Tool for processing mapping clusters (boomer reports)

[cmungall]

Currently tightly coupled with boomer.

Added a datamodel for boomer results: https://github.com/INCATools/ontology-access-kit/blob/0a1d53cfe0732f8834e703c18683ceabbf366eb1/src/oaklib/datamodels/mapping_cluster_datamodel.yaml

CLI:

Usage: boomerang export [OPTIONS] INPUT_REPORT

  Exports mappings from a boomer report.

  boomerang export tests/input/boomer-example.md

Options:
  -L, --minimum-confidence FLOAT  Do not show mappings with lower confidence
  -H, --maximum-confidence FLOAT  Do not show mappings with higher confidence
  --help                          Show this message and exit.

Example:

boomerang export tests/input/boomer-example-larger.md  -H 0.6
# curie_map: {}
# license: UNSPECIFIED
# mapping_set_id: temp
subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	confidence
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:exactMatch	http://identifiers.org/mesh/D008202	MESH:D008202	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:closeMatch	http://identifiers.org/snomedct/400178008	SCTID:400178008	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:exactMatch	http://identifiers.org/snomedct/254836000	SCTID:254836000	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:exactMatch	http://purl.obolibrary.org/obo/NCIT_C8965	Lymphangioma	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:exactMatch	http://www.orpha.net/ORDO/Orphanet_2415	Orphanet:2415	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:exactMatch	http://linkedlifedata.com/resource/umls/id/CN201700	UMLS:CN201700	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0002013	lymphangioma	skos:exactMatch	http://purl.obolibrary.org/obo/DOID_1475	DOID:1475	semapv:CompositeMatching	0.5000000000000002
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:exactMatch	http://purl.obolibrary.org/obo/DOID_0090142	DOID:0090142	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:closeMatch	http://linkedlifedata.com/resource/umls/id/C0268616	UMLS:C0268616	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:exactMatch	http://purl.obolibrary.org/obo/NCIT_C129070	Cystathioninuria	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:closeMatch	http://linkedlifedata.com/resource/umls/id/C0220993	UMLS:C0220993	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:exactMatch	http://linkedlifedata.com/resource/umls/id/C3495552	UMLS:C3495552	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:exactMatch	http://identifiers.org/snomedct/13003007	SCTID:13003007	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:exactMatch	https://omim.org/entry/219500	OMIM:219500	semapv:CompositeMatching	0.5
http://purl.obolibrary.org/obo/MONDO_0009058	cystathioninuria	skos:exactMatch	http://www.orpha.net/ORDO/Orphanet_212	Cystathioninuria	semapv:CompositeMatching	0.5

note: cluster IDs pending INCATools/boomer#332

[codecov-commenter]

Codecov Report

Base: 80.03% // Head: 80.05% // Increases project coverage by +0.02% 🎉

Coverage data is based on head (0e4c4df) compared to base (24cd1d1).
Patch coverage: 79.59% of modified lines in pull request are covered.

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #440      +/-   ##
==========================================
+ Coverage   80.03%   80.05%   +0.02%     
==========================================
  Files         195      201       +6     
  Lines       21501    22235     +734     
==========================================
+ Hits        17208    17800     +592     
- Misses       4293     4435     +142     

Impacted Files	Coverage Δ
src/oaklib/datamodels/cross_ontology_diff.py	88.60% <ø> (ø)
src/oaklib/datamodels/lexical_index.py	96.81% <ø> (ø)
src/oaklib/datamodels/mapping_rules_datamodel.py	81.37% <ø> (ø)
src/oaklib/datamodels/obograph.py	88.48% <ø> (ø)
src/oaklib/datamodels/oxo.py	90.06% <ø> (ø)
src/oaklib/datamodels/search_datamodel.py	77.82% <ø> (ø)
.../oaklib/datamodels/summary_statistics_datamodel.py	84.02% <ø> (+0.23%)	⬆️
src/oaklib/datamodels/taxon_constraints.py	88.02% <ø> (ø)
src/oaklib/datamodels/validation_datamodel.py	82.17% <ø> (ø)
src/oaklib/datamodels/value_set_configuration.py	89.62% <ø> (ø)
... and 39 more

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[matentzn]

Will we switch the input of boomerang to the json file we discussed yesterday?

[cmungall]

Will we switch the input of boomerang to the json file we discussed yesterday?

Like everything in OAK, this has a linkml datamodel that can be exported in all the usual formats. All that would need to be done here is to follow the get_writer pattern in the main cli, @hrshdhgd can do this

[cmungall]

I added a first pass at INCATools/boomer#334

The format is a little custom but this is easily changed

For most ontologies where xref means exact we can do:

boomerang compare tests/input/boomer-fake-go-example.md -i tests/input/go-nucleus.db --reject-non-exact --promote-xref-to-exact -L 0.95

and get back:

type	info	confidence	predicate_id	subject_id	object_id
NEW	None	0.95	skos:exactMatch	GO:0005634	FAKE:1
REJECT	skos:closeMatch	0.95	skos:exactMatch	GO:0005634	Wikipedia:Cell_nucleus
OK	None	0.95	skos:exactMatch	GO:0005773	Wikipedia:Vacuole

if you store non-exacts in the source ontology then the output is a little more complex, and this is compounded by the fact that OAK doesn't yet auto-promote hacky xref annotations as used in mondo/go. I recommend these are switched to skos at source (cc @balhoff @hrshdhgd @matentzn).

If skos annotations are stored directly then just use the plain options, and any CONFLICT line will report a diff between predicate that needs to be enacted

next steps:

• export as sssom in separate accept/reject files
• export as kgcl?