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Update bridging relations in cross-species bridges #3466

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merged 4 commits into from
Jan 30, 2025
Merged

Update bridging relations in cross-species bridges #3466

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aefc79a
Use 'in_taxon' as the main cross-species bridging relation.
gouttegd Jan 23, 2025
3fc08d1
Unfold composite ontologies over 'in taxon'.
gouttegd Jan 23, 2025
3313df2
Import RO:0002012 (occurrent part of).
gouttegd Jan 23, 2025
8ffcbd4
Update documentation.
gouttegd Jan 23, 2025
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6 changes: 3 additions & 3 deletions docs/bridges.md
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Expand Up @@ -8,14 +8,14 @@ Uberon term and a term from the foreign ontology.
For example, the `uberon-bridge-to-zfa` bridge contains axioms such as
this one:

> ZFA:0001262 EquivalentTo: UBERON:0005564 and (BFO:0000050 some NCBITaxon:7954)
> ZFA:0001262 EquivalentTo: UBERON:0005564 and (RO:0002162 some NCBITaxon:7954)

which states that ZFA’s [gonad
primordium](http://purl.obolibrary.org/obo/ZFA_0001262) (ZFA:0001262) is
equivalent to a Uberon’s [gonad
primordium](http://purl.obolibrary.org/obo/UBERON_0005564)
(UBERON:0005564) that is [part
of](http://purl.obolibrary.org/obo/BFO_0000050) a
(UBERON:0005564) that is [in
taxon](http://purl.obolibrary.org/obo/RO_0002162) some
[Danio](http://purl.obolibrary.org/obo/NCBITaxon_7954) (NCBITaxon:7954).

Such a bridge may be used by anyone who wants to merge Uberon and ZFA to
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4 changes: 2 additions & 2 deletions docs/combined_multispecies.md
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Expand Up @@ -113,7 +113,7 @@ that `collected-drosophila` contains the following axiom (provided by the
bridge between Uberon and FBbt):

```
FBbt:00004865 EquivalentTo: UBERON:0000992 and (part_of some NCBITaxon:7227)
FBbt:00004865 EquivalentTo: UBERON:0000992 and (in_taxon some NCBITaxon:7227)
```

(`NCBITaxon:7227` being the identifier for the _Drosophila melanogaster_
Expand All @@ -132,7 +132,7 @@ FBbt:00004911 SubClassOf: continuous_with some FBbt:00004865
gets rewritten as

```
FBbt:00004911 SubClassOf: continous_with some (UBERON:00009992 and (part_of some NCBITaxon:7227))
FBbt:00004911 SubClassOf: continous_with some (UBERON:00009992 and (in_taxon some NCBITaxon:7227))
```

The figure below illustrates the resulting differences between a
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3 changes: 1 addition & 2 deletions src/ontology/config/taxa.yaml
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@@ -1,8 +1,7 @@
defaults:
compositing:
unfold_over:
- BFO:0000050
- BFO:0000066
- RO:0002162
species:
- taxon_id: NCBITaxon:9606
label: human
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1 change: 1 addition & 0 deletions src/ontology/imports/ro_terms.txt
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@@ -1,4 +1,5 @@
BFO:0000050
RO:0002012
RO:0002202
RO:0002158
RO:0002476
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10 changes: 8 additions & 2 deletions src/scripts/taxa.py
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Expand Up @@ -65,11 +65,17 @@ def generate_bridging_rules(f, taxa):
f.write(f"""
[{name}-uberon] subject=={prefix}:* object==UBERON:* {{
predicate==* -> annotate(%{{subject_id}}, IAO:0000589, "%{{object_label}} ({label})");
predicate==semapv:crossSpeciesExactMatch -> create_axiom("%subject_id EquivalentTo: %object_id and (%TAXREL some {taxon_id})");
predicate==semapv:crossSpeciesExactMatch -> {{
create_axiom("%subject_id EquivalentTo: %object_id and (RO:0002162 some {taxon_id})");
create_axiom("%subject_id SubClassOf: %TAXREL some {taxon_id}");
}}
}}
[{name}-cl] subject=={prefix}:* object==CL:* {{
predicate==* -> annotate(%{{subject_id}}, IAO:0000589, "%{{object_label}} ({label})");
predicate==semapv:crossSpeciesExactMatch -> create_axiom("%subject_id EquivalentTo: %object_id and (%TAXREL some {taxon_id})");
predicate==semapv:crossSpeciesExactMatch -> {{
create_axiom("%subject_id EquivalentTo: %object_id and (RO:0002162 some {taxon_id})");
create_axiom("%subject_id SubClassOf: %TAXREL some {taxon_id}");
}}
}}
""")

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