Unsatisfiable classes introduced by phenoscape-ext-zfa-bridge

[balhoff]

This ontology has 10 unsatisfiable classes (I haven't been able to get an explanation from Protege, but phenoscape-ext need not be included):

Prefix(owl:=http://www.w3.org/2002/07/owl#) Prefix(rdf:=http://www.w3.org/1999/02/22-rdf-syntax-ns#) Prefix(xml:=http://www.w3.org/XML/1998/namespace) Prefix(xsd:=http://www.w3.org/2001/XMLSchema#) Prefix(rdfs:=http://www.w3.org/2000/01/rdf-schema#)

Ontology(http://www.semanticweb.org/ontologies/2012/11/untitled-ontology-168 Import(http://purl.obolibrary.org/obo/zfa.owl) Import(http://purl.obolibrary.org/obo/uberon/merged.owl) Import(http://purl.obolibrary.org/obo/uberon/bridge/uberon-ext-bridge-to-zfa.owl) )

[cmungall]

We have a separate check for core - http://build.berkeleybop.org/job/check-uberon-zfa/

But not yet for ext. Multi-ontology combinatorics.. this will be easier when the ext/core distinction becomes purely editorial..

In the meantime we should have a separate check that runs. Will leave this open til this is done and these 10 are reolved. If the URIs are handy can you paste them in here?

[balhoff]

http://purl.obolibrary.org/obo/ZFA_0000467 anguloarticular http://purl.obolibrary.org/obo/ZFA_0001592 claustrum bone http://purl.obolibrary.org/obo/ZFA_0005298 cranial lymph vessel http://purl.obolibrary.org/obo/ZFA_0005108 facial lymphatic vessel http://purl.obolibrary.org/obo/ZFA_0001406 kinethmoid bone http://purl.obolibrary.org/obo/ZFA_0001601 manubrium http://purl.obolibrary.org/obo/ZFA_0001171 os suspensorium http://purl.obolibrary.org/obo/ZFA_0001599 os suspensorium medial flange http://purl.obolibrary.org/obo/ZFA_0001630 perichondral bone http://purl.obolibrary.org/obo/ZFA_0000698 tripus

[balhoff]

This is producing crazy results in the Phenoscape RDF KB.

[cmungall]

I thought this was actually resolved recently through relaxation of some disjointness axioms and fixes in ZFA. I can't seem to reproduce this using Elk.

See: edit/phenoscape-ext-plus-zfa-READONLY.owl in the phenoscape svn

[balhoff]

Maybe it's not inconsistent anymore, but I am finding that these classes are subclasses of "pinhole eye" (for example) in my KB, resulting in some weird query results. I am having a really hard time pinning down where this inference happens, however. But it struck me that it is the same list of classes. I'll continue investigating.

[balhoff]

Add an import of http://purl.obolibrary.org/obo/uberon/bridge/uberon-ext-bridge-to-zfa.owl to phenoscape-ext-plus-zfa-READONLY.owl and these classes will be unsatisfiable.

[cmungall]

OK, thanks. The pipeline now detects these. May take a while to fix - if we're to retain the disjoints then ZFA may have to change. For you, removing all disjointness axioms should solve

[cmungall]

I think this line in tao-obsoletions was largely to blame:

[Term]
id: TAO:0001637 ! replacement bone
is_obsolete: true
replaced_by: UBERON:0004763 ! endochondral bone tissue

I'm changing this to:

[Term]
id: TAO:0001637 ! replacement bone
is_obsolete: true
replaced_by: UBERON:0012075 ! replacement bone

and rebuilding the equivs.

Note that VSAO opted not to have a 'replacement bone' term, but this omission was never coordinated with ZFA which retains it. We keep it in uberon until this is resolved.

Hopefully this should fix the majority of them...

For the really gory details see this explanation:

Basically uberon allows bone elements to be classified as both endochondral and intramembranous (some bones are composed of both tissue types), but forces the tissue types to be disjoint.

[cmungall]

Down to 3, hurrah!

UNSAT: ZFA:0005573 'zonule'
UNSAT: ZFA:0005298 'cranial lymph vessel'
UNSAT: ZFA:0005108 'facial lymphatic vessel'

[cmungall]

the culprit:

[Term]
id: TAO:0001682 ! ligament
is_obsolete: true
replaced_by: UBERON:0000211 ! ligament
replaced_by: UBERON:0008846 ! skeletal ligament

[cmungall]

and the last two:

Source of this issue:

[Term]
id: ZFA:0005249
name: vasculature
namespace: zebrafish_anatomy
def: "Is an interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism." [ZFIN:curator]
xref: TAO:0001079 ! blood vasculature
xref: TAO:0005249 ! vasculature
xref: ZFIN:ZDB-ANAT-091221-27
is_a: ZFA:0001488  ! multi-tissue structure
relationship: end ZFS:0000044 ! Adult
relationship: part_of ZFA:0000010 ! cardiovascular system
relationship: start ZFS:0000027 ! Segmentation:20-25 somites

We are still reliant on ZFA-maintained xrefs for transitively connecting to non-core uberon classes. Solution: we take over management of these within core.