ring canal

[gocentral]

Consider either adding a synonym "germline ring canal formation" to GO:0030725 ! ring canal formation

or adding a synonym "ring canal" to GO:0045172 ! germline ring canal

(presuming these are all refering to the same entitiy)

Also I think the terminology needs better aligned with FBbt, and xrefs need to be added to FBbt.

does this GO:0007301 ! ovarian ring canal formation refer to this FBbt:00004879 ! nurse cell ring canal ?

does this GO:0030726 ! testicular ring canal formation refer to this FBbt:00004939 ! spermatocyte ring canal ?

Consider adding these two subtypes to CC

Reported by: cmungall

Original Ticket: geneontology/ontology-requests/7047

[gocentral]

• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

[gocentral]

Susan is discussing this with DavidOS, so please consult her when you work on this.

cheers, m

Original comment by: mah11

[gocentral]

They are the same thing. How about doing the following?:

1. remove the following terms from FBbt because they are all cellular components:

nurse cell ring canal ; FBbt:00004879 nurse cell ring canal rim ; FBbt:00004880 inner nurse cell ring canal rim ; FBbt:00004881 outer nurse cell ring canal rim ; FBbt:00004882 nurse cell fusome ; FBbt:00004884 spermatocyte ring canal ; FBbt:00004939 ring canal ; FBbt:00005409

2. (Add synonyms) and change the names of the following GO terms to reflect the fact that: a. ring canals exist between cystocytes i.e. before these cells develop into (oocytes, nurse cells, spermatocytes) and perhaps before the germline cyst is considered to be a true ovary b. flies don't have testicles so testicular is maybe not the best choice in term name c. nurse cells are found in other contexts

testicular ring canal formation ; GO:0030726 > male germline ring canal formation ; GO:0030726 exact_synonym: testicular ring canal formation exact_synonym: spermatocyte ring canal formation

ovarian ring canal formation ; GO:0007301 > female germline ring canal formation ; GO:0007301 exact_synonym: ovarian ring canal formation exact_synonym: nurse cell ring canal formation

ovarian ring canal stabilization ; GO:0008335 > female germline ring canal stabilization ; GO:0008335 exact_synonym: ovarian ring canal stabilization exact_synonym: nurse cell ring canal stabilization

ring canal formation ; GO:0030725 > germline ring canal formation ; GO:0030725 (makes this consistent with cc terms)

ring canal formation, actin assembly ; GO:0008302 > female germline ring canal formation, actin assembly ; GO:0008302 (current def is female specific) exact_synonym: ovarian ring canal formation, actin assembly exact_synonym: nurse cell ring canal formation, actin assembly

germline ring canal inner rim ; GO:0035183 > female germline ring canal inner rim ; GO:0035183 (current def refers to female) exact_synonym: ovarian ring canal inner rim exact_synonym: nurse cell ring canal inner rim

germline ring canal outer rim ; GO:0035182 > female germline ring canal outer rim ; GO:0035182 (current def refers to female) exact_synonym: ovarian ring canal outer rim exact_synonym: nurse cell ring canal outer rim

fusome ; GO:0045169 add narrow_synonym: nurse cell fusome

3. Add new GO terms

female germline ring canal male germline ring canal both is_a germline ring canal with synonyms as above

female germline ring canal rim exact_synonym: nurse cell ring canal rim exact_synonym: ovarian ring canal rim

Tweak parentage to accommodate new terms.

What do you think David? Susan

Original comment by: stweedie

[gocentral]

Hi Susan,

Your suggestions look pretty good to me. Few comments in-line.

> 1. remove the following terms from FBbt because they are all cellular > components: > > nurse cell ring canal ; FBbt:00004879 > nurse cell ring canal rim ; FBbt:00004880 > inner nurse cell ring canal rim ; FBbt:00004881 > outer nurse cell ring canal rim ; FBbt:00004882 > nurse cell fusome ; FBbt:00004884 > spermatocyte ring canal ; FBbt:00004939 > ring canal ; FBbt:00005409 >

OK. This means we lose the ability to group some phenotypes via part_of (e.g.- a phenotype in a spermatocyte ring canal is a phenotype in a spermtocyte cyst.) But I guess I can live with that.

> 2. (Add synonyms) and change the names of the following GO terms to > reflect the fact that: > a. ring canals exist between cystocytes i.e. before these cells develop > into (oocytes, nurse cells, spermatocytes) and perhaps before the germline > cyst is considered to be a true ovary.

Sounds good except that I'm confused by this last bit. In insects at least, the ovary is a structure containing many cysts. Isn't this also true in vertebrates?

> b. flies don't have testicles so testicular is maybe not the best choice > in term name

If testicle is synonymous with testis, then they do (I initially wrongly assumed otherwise)

> c. nurse cells are found in other contexts > > testicular ring canal formation ; GO:0030726 > > > male germline ring canal formation ; GO:0030726 > exact_synonym: testicular ring canal formation > exact_synonym: spermatocyte ring canal formation >

Agreed.

> ovarian ring canal formation ; GO:0007301 > > > female germline ring canal formation ; GO:0007301 > exact_synonym: ovarian ring canal formation > exact_synonym: nurse cell ring canal formation >

Shouldn't these be narrow synonyms?

> ovarian ring canal stabilization ; GO:0008335 > > > female germline ring canal stabilization ; GO:0008335 > exact_synonym: ovarian ring canal stabilization > exact_synonym: nurse cell ring canal stabilization > > ring canal formation ; GO:0030725 > > > germline ring canal formation ; GO:0030725 > (makes this consistent with cc terms) > Shouldn't these be narrow synonyms?

> ring canal formation, actin assembly ; GO:0008302 > > > female germline ring canal formation, actin assembly ; GO:0008302 > (current def is female specific) > exact_synonym: ovarian ring canal formation, actin assembly > exact_synonym: nurse cell ring canal formation, actin assembly > Shouldn't these be narrow synonyms?

> germline ring canal inner rim ; GO:0035183 > > > female germline ring canal inner rim ; GO:0035183 > (current def refers to female) > exact_synonym: ovarian ring canal inner rim > exact_synonym: nurse cell ring canal inner rim > Shouldn't these be narrow synonyms?

> germline ring canal outer rim ; GO:0035182 > > > female germline ring canal outer rim ; GO:0035182 > (current def refers to female) > exact_synonym: ovarian ring canal outer rim > exact_synonym: nurse cell ring canal outer rim > Shouldn't these be narrow synonyms?

> fusome ; GO:0045169 > add narrow_synonym: nurse cell fusome >

Note - we have a whole zoo of fusome terms in FBbt: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=FBbt&termId=FBbt%3A00004862&termName=fusome

Could the rest of these find a home in GO?

> 3. Add new GO terms > > female germline ring canal > male germline ring canal > both is_a germline ring canal with synonyms as above > > female germline ring canal rim > exact_synonym: nurse cell ring canal rim > exact_synonym: ovarian ring canal rim

Shouldn't these be narrow synonyms?

Cheers,

David

Original comment by: dosumis

[gocentral]

please keep the part_of links around somewhere

we could add them to cellular_component_links_cell, but you'd need to make sure all fly cells are in CL first

Original comment by: cmungall

[gocentral]

If you don't want to take the terms out of FBbt yer maybe you could just change the names to match GO and add def.

It seems a bit odd changing a term name and not making the original name an exact synonym but I don't have strong feelings if you think narrow is correct. If the female synonyms should be narrow should the male ones be narrow too?

Ignore my comment about the ovary - brain fade on my part.

We can look at the other fusome terms - I'll add a separate SF item for these.

Looks like we are pretty much agreed Becky.

Original comment by: stweedie

[gocentral]

Added 2 new component terms: male germline ring canal ; GO:00035323 female germline ring canal ; GO:0003524

Changed all ovarian ring canal GO terms to female germline ring canal terms, with narrow ovarian and nurse cell synonyms.

Changed all testicular ring canal GO terms to male germline ring canal terms, with narrow testicular and spermatocyle synonyms.

If the ring canal terms are staying in the FlyBase anatomy, X-refs to the new GO terms can now be added.

Thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-accepted

Original comment by: rebeccafoulger