Single Exon node with the name `Exon`

[dkoslicki]

I might have mentioned it before, but there is only a single node with the category biolink:Exon: a node with the name Exon. I think either the ETL-ing of whatever KP has exon info is borked, or something else fishy might be going on. Otherwise, should this node (and the category) just be removed?

[ecwood]

This is the single biolink:Exon node in KG2 (checked in RTX-KG2.9.0pre):

{
  "iri": "http://www.ebi.ac.uk/efo/EFO_0004423",
  "synonym": [
    "exonic region"
  ],
  "category_label": "exon",
  "deprecated": "False",
  "name": "exon",
  "description": "An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule either after portions of a precursor RNA (introns) have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing.",
  "provided_by": "['infores:efo']",
  "id": "EFO:0004423",
  "category": "biolink:Exon",
  "update_date": "3630"
}

This node comes from EFO, which is in the multi ont load process. I would not be surprised if that ETL is "borked". I will take a look to see where this is coming from.

[ecwood]

Here is the term in efo.owl:

    <!-- http://www.ebi.ac.uk/efo/EFO_0004423 -->

    <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0004423">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                <owl:someValuesFrom rdf:resource="http://www.ebi.ac.uk/efo/EFO_0004422"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <obo:IAO_0000115>An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule either after portions of a precursor RNA (introns) have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing.</obo:IAO_0000115>
        <oboInOwl:hasDbXref>NCIt:C13231</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>SNOMEDCT:33091005</oboInOwl:hasDbXref>
        <oboInOwl:hasExactSynonym>exonic region</oboInOwl:hasExactSynonym>
        <rdfs:label>exon</rdfs:label>
    </owl:Class>

[ecwood]

EFO:0004423 is a subclass of material entity (BFO:0000040), along with several other similar terms. It looks like the same issue also shows up with a different subclass of material entity like enzyme:

{
  "iri": "http://purl.obolibrary.org/obo/OBI_0000427",
  "category_label": "protein",
  "deprecated": "False",
  "name": "enzyme",
  "description": "(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity); (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)",
  "provided_by": "['infores:efo', 'infores:genepio']",
  "id": "OBI:0000427",
  "category": "biolink:Protein",
  "update_date": "2024-02-21 01:39:56 GMT"
}

These are all of the subclasses of material entity:

Running

match (n) where n.iri in ["http://purl.obolibrary.org/obo/BTO_0002690", "http://www.ebi.ac.uk/efo/EFO_0004446", "http://purl.obolibrary.org/obo/BTO_0000214", "http://www.ebi.ac.uk/efo/EFO_0000324", "http://purl.obolibrary.org/obo/GO_0005575", "http://www.ebi.ac.uk/efo/EFO_0006794", "http://purl.obolibrary.org/obo/CHEBI_24431", "http://www.ebi.ac.uk/efo/EFO_0005066", "http://www.ebi.ac.uk/efo/EFO_0000469", "http://purl.obolibrary.org/obo/OBI_0000427", "http://www.ebi.ac.uk/efo/EFO_0004422", "http://www.ebi.ac.uk/efo/EFO_0004423", "http://purl.obolibrary.org/obo/SO_0000704", "http://www.ebi.ac.uk/efo/EFO_0004420", "http://www.ebi.ac.uk/efo/EFO_0000548", "http://www.ebi.ac.uk/efo/EFO_0005060", "http://purl.obolibrary.org/obo/OBI_0100026", "http://www.ebi.ac.uk/efo/EFO_0000635", "http://purl.obolibrary.org/obo/OBI_0000245", "http://purl.obolibrary.org/obo/MPATH_0", "http://www.ebi.ac.uk/efo/EFO_0000663", "http://purl.obolibrary.org/obo/OBI_0000181", "http://www.ebi.ac.uk/efo/EFO_0010579", "http://purl.obolibrary.org/obo/OBI_0100051", "http://www.ebi.ac.uk/efo/EFO_0004359", "http://purl.obolibrary.org/obo/BTO_0001384", "http://purl.obolibrary.org/obo/OBI_0100051"] return n.id, n.name, n.category, n.provided_by

on kg2endpoint-kg2-9-0.rtx.ai we get:

n.id	n.name	n.category	n.provided_by
"GO:0005575"	"cellular_component"	"biolink:CellularComponent"	"['infores:efo', 'infores:cl', 'infores:go-plus', 'infores:hpo', 'infores:mondo', 'infores:nbo', 'infores:pato', 'infores:pr', 'infores:uberon', 'infores:go']"
"CHEBI:24431"	"chemical entity"	"biolink:MolecularEntity"	"['infores:efo', 'infores:chebi', 'infores:cl', 'infores:disease-ontology', 'infores:foodon', 'infores:genepio', 'infores:go-plus', 'infores:hpo', 'infores:mondo', 'infores:nbo', 'infores:pato', 'infores:pr', 'infores:uberon']"
"OBI:0100026"	"organism"	"biolink:PhysicalEntity"	"['infores:efo', 'infores:foodon', 'infores:genepio', 'infores:go-plus', 'infores:pato', 'infores:pr', 'infores:ro']"
"SO:0000704"	"gene"	"biolink:Gene"	"['infores:efo', 'infores:disease-ontology', 'infores:go-plus', 'infores:mondo', 'infores:pr', 'infores:uberon']"
"OBI:0100051"	"specimen"	"biolink:PhysicalEntity"	"['infores:efo', 'infores:genepio']"
"EFO:0006794"	"cerebrospinal fluid biomarker measurement"	"biolink:InformationContentEntity"	"['infores:efo']"
"EFO:0000635"	"organism part"	"biolink:AnatomicalEntity"	"['infores:efo']"
"EFO:0000663"	"pool"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0005060"	"instrument part"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0005066"	"collection of material"	"biolink:MaterialSample"	"['infores:efo']"
"BTO:0000214"	"cell culture"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0004423"	"exon"	"biolink:Exon"	"['infores:efo']"
"EFO:0004422"	"exome"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0004420"	"genome"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0004446"	"biological macromolecule"	"biolink:MolecularEntity"	"['infores:efo']"
"EFO:0000324"	"cell type"	"biolink:Cell"	"['infores:efo']"
"EFO:0000548"	"instrument"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0000469"	"environmental factor"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0010579"	"proteome"	"biolink:PhysicalEntity"	"['infores:efo']"
"OBI:0000245"	"organization"	"biolink:PhysicalEntity"	"['infores:efo', 'infores:foodon', 'infores:genepio']"
"MPATH:0"	"pathological entity"	"biolink:BiologicalEntity"	"['infores:efo', 'infores:genepio', 'infores:hpo']"
"OBI:0000427"	"enzyme"	"biolink:Protein"	"['infores:efo', 'infores:genepio']"
"BTO:0001384"	"tissue culture"	"biolink:PhysicalEntity"	"['infores:efo']"
"EFO:0004359"	"telomere"	"biolink:PhysicalEntity"	"['infores:efo']"
"OBI:0000181"	"population"	"biolink:PhysicalEntity"	"['infores:efo', 'infores:genepio']"
"BTO:0002690"	"biofilm"	"biolink:PhysicalEntity"	"['infores:efo']"

Many of these seem to be problematic.