Bronchomotor model contains non UBERON/ILX terms.

[dbrnz]

My understanding is that only UBERON and ILX terms are to be used for connectivity model annotation and that part of the August QC process was to ensure that this was the case.

---

[tgbugs]

We switched out all the non Uberon/ILX terms that were used for regions and layers, but we explicitly did not switch out the identifiers used for materials, which is why there are lingering FMA ids. This will be addressed in the next release.

[dbrnz]

In which case why are FMA terms appearing for region/layer ids, as shown above??

[tgbugs]

In both cases the wall is appearing as a layer (region is on the bottom), and the layer was specified as being composed of a material and we walk up the partonomy and find the ontology id attached to the material, or the lyph referenced a material as the id for a layer and a new layer was constructed using the material as the template.

[dbrnz]

Or turning the question around, why are material identifiers appearing in nodes of the simplified path? Should they be filtered out??

[tgbugs]

They are appearing because they are the identifier that winds up being associated with the layer because of how the layer is specified. This particular case is a bit tricky because there is some confusion between whether the trachea is just the material biological part or whether it also includes the air that passes through it. In the ApiNATOMY model @bdebono uses trachea to refer to both together, but in uberon it is usually just the material portion. As a result, in the ApiNATOMY model the wall of the trachea was given an additional identifier (which FMA happened to already have). Another way to model it would be to use the id for trachea as the id for the layer(s) and create a new id for the air + trachea region. In either case the only thing we really care about is the trachea, but we can't filter out the layer ids because in some cases they are necessary.

[memartone]

Let us discuss this Tom on Thursday. I don't understand why the materials are there either. We should simplify.

[bdebono]

A lyph will contain layers that includes (i) materials of the wall conduit, as well as (ii) the material (typically in the innermost layer) of the fluid conveyed. This approach is well documented and applies to blood vessels, airways, digestive tract, etc.

All the best,

Bernard

On Mon, 19 Sept 2022 at 15:51, Maryann E. Martone @.***> wrote:

Let us discuss this Tom on Thursday. I don't understand why the materials are there either. We should simplify.

— Reply to this email directly, view it on GitHub https://github.com/open-physiology/apinatomy-models/issues/26#issuecomment-1251476479, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGMRLFDJT7G6ONRZFSNHKDV7C74FANCNFSM6AAAAAAQOYUALQ . You are receiving this because you were mentioned.Message ID: @.***>

[memartone]

But do they matter for the connectivity visualization? I don't think so.

[memartone]

What about Ardell 6? Was that problem resolved?

[tgbugs]

In some cases materials might matter for visualization, e.g. the layers of the stomach, or sometime they might not, e.g. air.

[memartone]

But the visualization can be done whether or not it is a material, can it not? Or is the material designation essential for handling layers?

[tgbugs]

The material designation is essential for how ApiNATOMY generates layers along longitudinal structures. For many models it is required to be able to have the correct visualization, and without it it would be impossible for a model author to create and maintain the model because the cartesian product between regions and materials would be too large to maintain as explicit layers.

[tgbugs]

One set of replacements.

FMA:64182   ILX:0738326
FMA:7470    ILX:0793684
FMA:67480   ILX:0793764
FMA:74655   ILX:0793765
FMA:62792   ILX:0775392

[tgbugs]

for bolew we have made these changes

FMA:64182   ILX:0738326
FMA:7470    ILX:0793684
FMA:54807   UBERON:0005020
FMA:4668    UBERON:0000378
FMA:55112   UBERON:0001742