Alignments: create new type of mapping to help with curations?

[sabrinatoro]

I am looking at the slurp file : https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/slurp/doid.tsv

Many of the terms in this list (suggested to be new terms in Mondo) already exist in Mondo. For example:

mondo_id	mondo_label	xref	xref_source	original_label	definition	parents
MONDO:0850393	intracranial berry aneurysm 1	DOID:0080964	MONDO:equivalentTo	intracranial berry aneurysm 1	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 7q11.2.	MONDO:0016483|MONDO:0000426
MONDO:0850394	intracranial berry aneurysm 2	DOID:0080965	MONDO:equivalentTo	intracranial berry aneurysm 2	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 19q13.	MONDO:0016483
MONDO:0850395	intracranial berry aneurysm 3	DOID:0080966	MONDO:equivalentTo	intracranial berry aneurysm 3	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 1p36.	MONDO:0016483|MONDO:0000426
MONDO:0850396	intracranial berry aneurysm 4	DOID:0080967	MONDO:equivalentTo	intracranial berry aneurysm 4	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 5p15.2-p14.3.	MONDO:0016483
MONDO:0850397	intracranial berry aneurysm 5	DOID:0080968	MONDO:equivalentTo	intracranial berry aneurysm 5	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome Xp22.	MONDO:0016483
MONDO:0850398	intracranial berry aneurysm 6	DOID:0080969	MONDO:equivalentTo	intracranial berry aneurysm 6	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 9p21.	MONDO:0016483
MONDO:0850399	intracranial berry aneurysm 7	DOID:0080970	MONDO:equivalentTo	intracranial berry aneurysm 7	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 11q24-q25.	MONDO:0016483
MONDO:0850400	intracranial berry aneurysm 8	DOID:0080971	MONDO:equivalentTo	intracranial berry aneurysm 8	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 14q23.	MONDO:0016483
MONDO:0850401	intracranial berry aneurysm 9	DOID:0080972	MONDO:equivalentTo	intracranial berry aneurysm 9	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 2q33.1.	MONDO:0016483
MONDO:0850402	intracranial berry aneurysm 10	DOID:0080973	MONDO:equivalentTo	intracranial berry aneurysm 10	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 8q12.1.	MONDO:0016483
MONDO:0850403	intracranial berry aneurysm 11	DOID:0080974	MONDO:equivalentTo	intracranial berry aneurysm 11	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 8p22.	MONDO:0016483
MONDO:0850404	intracranial berry aneurysm 12	DOID:0080975	MONDO:equivalentTo	intracranial berry aneurysm 12	An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and that has_material_basis_in heterozygous mutation in the THSD1 gene on chromosome 13q14.	MONDO:0016483

These are probably the same as:

Could we set up additional mapping rules or reports that could help or support curation? (so I don't have to manually check every 12 types of intracranial berry aneurysm to ensure they are the same in DO and Mondo; and the same with other terms)

Some ideas would be:

• mapping on OMIM x-ref (only omim x-ref).
• lex matching when the words are "mix up". ?

Note: if this work would take longer than me doing it manually, I can do it manually. But it might help us in the long term.

[sabrinatoro]

another example:

mondo_id	mondo_label	xref	xref_source	original_label
MONDO:0850061	nipah virus encephalitis	DOID:0050192	MONDO:equivalentTo	Nipah virus encephalitis

This term is probably the same as 'Nipah virus disease' (MONDO:0020499)

For this one, the exact synonym is: 'Nipah encephalitis' We decided to only match if all the words were in the label/synonym. However, if we could have a simple report with these "not exactly exact match for the potential new terms in the slurp file" that we can review, it would help

[matentzn]

intracranial berry aneurysm 12 aneurysm, intracranial berry, type 12

This should be doable.

Solution 1: Matching rules/synonymiser

1. "type ([0-9IXV])" should be rewritten to $1 (aneurysm, intracranial berry, type 12 - aneurysm, intracranial berry, 12)
2. commas should stripped (aneurysm intracranial berry 12)
3. Word order should be normalised (bag of words matching)

@hrshdhgd what do you think? Any other way we can go about this?

Solution 2: Preprocessing

If there is any flaw in my thinking above, there is an easy way to solve this ticket:

During preprocessing, declare OMIM xrefs in DOID as "exactMatch". That way the current matching infrastructure will work without any changes, as we already "match on skos:exactMatch".

[matentzn]

@hrshdhgd Example to start with:

http://purl.obolibrary.org/obo/MONDO_0007111         <skos:exactMatch rdf:resource="https://omim.org/entry/105800"/>
http://purl.obolibrary.org/obo/DOID_0080964         <skos:exactMatch rdf:resource="https://omim.org/entry/105800"/>

Why is the lexmatch pipeline not finding that MONDO_0007111 -exactMatch-> DOID_0080964?

[hrshdhgd]

DOID:0080964    intracranial berry aneurysm 1   skos:closeMatch MONDO:0007111   aneurysm, intracranial berry type 1 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:105800     

This is because lexmatch tags it as a skos:closeMatch in the mondo-sources-all-lexical.sssom.tsv file (not version controlled since it is too large).

[hrshdhgd]

Full mention

subject_id  subject_label   predicate_id    object_id   object_label    mapping_justification   mapping_tool    confidence  subject_match_field object_match_field  match_string    subject_preprocessing   object_preprocessing
DOID:0080964    intracranial berry aneurysm 1   skos:closeMatch MONDO:0007111   aneurysm, intracranial berry type 1 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:105800     
DOID:0080964    intracranial berry aneurysm 1   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:105800     
DOID:0080965    intracranial berry aneurysm 2   skos:closeMatch MONDO:0012053   aneurysm, intracranial berry, 2 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:608542     
DOID:0080965    intracranial berry aneurysm 2   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:608542     
DOID:0080966    intracranial berry aneurysm 3   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:609122     
DOID:0080966    intracranial berry aneurysm 3   skos:closeMatch MONDO:0012194   aneurysm, intracranial berry, 3 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:609122     
DOID:0080967    intracranial berry aneurysm 4   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:610213     
DOID:0080967    intracranial berry aneurysm 4   skos:closeMatch MONDO:0012443   aneurysm, intracranial berry, 4 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:610213     
DOID:0080968    intracranial berry aneurysm 5   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:300870     
DOID:0080968    intracranial berry aneurysm 5   skos:closeMatch MONDO:0010468   aneurysm, intracranial berry, 5 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:300870     
DOID:0080969    intracranial berry aneurysm 6   skos:closeMatch MONDO:0012752   aneurysm, intracranial berry, 6 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:611892     
DOID:0080969    intracranial berry aneurysm 6   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:611892     
DOID:0080970    intracranial berry aneurysm 7   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612161     
DOID:0080970    intracranial berry aneurysm 7   skos:closeMatch MONDO:0012810   aneurysm, intracranial berry, 7 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612161     
DOID:0080971    intracranial berry aneurysm 8   skos:closeMatch MONDO:0012811   aneurysm, intracranial berry, 8 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612162     
DOID:0080971    intracranial berry aneurysm 8   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612162     
DOID:0080972    intracranial berry aneurysm 9   skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612586     
DOID:0080972    intracranial berry aneurysm 9   skos:closeMatch MONDO:0012949   aneurysm, intracranial berry, 9 semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612586     
DOID:0080973    intracranial berry aneurysm 10  skos:closeMatch MONDO:0012950   aneurysm, intracranial berry, 10    semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612587     
DOID:0080973    intracranial berry aneurysm 10  skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:612587     
DOID:0080974    intracranial berry aneurysm 11  skos:closeMatch MONDO:0013654   aneurysm, intracranial berry, 11    semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:614252     
DOID:0080974    intracranial berry aneurysm 11  skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:614252     
DOID:0080975    intracranial berry aneurysm 12  skos:closeMatch Orphanet:231160 Familial cerebral saccular aneurysm semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:618734     
DOID:0080975    intracranial berry aneurysm 12  skos:closeMatch MONDO:0032891   aneurysm, intracranial berry, 12    semapv:LexicalMatching  oaklib  0.5 oio:hasDbXref   oio:hasDbXref   omim:618734     

[matentzn]

But the config says "exact": https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/config/mondo-match-rules.yaml#L42

Can you change this so that match on exact match is "exact"?

[hrshdhgd]

In tmp/mondo.sssom.tsv

subject_id  subject_label   predicate_id    object_id   object_label    mapping_justification
MONDO:0016483   intracranial berry aneurysm skos:exactMatch OMIMPS:105800       semapv:UnspecifiedMatching
MONDO:0007111   aneurysm, intracranial berry type 1 skos:exactMatch OMIM:105800     semapv:UnspecifiedMatching

The prefixes are different. Is that expected?

[hrshdhgd]

But the config says "exact": https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/config/mondo-match-rules.yaml#L42

That's because - oio:hasDbXref was commented out based on some discussion in the past. I'll uncomment it and run again to see what happens.

[matentzn]

No, they are both skos exaxt match. Don't use hasDbXref! Something is going wrong if not both sources have skos exact match!

[hrshdhgd]

Digging deeper...

These are parts of the merged.db.lexical.yaml which is the lexical_index of merged.db. I did a search for 105800 and these were what I found.

omimps:105800:
    term: omimps:105800
    relationships:
    - predicate: oio:hasDbXref
      element: DOID:0060228
      element_term: OMIMPS:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: MONDO:0016483
      element_term: OMIMPS:105800
      pipeline:
      - default
      synonymized: false

omim:105800:
    term: omim:105800
    relationships:
    - predicate: oio:hasDbXref
      element: DOID:0080964
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: MONDO:0007111
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: Orphanet:231160
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false

aneurysm, intracranial berry, 1:
    term: aneurysm, intracranial berry, 1
    relationships:
    - predicate: oio:hasRelatedSynonym
      element: MONDO:0007111
      element_term: aneurysm, intracranial berry, 1
      pipeline:
      - default
      synonymized: false
    - predicate: rdfs:label
      element: OMIM:105800
      element_term: aneurysm, intracranial berry, 1
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasExactSynonym
      element: OMIM:105800
      element_term: aneurysm, intracranial berry, 1
      pipeline:
      - default
      synonymized: false

aneurysmal subarachnoid hemorrhage, familial:
    term: aneurysmal subarachnoid hemorrhage, familial
    relationships:
    - predicate: oio:hasRelatedSynonym
      element: MONDO:0007111
      element_term: aneurysmal subarachnoid hemorrhage, familial
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasExactSynonym
      element: OMIM:105800
      element_term: aneurysmal subarachnoid hemorrhage, familial
      pipeline:
      - default
      synonymized: false

anib1:
    term: anib1
    relationships:
    - predicate: oio:hasExactSynonym
      element: OMIM:105800
      element_term: ANIB1
      pipeline:
      - default
      synonymized: false

And a quick search of DOID:0080964 revealed:

intracranial berry aneurysm 1:
    term: intracranial berry aneurysm 1
    relationships:
    - predicate: rdfs:label
      element: DOID:0080964
      element_term: intracranial berry aneurysm 1
      pipeline:
      - default
      synonymized: false

  omim:105800:
    term: omim:105800
    relationships:
    - predicate: oio:hasDbXref
      element: DOID:0080964
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: MONDO:0007111
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: Orphanet:231160
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false

Am I missing something? I do not see an exactMatch predicate for the rules to kick in. I only see oio:hasDbXref which is commented in the rules file.

[matentzn]

Well they should be there! The exact matches.. check the raw owl files going in before db state and see if they are in there.

[hrshdhgd]

merged.owl

<!-- http://purl.obolibrary.org/obo/MONDO_0007111 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0007111">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MONDO_0016483"/>
        <oboInOwl:hasDbXref>MESH:C566284</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>OMIM:105800</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>UMLS:C1862932</oboInOwl:hasDbXref>
        <oboInOwl:hasRelatedSynonym>aneurysm, intracranial berry, 1</oboInOwl:hasRelatedSynonym>
        <oboInOwl:hasRelatedSynonym>aneurysmal subarachnoid hemorrhage, familial</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id>MONDO:0007111</oboInOwl:id>
        <rdfs:label>aneurysm, intracranial berry type 1</rdfs:label>
        <skos:exactMatch rdf:resource="http://identifiers.org/mesh/C566284"/>
        <skos:exactMatch rdf:resource="http://linkedlifedata.com/resource/umls/id/C1862932"/>
        <skos:exactMatch rdf:resource="https://omim.org/entry/105800"/>
    </owl:Class>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
        <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/MONDO_0016483"/>
        <oboInOwl:source>DC-OMIM:105800</oboInOwl:source>
        <oboInOwl:source>OMIM:105800</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
        <owl:annotatedTarget>MESH:C566284</owl:annotatedTarget>
        <oboInOwl:source>MONDO:equivalentTo</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
        <owl:annotatedTarget>OMIM:105800</owl:annotatedTarget>
        <oboInOwl:source>MONDO:equivalentTo</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
        <owl:annotatedTarget>UMLS:C1862932</owl:annotatedTarget>
        <oboInOwl:source>MONDO:equivalentTo</oboInOwl:source>
        <oboInOwl:source>MONDO:ncbi_mim2gene_medline</oboInOwl:source>
        <oboInOwl:source>OMIM:105800</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
        <owl:annotatedTarget>aneurysm, intracranial berry, 1</owl:annotatedTarget>
        <oboInOwl:hasDbXref>MONDO:Lexical</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>OMIM:105800</oboInOwl:hasDbXref>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
        <owl:annotatedTarget>aneurysmal subarachnoid hemorrhage, familial</owl:annotatedTarget>
        <oboInOwl:hasDbXref>OMIM:105800</oboInOwl:hasDbXref>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2004/02/skos/core#exactMatch"/>
        <owl:annotatedTarget rdf:resource="http://identifiers.org/mesh/C566284"/>
        <sssom:mapping_justification rdf:resource="https://w3id.org/semapv/UnspecifiedMatching"/>
        <sssom:subject_label>aneurysm, intracranial berry type 1</sssom:subject_label>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2004/02/skos/core#exactMatch"/>
        <owl:annotatedTarget rdf:resource="http://linkedlifedata.com/resource/umls/id/C1862932"/>
        <sssom:mapping_justification rdf:resource="https://w3id.org/semapv/UnspecifiedMatching"/>
        <sssom:subject_label>aneurysm, intracranial berry type 1</sssom:subject_label>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0007111"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2004/02/skos/core#exactMatch"/>
        <owl:annotatedTarget rdf:resource="https://omim.org/entry/105800"/>
        <sssom:mapping_justification rdf:resource="https://w3id.org/semapv/UnspecifiedMatching"/>
        <sssom:object_label>aneurysm, intracranial berry, 1</sssom:object_label>
        <sssom:subject_label>aneurysm, intracranial berry type 1</sssom:subject_label>
    </owl:Axiom>

<!-- http://purl.obolibrary.org/obo/MONDO_0016483 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0016483">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MONDO_0003847"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MONDO_0005291"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MONDO_0015145"/>
        <obo:IAO_0000115>An intracranial aneurysm with a characteristic rounded shape; the most common form of cerebral aneurysm.</obo:IAO_0000115>
        <mondo:excluded_from_qc_check rdf:resource="http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql"/>
        <mondo:should_conform_to rdf:resource="http://purl.obolibrary.org/obo/mondo/patterns/OMIM_phenotypic_series.yaml"/>
        <oboInOwl:hasDbXref>DOID:0060228</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>HP:0007029</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>OMIMPS:105800</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>Orphanet:231160</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>SCTID:703226008</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>UMLS:CN230268</oboInOwl:hasDbXref>
        <oboInOwl:hasExactSynonym>aneurysm, intracranial berry</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>familial aneurysmal subarachnoid hemorrhage</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>familial berry aneurysm</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>familial intracranial saccular aneurysm</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>saccular cerebral aneurysm</oboInOwl:hasExactSynonym>
        <oboInOwl:hasRelatedSynonym>familial cerebral saccular aneurysm</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id>MONDO:0016483</oboInOwl:id>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mondo#ordo_disease"/>
        <rdfs:label>intracranial berry aneurysm</rdfs:label>
        <skos:exactMatch rdf:resource="http://identifiers.org/snomedct/703226008"/>
        <skos:exactMatch rdf:resource="http://linkedlifedata.com/resource/umls/id/CN230268"/>
        <skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/DOID_0060228"/>
        <skos:exactMatch rdf:resource="http://www.orpha.net/ORDO/Orphanet_231160"/>
        <skos:exactMatch rdf:resource="https://omim.org/phenotypicSeries/PS105800"/>
    </owl:Class>

    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0016483"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
        <owl:annotatedTarget>OMIMPS:105800</owl:annotatedTarget>
        <oboInOwl:source>MONDO:cjm</oboInOwl:source>
        <oboInOwl:source>MONDO:equivalentTo</oboInOwl:source>
    </owl:Axiom>

    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0016483"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2004/02/skos/core#exactMatch"/>
        <owl:annotatedTarget rdf:resource="https://omim.org/phenotypicSeries/PS105800"/>
        <sssom:mapping_justification rdf:resource="https://w3id.org/semapv/UnspecifiedMatching"/>
        <sssom:subject_label>intracranial berry aneurysm</sssom:subject_label>
    </owl:Axiom>

DOID_0080964

<!-- http://purl.obolibrary.org/obo/DOID_0080964 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_0080964">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_0050736"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_0060228"/>
        <obo:IAO_0000115>An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 7q11.2.</obo:IAO_0000115>
        <oboInOwl:hasDbXref>OMIM:105800</oboInOwl:hasDbXref>
        <rdfs:label>intracranial berry aneurysm 1</rdfs:label>
        <skos:exactMatch rdf:resource="https://omim.org/entry/105800"/>
    </owl:Class>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/DOID_0080964"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
        <owl:annotatedTarget>An intracranial berry aneurysm that is characterized by rupture of an intracranial aneurysm, an outpouching or sac-like widening of a cerebral artery, leads to a subarachnoid hemorrhage, a sudden-onset disease that can lead to severe disability and death and has been mapped to chromosome 7q11.2.</owl:annotatedTarget>
        <oboInOwl:hasDbXref>url:https://pubmed.ncbi.nlm.nih.gov/16736093/</oboInOwl:hasDbXref>
    </owl:Axiom>

[hrshdhgd]

Here's what the lexical index file shows:

omim:105800:
    term: omim:105800
    relationships:
    - predicate: oio:hasDbXref
      element: DOID:0080964
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: MONDO:0007111
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false
    - predicate: oio:hasDbXref
      element: Orphanet:231160
      element_term: OMIM:105800
      pipeline:
      - default
      synonymized: false

So if hasDbXref is uncommented in the match_rules.yaml, the skos:exactMatch should automatically appear (theoretically speaking).

[matentzn]

This still seems strange - we do not want to match on hasDbXref, just skos exactMatch. To me it seems that oak Lexmatch does not know how to take skos exact match into account when building the lexical index..