
              "t": [ ],
              "c": {  
                "gp": null,
                "dc": null
              }
            },
            {  
              "i": "MESH:C029371",
              "l": "hydroxyethyloxamic acid",
              "d": [ ],
              "t": [ ],
              "c": {  
                "gp": null,
                "dc": null
              }
            },
            {  
              "i": "CAS:5270-73-5",
              "l": "",
              "d": [ ],
              "t": [ ],              ],
              "c": { 
                "gp": null,
                "dc": null
              }
            },
            {
              "i": "INCHIKEY:IYENBEYPOIXIHY-UHFFFAOYSA-N",
              "l": "",
              "d": [ ],
              "t": [ ],
              "c": { 
                "gp": null,
                "dc": null
              }
            }
          ],
          "preferred_name": "hydroxyethyloxamic acid",
          "taxa": [ ]
        }
      },
      {
        "_index": "nodenorm_20251106_lv86fxt0",
        "_id": "NCBITaxon:2",
        "_score": 0,
        "_source": {
          "type": "biolink:OrganismTaxon",
          "ic": 12.303639894221472,
          "identifiers": [ 
            {
              "i": "NCBITaxon:2",
              "l": "Bacteria (eubacteria)",
              "d": [ ],
              "t": [ ],
              "c": {
                "gp": null,
                "dc": null
              }
            },
            {
              "i": "MESH:D001419",
              "l": "Bacteria",
              "d": [ ],
              "t": [ ],
              "c": { 
                "gp": null,
                "dc": null
              }
            },
            { 
              "i": "UMLS:C0004611",
              "l": "Bacteria",
              "d": [ ],
              "t": [ ],
              "c": {  
                "gp": null,
                "dc": null
              }
            }
          ],
          "preferred_name": "Bacteria",
          "taxa": [ ]
        }
      }
    ]
  }
}

We specify the size to the number of CURIE's we expect, so the MESH identifier is truncated from the response. This should have been handled by our curie duplication merging prior to indexing, so their may be an error in our logic there. Going to investigate that next

[gaurav]

This issue should probably be moved to https://github.com/biothings/NodeNormalizationAPI/issues to keep all the NodeNorm issues together.