Should fissures/sulcus/incisure be material or immaterial?

[shawntanzk]

Related to https://github.com/obophenotype/uberon/pull/2633

Thanks to @bvarner-ebi for bringing this up

Currently it is unclear in uberon if fissures/sulcus/incisure should be material or immaterial - do they refer to the fold itself or do they refer to the space

Currently there are examples of both. Examples:

immaterial: http://purl.obolibrary.org/obo/UBERON_0014466 http://purl.obolibrary.org/obo/UBERON_0000093

material: terms under surface groove(http://purl.obolibrary.org/obo/UBERON_0006846): http://purl.obolibrary.org/obo/UBERON_0005412 http://purl.obolibrary.org/obo/UBERON_0005478

Need input on this @cmungall & @dosumis

[shawntanzk]

From UBERON call:

In Allen Brain Atlas, it is not "represented" in the atlas - as in there is the term, but not mapped on the atlas. This should (at least in my mind) be immaterial. See examples by @patrick-lloyd-ray

However, @cmungall did mention that there is utility of being in the material branch as that is more used by people.

My take: We follow atlas and make all the above as immaterial unless we have a use case for making it material

Plan: Will make a go and moving them all to immaterial and see if uberon breaks and figure out from there

[shawntanzk]

Using the following in ubergraph to find all material terms with sulcus, fissure, incisure in uberon:

SPARQL query

```SPARQL # adding prefixes used prefix owl: prefix rdfs: prefix IAO: prefix BFO: # selecting only unique instances of the three variables SELECT DISTINCT ?entity ?label WHERE { # the variable label is a rdfs:label VALUES ?property { rdfs:label } # only look for uberon terms ?entity rdfs:isDefinedBy . # defining the order of variables in the triple ?entity ?property ?label . # entity must be material ?entity rdfs:subClassOf BFO:0000040 # filtering out triples where the variable label has sulcus in it FILTER(contains(STR(?label), "sulcus")||contains(STR(?label), "incisure")||contains(STR(?label), "fissure")) } # arrange report by entity variable ORDER BY ?entity ```

Results in the following

Table of material sulcus, incisure, fissure

entity | label -- | -- http://purl.obolibrary.org/obo/UBERON_0001819 | palpebral fissure http://purl.obolibrary.org/obo/UBERON_0005412 | optic fissure http://purl.obolibrary.org/obo/UBERON_0005478 | sulcus limitans of neural tube http://purl.obolibrary.org/obo/UBERON_0005480 | superior orbital fissure http://purl.obolibrary.org/obo/UBERON_0005489 | anterior interventricular sulcus http://purl.obolibrary.org/obo/UBERON_0005490 | posterior interventricular sulcus http://purl.obolibrary.org/obo/UBERON_0006271 | orbital fissure http://purl.obolibrary.org/obo/UBERON_0009570 | spinal cord sulcus limitans http://purl.obolibrary.org/obo/UBERON_0009576 | medulla oblongata sulcus limitans http://purl.obolibrary.org/obo/UBERON_0009577 | metencephalon sulcus limitans http://purl.obolibrary.org/obo/UBERON_0009578 | myelencephalon sulcus limitans http://purl.obolibrary.org/obo/UBERON_0014628 | vestibular fissure of the cochlear canal http://purl.obolibrary.org/obo/UBERON_0014870 | inferior orbital fissure http://purl.obolibrary.org/obo/UBERON_0018339 | metotic fissure http://purl.obolibrary.org/obo/UBERON_0036014 | gluteal sulcus http://purl.obolibrary.org/obo/UBERON_0036212 | intertragic incisure http://purl.obolibrary.org/obo/UBERON_2000305 | ventral sulcus http://purl.obolibrary.org/obo/UBERON_2000589 | sulcus ypsiloniformis http://purl.obolibrary.org/obo/UBERON_3000803 | sulcus articularis lateralis http://purl.obolibrary.org/obo/UBERON_3000804 | sulcus articularis medialis http://purl.obolibrary.org/obo/UBERON_3000844 | sulcus longitudinalis http://purl.obolibrary.org/obo/UBERON_3000906 | sulcus pro musculo extensori cruris brevis http://purl.obolibrary.org/obo/UBERON_3000908 | sulcus distalis ossis cruris http://purl.obolibrary.org/obo/UBERON_3000909 | sulcus proximalis ossis cruris http://purl.obolibrary.org/obo/UBERON_3010829 | sulcus intermedius

[shawntanzk]

missed groove - are they material or immaterial? I personally would like it to all be immaterial, but there's also a lot of part_of stuff with material that we need to deal with.

I see how groove can be considered material (as it can represent the fold itself rather than the space, but if we want consistency with the rest, making it immaterial is ALOT easier)

[shawntanzk]

Groove that are material:

entity | label -- | -- http://purl.obolibrary.org/obo/UBERON_0004056 | primitive groove http://purl.obolibrary.org/obo/UBERON_0005061 | neural groove http://purl.obolibrary.org/obo/UBERON_0005455 | interventricular groove http://purl.obolibrary.org/obo/UBERON_0006212 | bulbo-ventricular groove http://purl.obolibrary.org/obo/UBERON_0006257 | laryngotracheal groove http://purl.obolibrary.org/obo/UBERON_0006266 | nasolacrimal groove http://purl.obolibrary.org/obo/UBERON_0006846 | surface groove http://purl.obolibrary.org/obo/UBERON_0010229 | ruminant esophageal groove http://purl.obolibrary.org/obo/UBERON_0013241 | embryonic urethral groove http://purl.obolibrary.org/obo/UBERON_0018314 | choanal groove http://purl.obolibrary.org/obo/UBERON_3000785 | trochlear groove of humerus http://purl.obolibrary.org/obo/UBERON_3010175 | circumferential groove http://purl.obolibrary.org/obo/UBERON_3010229 | costal grooves http://purl.obolibrary.org/obo/UBERON_3010235 | nuchal groove http://purl.obolibrary.org/obo/UBERON_3010239 | subocular groove http://purl.obolibrary.org/obo/UBERON_3010242 | nasolabial groove

[ghost]

Based on Uberon's text definitions invoking "mass" to differentiate material from immaterial anatomical entities, I propose groove, fissure, sulcus, etc are immaterial.

[shawntanzk]

41 terms to deal with, will make plans on this google sheets and work from there https://docs.google.com/spreadsheets/d/1pLezAT_LHJUA5JIxszNnRdodeDwC8t7GWHUZ4xHJ0Kw/edit?usp=sharing Probably will take awhile given they need to be manually looked and axioms to material stuff need to be changed accordingly

[shawntanzk]

just centralising stuff from https://github.com/obophenotype/uberon/pull/2689: 1) material entity and immaterial entity are not disjoint which feels like they should 2) immaterial anatomical entity in uberon does not seem to be subclass_of immaterial entity in uberon, but in OLS it seems to be, not sure why 3) http://purl.obolibrary.org/obo/UBERON_0013118 sulcus of brain seems to be both immaterial and material (see horribly complicated graph showing route from sulcus of brain to both material and immaterial anatomical entity

[shawntanzk]

More thoughts: Can an immaterial anatomical entity be part of a material anatomical entity? Saying something like a ventricle is part of the brain seems to make sense to me, yet that is immaterial being part of material, perhaps this is the reason there isn't a disjoint? but modelling wise how are the boundaries drawn etc? There are currently 111 terms (accordingly to ubergraph) that are part of both material and immaterial anatomical entities (though nothing is both a subclass_of both)

Answer: According to Barry Smtih - immaterial can be part of material, not a problem. other way around should be located

[cmungall]

Yes immaterial can be part of material, but not the other way around.

Debugging disjointness is one of the few times you want to omit part-ofs in graph displays - if in your diagram you ignore the blue edges it is consistent