CCF validation invalids picked up

[Shawn Tan]

@dosumis I'm using this ticket for examples that are picked up that I think are good: (still working on it, I've just gotten a version with labels for the aba stuff, so might do a better job here)

1. Uncurated entities get mapped to regional part of brain
   Currently the most amount of non_valids are coming from terms that are mapped to regional part of brain
   Regional part of brain cannot be part of a smaller unit. example:

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0007225	UBERON:0002616	lateral entorhinal cortex	regional part of brain	http://purl.obolibrary.org/obo/MBA_918	http://purl.obolibrary.org/obo/MBA_312

2. Developmental structure as part_of any part of the brain
   Example: mesomere 1 part_of midbrain (also part_of regional part of brain)
   In Uberon developmental parts are subclassof future brain rather than brain

3. Looks like a good one but I need to do more research (leave this with me, I'll figure this out):

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002714	UBERON:0002615	rubrospinal tract	ventral tegmental decussation	http://purl.obolibrary.org/obo/MBA_863	http://purl.obolibrary.org/obo/MBA_397

5. Should be overlap instead of part_of - esp prominent in spinal cord stuff
   Examples:

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002616	UBERON:0002707	regional part of brain	corticospinal tract	http://purl.obolibrary.org/obo/MBA_784	http://purl.obolibrary.org/obo/MBA_190
UBERON:0002272	UBERON:0001935	medial zone of hypothalamus	ventromedial nucleus of hypothalamus	http://purl.obolibrary.org/obo/MBA_467	http://purl.obolibrary.org/obo/MBA_693
UBERON:0002616	UBERON:0002291	regional part of brain	central canal of spinal cord	http://purl.obolibrary.org/obo/MBA_73	http://purl.obolibrary.org/obo/MBA_164

6a. Should be (I THINK) connected_to instead of part_of (will make sure this is not overlaps too, but I'm guessing lateral and posterior would be separate

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002736	UBERON:0002709	lateral nuclear group of thalamus	posterior nuclear complex of thalamus	http://purl.obolibrary.org/obo/MBA_138	http://purl.obolibrary.org/obo/MBA_1020

6b. Things that are not in the brain (I'm guessing its an issue of connected_to also)

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002616	UBERON:0001646	regional part of brain	abducens nerve	http://purl.obolibrary.org/obo/MBA_967	http://purl.obolibrary.org/obo/MBA_710
UBERON:0002616	UBERON:0001647	regional part of brain	facial nerve	http://purl.obolibrary.org/obo/MBA_967	http://purl.obolibrary.org/obo/MBA_798

[Shawn Tan]

1. CCF validation correcting a part_of to connected_to
   

2. CCF validation showing invalid due to uberon not having relation:
   MAYBE

-- | -- | -- | -- | -- | --
lateral zone of hypothalamus | zona incerta | http://purl.obolibrary.org/obo/MBA_290 | Hypothalamic lateral zone | http://purl.obolibrary.org/obo/MBA_797 | Zona incerta

[Chris Mungall]

Is there a quick summary of how to read these?

For the first one it seems there is an implicit rdfs:subClassOf between s and o? And 'user' is a user's mapping?

Regional part of brain cannot be part of a smaller unit

Which OWL axiom is this?

Is the root of this issue:

id: UBERON:0007225
name: lateral entorhinal cortex
...
is_a: UBERON:0000064 ! organ part

Which is a little odd - some regions are "organ part" some are "regional part of brain". I think we could do a search and replace on these just for structural consistency

[Shawn Tan]

Is there a quick summary of how to read these?

o is object and s is subject - so it looks for s part_of o (or subclass of, overlaps, connected to, develops from)
user_olabel/user_slabel is the mba mapping to the uberon term

In general I wouldn't bother looking too much into this for now - we have a new list of expert curated bridge that I'm working on to update the bridge file. After which we plan to re-run the CCF validation on that, so hopefully all these will be gone after that :)

[Chris Mungall]

I'm also thinking of running boomer on Uberon + ABAs which may overlap with this QC check

[David Osumi-Sutherland]

Is there a quick summary of how to read these?

The headers were designed for reporting on ASCT+B tables user_slabel and user_olabel = the names given to subject and object of the relationship in the tables. In our repurposing, these correspond to child and parent term in the structureGraph. I think these would be easier to read if the user_olabel and user_slabel had the form 'label ; id'

Note - invalid is an overstatement. All the reports test is for whether child --> parent in the structureGraph corresponds to a 'relationship' (asserted or inferred) between the Uberon mapping of child and the Uberon mapping of parent where that relationship might be subClassOf or an existential restriction on part_of, overlaps or connected_to. Maybe non-validated would be a more accurate term to use.

[David Osumi-Sutherland]

Working through some examples (just documenting - no need to reply)

Looks like this might be a genuine difference in definition and composition of zones between ABA and Uberon

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002272	UBERON:0001935	medial zone of hypothalamus	ventromedial nucleus of hypothalamus	http://purl.obolibrary.org/obo/MBA_467	http://purl.obolibrary.org/obo/MBA_693

---

This one could also be a genuine difference in how nuclei are grouped, this time by partitioning of the thalamus (or it could be that Uberon just didn't partition this nucleus.

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002736	UBERON:0002709	lateral nuclear group of thalamus	posterior nuclear complex of thalamus	http://purl.obolibrary.org/obo/MBA_138	http://purl.obolibrary.org/obo/MBA_1020

---

This one might be overlap:

o	s	olabel	slabel	user_olabel	user_slabel
UBERON:0002714	UBERON:0002615	rubrospinal tract	ventral tegmental decussation	http://purl.obolibrary.org/obo/MBA_863	http://purl.obolibrary.org/obo/MBA_397