ntr: Dense Core Granule ; similar to GO:0020026

[gocentral]

Hi all,

I'm working on GO annotations for a number of proteins found in "dense core granules", a type of secretory granule found in ciliates. These structures resemble the "dense granules" of Apicomplexans.

GO term: dense granule (sensu Apicomplexa) Synonyms: dense body Definition: Electron-dense organelle with a granular internal matrix found throughout the merozoite life cycle stage of apicomplexan parasites; contains proteins destined to be secreted into the parasitophorous vacuole following parasite invasion of a host cell. As in, but not restricted to, the apicomplexans (Apicomplexa, ncbi_taxonomy_id:5794). Ontology: Cellular Component (GO:0020026)

Despite the fact that Ciliates and Apicomplexans are fairly closely related, it's still not clear if these structures are orthologous their cargoes are certainly different, and the proteins that make up the lattice inside arent similar. A previous discussion led to the creation of separate sensu Apicomplexa and platelet (GO: 0042827) dense granule terms (request ID: 785248). The ciliate and apicomplexan granules could be as different as the mammalian and apicomplexan ones.

To maintain the current architecture, I should request a separate term for the ciliate granules.

The dense granule (sensu Apicomplexa) term, which Im trying to model my new definition after, is confusing me. Since the definition is loaded with apicomplexan-specific qualifiers, the sensu tag seems unnecessary, and the not restricted to the apicomplexans line is kinda funny at the end. But its got me worried that the definition Ive come up with for the new term Im requesting isnt adequate:

(new) GO term: dense core granule (sensu Ciliophora) Synonyms: dense core vesicle ; mucocyst Definition: Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. As in, but not restricted to, the ciliates (Ciliophora, ncbi_taxonomy_id: 5878). Ontology: Cellular Component Relationship: is_a GO:0030141 (reference: PMID: 14690495)

This new term would work for us, but if anyone favors another solution, please let me know.

Thanks, Nick

Reported by: nastover

Original Ticket: "geneontology/ontology-requests/2055":https://sourceforge.net/p/geneontology/ontology-requests/2055

[gocentral]

• labels: --> New term request
• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

You've presented a very good, clear explanation of why a new term is warranted -- I'm convinced! I wish all of our SourceForge entries were so complete :)

And your suggested definition looks very good from a GO point of view. The new term may not have to be 'sensu Ciliophora' after all, though, because we don't have any other terms with 'dense core granule' in the names (the platelet and apicomplexan terms say 'dense granule' rather than 'dense CORE granule).

I'm going to try to clear up some of the confusion about 'sensu' terms. I hope I succeed ...

The reason to include 'sensu Apicomplexa' in the term name for GO:0020026 is to avoid confusion with other structures that have been called dense granules but are very different, such as the platelet or ciliate examples. Without the 'sensu' qualfier, we would have two different concepts represented by identical text strings. This particular example is perhaps not the most obvious or the most illustrative, since we can use 'platelet' as the distinguishing text feature for the platelet dense granule instead of having to use another 'sensu' tag naming a different taxon. And although it may seem redundant to use 'sensu Apicomplexa' when the definition is so full of protozoan-specific information, it's another little help to reduce confusion -- seeing the 'sensu Apicomplexa' tag, one knows to expect the protozoan biology.

The 'as in, but not restricted to, the taxon [blah]' passages have a history of their own. Strictly speaking, they're not necessary, but we (meaning the whole GO consortium) decided to put them in because we saw that a lot of people, even curators doing GO annotation regularly, were confused about what we mean by 'sensu'. It means 'as observed in' a given taxon, but the sensu terms are meant to be available to use for organisms that aren't in the named taxon, if they do have the same activity, process, or structure. For example, if someone discovers that jellyfish have dense granules that look and act exactly like the Apicomplexan dense granules, an annotator could use the 'sensu Apicomplexa' GO term to annotate the relevant gene products.

If this is still clear as mud, we can talk at the meeting.

Oh yes, one more thing: the new term is 'dense core granule' for the moment, and it can be renamed to add a 'sensu' qualifier if the need arises.

id: GO:0031045 name: dense core granule namespace: component def: "Electron-dense organelle found in ciliates, with a granular internal matrix; contains proteins destined to be secreted." [PMID:14690495] is_a: GO:0030141 ! secretory granule

Cheers, midori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

Hi Nick,

Remember this one? A recent SF request (1522488) has made me notice that there are a few papers that refer to some kinds of "higher"-eukaryote secretory granules as "dense core granules". Do you think we could broaden the definition of GO:0031045, or will we need separate terms? If we do add a new term, it could be a parent of the ciliate dense core granule term and of platelet dense granule.

(In fact, I should've noticed this when I did SF 1522491, but I must have been in a hurry that day ...)

links: https://sourceforge.net/tracker/? func=detail&atid=440764&aid=1522488&group_id=36855 https://sourceforge.net/tracker/index.php? func=detail&aid=1522491&group_id=36855&atid=440764

cheers, midori

Original comment by: mah11

[gocentral]

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Hi Midori,

"Dense granules" of all sorts get their names because the dense cargo they carry is shows up as a dark spot under a microscope. This is a weird way to classify structures since their actual cargoes, functions, and evolutionary relationships aren't necessarily related because of this similar look. I'd hesistate to group any of these structures, and I believe the "dense granules" of ciliates and platelets should continue to be separate terms under "secretory granule".

Does that sound reasonable to you?

Nick

Original comment by: nastover

[gocentral]

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Hi Nick,

Thanks, and yes, it makes sense to keep separate terms. Now I need to figure out how to get the point across that the GO term 'dense core granule' is ciliate-specific. We're trying to avoid using the 'sensu' wording these days, so is there anything else I could add to the term name to help make the distinction, and prevent people overlooking that word 'ciliates' in the definition?

I'd also like to be able to add 'dense core granule' as a related synonym for some of the other terms, but only if we can reword the ciliate term (I hate having one string be both a term name and any type of synonym).

Background on why we'd prefer to avoid going sensu: http://wiki.geneontology.org/index.php/Sensu\_Plans

cheers, m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

p.s. also, if there's anything about structural proteins or cargo that I could add to the def, that'll help too.

m

Original comment by: mah11