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INCATools / boomer

Bayesian OWL ontology merging
https://incatools.github.io/boomer/
BSD 3-Clause "New" or "Revised" License
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Incoherent results in output.txt with equivalence triads #49

Closed cmungall closed 3 years ago

cmungall commented 4 years ago

triad.tsv:

X:1 Y:1 0.01    0.01    0.97    0.01
Y:1 Z:1 0.01    0.01    0.97    0.01
X:1 Z:1 0.2 0.2 0.01    0.59

empty.rdf:

prefix X: <http://purl.obolibrary.org/obo/X_>
prefix Y: <http://purl.obolibrary.org/obo/Y_>
prefix Z: <http://purl.obolibrary.org/obo/Z_>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
prefix owl: <http://www.w3.org/2002/07/owl#>

X:1 a owl:Class .

prefixes.yaml:

X: http://purl.obolibrary.org/obo/X_
Y: http://purl.obolibrary.org/obo/Y_
Z: http://purl.obolibrary.org/obo/Z_

run:

$ boomer --ptable triad.tsv --ontology empty.rdf --prefixes prefixes.yaml --runs 5 --window-count 2
2020.04.27 19:57:25 [INFO] org.monarchinitiative.boomer.Boom.evaluate:21:18 - Bin size: 3; Most probable: 0.97
2020.04.27 19:57:25 [INFO] org.monarchinitiative.boomer.Boom.evaluate:24:16 - Max possible joint probability: -0.5885511570517892
2020.04.27 19:57:26 [INFO] org.monarchinitiative.boomer.Boom.evaluateInOrder:39:20 - Found joint probability: -4.666088600957509
2020.04.27 19:57:26 [INFO] org.monarchinitiative.boomer.Boom.evaluateInOrder:39:20 - Found joint probability: -4.666088600957509
2020.04.27 19:57:26 [INFO] org.monarchinitiative.boomer.Boom.evaluateInOrder:39:20 - Found joint probability: -5.163262135555172
2020.04.27 19:57:26 [INFO] org.monarchinitiative.boomer.Boom.evaluateInOrder:39:20 - Found joint probability: -5.163262135555172
2020.04.27 19:57:26 [INFO] org.monarchinitiative.boomer.Boom.evaluateInOrder:39:20 - Found joint probability: -5.163262135555172
2020.04.27 19:57:26 [INFO] org.monarchinitiative.boomer.Main.$anonfun:42:34 - Most probable: -6.731742884949919
2020.04.27 19:57:27 [INFO] org.monarchinitiative.boomer.Main.$anonfun:57:34 - 5s

output.txt:

X:1 EquivalentTo Z:1    false
Y:1 EquivalentTo Z:1    true
X:1 EquivalentTo Y:1    true

this is incoherent as equivalence is symmetric, transitive

I think this is just an error in reporting, because we have

output.ofn:

# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)

SubClassOf(<http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/Y_1>)
SubClassOf(<http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/Z_1>)

# Class: <http://purl.obolibrary.org/obo/Y_1> (<http://purl.obolibrary.org/obo/Y_1>)

SubClassOf(<http://purl.obolibrary.org/obo/Y_1> <http://purl.obolibrary.org/obo/X_1>)
SubClassOf(<http://purl.obolibrary.org/obo/Y_1> <http://purl.obolibrary.org/obo/Z_1>)

# Class: <http://purl.obolibrary.org/obo/Z_1> (<http://purl.obolibrary.org/obo/Z_1>)

SubClassOf(<http://purl.obolibrary.org/obo/Z_1> <http://purl.obolibrary.org/obo/X_1>)
SubClassOf(<http://purl.obolibrary.org/obo/Z_1> <http://purl.obolibrary.org/obo/Y_1>)

When I run through robot reason -A EquivalentClass -i output.ofn -s true -o ... I get the expected

EquivalentClasses(<http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/Y_1> <http://purl.obolibrary.org/obo/Z_1>)

balhoff commented 4 years ago

Sorry, this is just very confusing output. The result for each mapping is the relation (either EquivalentTo, SubClassOf, SuperClassOf, etc.). The true and false is whether the selected relation had the highest prior probability. Hope I didn't waste too much of your time. I can just drop that, or change the text to something more explicit.