hindgut contraction parentage

[gocentral]

Look at "hindgut contraction" (GO:0043133). Instead of being an aunt/uncle to "intestine smooth muscle contraction" (GO:0014827), it seems like GO:0043133 should be a child of GO:0014827.

Reported by: slaulederkind

Original Ticket: geneontology/ontology-requests/11590

[gocentral]

• labels: --> Other term-related request
• assigned_to: Stan Laulederkind --> Tanya Berardini

Original comment by: tberardini

[gocentral]

Hi Stan,

In UBERON, hindgut is not is_a intestine but rather is a sibling, they're both child terms of 'subdivision of digestive tract'. Our term placement for the GO term is consistent with this structure. If you think the the UBERON structure should be fixed, let's do that and then GO will change to reflect that base structure.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

Hi Stan,

Following up on this issue. I need some feedback.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

In UBERON "left colon" is both a child term and a great, great grandchild term of "hindgut". Meanwhile "left colon" is also great grandchild of "intestine", a sibling of "hindgut". With that kind of logic all over that branch, maybe someone involved with UBERON can shed some light on the apparent conundrum. In anticipation of some kind of "derives from" versus "part of" explanation, just retract my request.

Original comment by: slaulederkind

[gocentral]

• assigned_to: Tanya Berardini --> Chris Mungall

Original comment by: tberardini

[gocentral]

I'm going to reassign this to Chris, just in case there's a quick fix that I'm not seeing.

Chris, over to you for comment, please.

Original comment by: tberardini

[gocentral]

hindgut and intestine are pretty wishy washy terms when generalized to all bilateria, as GO seems to do (at least hindgut is used generically, not clear about intestine)

further wishy washyness in that sometimes the terms denote embryonic structures rather than adult (in which case proposed relationship would be wrong). However, GO seems to use these inclusively.

If we assume adult mammal, then the proposed placement is defensible. Others would have to comment on insects. But even if true for adults, is it true for embryos where the hindgut may precede the intestines?

I will need to consult with David OS+H on this one. It's tempting to redo this part of the GO hierarchy

As an aside, the definition of intestine SMC is wrong: "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry." (I am ignoring the gloss which is not part of the definition)

Original comment by: cmungall

[gocentral]

I picked the first annotation to hindgut contraction at random (there aren't many experimental). This one from rat:

http://www.ncbi.nlm.nih.gov/pubmed/19258489

Looks like a condom was inflated in the colon to test for contraction. No other parts of the "hindgut" were tested?

I think we get into a lot of trouble in GO making annotations to fuzzy genericized terms. I like having generic terms to do cross-species matching, but I think as far as possible direct annotations should be to specific unambiguous structures like 'colon'. That way it's easier for us to shuffle and even obsolete groupings if they appear to be at the wrong level of abstraction.

I suppose there is a useful generalization here with midgut in that I believe at least with mammals it has distinct innervation. But cross-bilaterian 'regulation of hindgut contraction' as a term for direct annotation feels wrong to me and I have the urge to obsolete.

Original comment by: cmungall

[gocentral]

I wonder if OBI has that balloon assay

Original comment by: cmungall

[gocentral]

https://github.com/obophenotype/uberon/issues/689

Original comment by: cmungall

[pgaudet]

@raymond91125 what do you think about this ?

[raymond91125]

hindgut contraction (its regulation) is used for rat, fly, and worm annotations, whereas intestine smooth muscle contraction is used for vertebrates only.

[raymond91125]

copied from Slack from @pgaudet for https://github.com/geneontology/go-ontology/issues/11758 I think we need to review the annotations before we can make a decision. from @cmungall These issues are a rabbit hole. In retrospect, any vague or imprecise term should have had a do-not-annotate. I wonder how much it’s worth doing this issue by issue vs closing old issues like this and having a propsective plan on how to do this kind of annotation better

[ValWood]

GO:0043133
hindgut contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine.

hindgut contraction has no annotations. Why not obsolete it and make it a synonym of "intestine muscle contraction"

[ValWood]

Should "intestine muscle contraction" have the parent "digestive system process"?

[raymond91125]

part_of, yes, probably for gastro-intestinal system smooth muscle contraction.

[balhoff]

It seems like is_a to me, but part_of 'digestion' (via 'digestive system process'). I'm not totally sure, but I do think we should get more of this automatically from the Uberon classification rather than asserting it. I was looking through this area and I think we probably need better design patterns here; we're missing a lot of connections to Uberon.

[raymond91125]

It seems like is_a to me, but part_of 'digestion' (via 'digestive system process'). I'm not totally sure, but I do think we should get more of this automatically from the Uberon classification rather than asserting it. I was looking through this area and I think we probably need better design patterns here; we're missing a lot of connections to Uberon.

Make sense. I won't do the manual connections then. Thanks.