Stomatogastric ganglion crab lobster

[stevewds]

Hi -

Here we add parts of the stomatogastric nervous system of crabs and lobsters.

1. We added a new "stomatogastric nervous system" term to cover both crabs and lobsters and insects. We updated the old term "insect stomatogastric nervous system" to be "part of" the stomatogastric nervous system.

2. We added some 14 parts of the stomatogastric nervous system of crabs and lobsters.

We discussed these changes at the November Uberon meeting.

Thanks
Dre and Steve

[stevewds]

Requesting @rays22 as a reviewer as discussed in the November meeting.

Best wishes
Steve

[rays22]

You need add your terms by editing the file uberon/src/ontology/uderon-edit.obo. The uberon.obo file will be automatically updated at the time of the next public release of Uberon. (FYI: The documentation incorrectly states that you edit the uberon-edit.owl file.)
Actions:

1. Undo your changes to uberon.obo.
2. Add your new terms to uberon/src/ontology/uderon-edit.obo.
3. I am not sure if the part_of relationships that you used is appropriate for the relationship between and the insect stomatogastric nervous system and the new stomatogastric nervous system. I think it should be a sub-class (is_a) relationship, i.e. the insect stomatogastric nervous system is_a stomatogastic nervous system.

id: UBERON:6005096
name: insect stomatogastric nervous system
...
relationship: part_of UBERON:8910000 ! stomatogastic nervous system

[stevevanhooser]

Thanks @rays22, revised as requested

Best
Steve

[rays22]

There are several non-standard characters in the uberon-edit.obo file. Please, remove them.
I would like to check the inferred relationships between the existing and the newly added terms, but Protege fails to open uberon-edit.obo from this github branch.
The error message in Protege is org.xml.sax.SAXParseException. Could the failure of Protege to parse uberon-edit.obo be related to the non-standard characters in the file?

[stevevanhooser]

@rays22 , sorry for that, I think I have removed them all. (I don't have a "special character detector" program but I saw the ones above.)

[rays22]

1. Fix the syntax for SubClass assertion (and typo in label).
   id: UBERON:6005096
   ...
   -relationship: is_a UBERON:8910000 ! stomatogastic nervous system

• correctly:

is_a: UBERON:8910000 ! stomatogastric nervous system

Fix syntax for SubClass assertion.

2. Use unique IDs. UBERON:8910013 has been used twice.

3. Fix "synonym" syntax (at several places).

e.g.

from synonym: "STG" to

synonym: "STG" EXACT []

[stevevanhooser]

Thanks @rays22, fixed and updated

[stevevanhooser]

Thanks @rays22 .

I'm a little confused. I've opened this in protoge, and I see it as a subclass, but I may not be viewing it the same way that you are. Sorry for my newbie issues!

Here if I'm looking at insect stomatogastric nervous system in Protoge it says it "is a some stomatogastric nervous system"

[rays22]

Thanks @rays22 .

I'm a little confused. I've opened this in protoge, and I see it as a subclass, but I may not be viewing it the same way that you are. Sorry for my newbie issues!

Here if I'm looking at insect stomatogastric nervous system in Protoge it says it "is a some stomatogastric nervous system"

It should look like this:

1. The insect somatogastric nervous system should be a branch of the somatogastrcic nervous system in the Class Hierarchy (left arrow).
2. The is_a some 'somatogastric nervous system' is a slightly but significantly different axiom from what we want here (right arrow).

[stevevanhooser]

Thanks Ray. Do you know how I should fix it? I'm not sure which language the .obo file is.

[rays22]

Thanks Ray. Do you know how I should fix it? I'm not sure which language the .obo file is.

You can replace line 219797 with my suggested fix. (You might be able to apply the suggested change directly here in the PR .

https://github.com/obophenotype/uberon/pull/3445/files#r1889024567

[stevevanhooser]

Ah, got it. Sorry, I didn't realize the word "relationship" messed it all up. It's now fixed and looks the same for me as it does for you in Protoge

Thanks
Steve

[rays22]

Sorry, I have some more (hopefully final) comments. We are getting there ... 😃

[rays22]

Suggested change

	relationship: part_of UBERON:8910000 ! stomatogastric nervous system
	relationship: part_of UBERON:8910001 ! stomatogastric ganglion
	relationship: part_of UBERON:8910001 ! stomatogastric ganglion

Keep only one of the two axioms.

• Explanation:
  If the stomatogastric ganglion is part of the stomatogastric nervous system, and another anatomical entity is part of the stomatogastric ganglion, then it is redundant to assert that the anatomical entity is also part of the stomatogastric nervous system. (The part of relationship is transitive.) Multiple classifications chains resulting from redundant assertions make the ontology difficult to edit and maintain in the long run.

[stevevanhooser]

This is an interesting question we should unpack further. Many of these nerves are partially comprised of processes that originate from the stomatogastric ganglion, but then they extend far outside the ganglion around other parts of the stomatogastric nervous system. If you cut out the stomatogastric ganglion, many of these processes would still be there and would still be part of the stomatogastric nervous system.

Is there a different way we should capture the relationship?

This comment is similar for the other cases...

[rays22]

This is an interesting question we should unpack further. Many of these nerves are partially comprised of processes that originate from the stomatogastric ganglion, but then they extend far outside the ganglion around other parts of the stomatogastric nervous system. If you cut out the stomatogastric ganglion, many of these processes would still be there and would still be part of the stomatogastric nervous system.

Is there a different way we should capture the relationship?

This comment is similar for the other cases...

I see. There is the RO:0002131 overlaps relationship that might capture this.

[rays22]

Suggested change

	relationship: part_of UBERON:8910000 ! stomatogastric nervous system
	relationship: part_of UBERON:8910001 ! stomatogastric ganglion
	relationship: part_of UBERON:8910001 ! stomatogastric ganglion

[rays22]

Suggested change

	relationship: part_of UBERON:8910000 ! stomatogastric nervous system
	relationship: part_of UBERON:8910001 ! stomatogastric ganglion
	relationship: part_of UBERON:8910001 ! stomatogastric ganglion

[stevevanhooser]

Yes, overlaps works. Changed!

[rays22]

Looks good.