How to handle MeSH supplemental concepts that only map to an AllowedDescriptorQualifierPair

[dhimmel]

Some supplemental concept records (SCRs) in MeSH only have a preferredMappedTo whose predicate is a AllowedDescriptorQualifierPair rather than the usual TopicalDescriptor

For example, the SCR Disease Familial spinal arachnoiditis has preferredMappedTo to an AllowedDescriptorQualifierPair Arachnoiditis/congenital. So Arachnoiditis is the parent topical descriptor and congenital is the qualifier.

Currently, these edges are dropped:

nxontology-data/nxontology_data/mesh/mesh.py

Lines 200 to 202 in 33ea9e9

	except nxontology.exceptions.NodeNotFound:
	# meshv:AllowedDescriptorQualifierPair nodes like D014199Q000031 aren't included as nodes
	pass

Need to investigate whether any of these AllowedDescriptorQualifierPair parents would break our is-a / parent assumption. If they are consistent with a hierarchical conceptual relationship, then I'm thinking we just add an edge from Arachnoiditis to Familial spinal arachnoiditis with an edge property that for the congenital qualifier.

[dhimmel]

Here's how the implementation looks like in the exproted node-link formatted JSON.

First the node JSON (all normal here):

    {
      "mesh_id": "C531624",
      "mesh_class": "SCR_Disease",
      "mesh_uri": "http://id.nlm.nih.gov/mesh/2023/C531624",
      "mesh_label": "Familial spinal arachnoiditis",
      "mesh_date_created": "2010-08-25",
      "mesh_date_revised": "2016-07-19",
      "mesh_date_established": null,
      "mesh_frequency": 68.0,
      "mesh_description": "A hereditary form of arachnoiditis that may appear as a thick fibrous band on the spinal arachnoid membrane. It is characterized by adult onset SPASTIC PARAPARESIS with prominent radicular pain and patchy numbness. OMIM: 182950",
      "tree_numbers": null,
      "id": "C531624"
    },

Now the edge JSON:

    {
      "relationship_type": "preferredMappedTo",
      "parent_qualified_id": "D001100Q000151",
      "parent_qualifier_id": "Q000151",
      "source": "D001100",
      "target": "C531624"
    },

Note how parent_qualified_id is different than source, since source is based only on the parent descriptor ID (it strips out the qualifier id). You can access the qualifier in parent_qualifier_id.

Expand for code

curl --silent --location https://github.com/related-sciences/nxontology-data/raw/5ca8a27b611499fc42b5cc29c624a341911fb9d4/mesh_topical_descriptor_descendants.json.gz | gunzip | grep --context=10 "C531624"