vacuole/sensu related

[gocentral]

I just got really confused by the vacuole terms that replaced the sensu terms.

membrane of vacuole with cell cycle-correlated morphology has the synonyn vacuolar membrane (sensu Fungi) so I thought this must in some way distinguish it from metazoan, but i think it is only to distinguish it from plant?

It just seems off when you first see it so it might be worth adding the additiaonal synonyms vacuolar membrane (sensu Metazoa)

...in these cases is it possible to add to the definition or a comment that this term is to distinguish fungal and metazoan vacuoles from plant.

also spotted that the plant one doesnt have storage vacuole as a parent?

and then I was wondering if the grouping term vacuole should exist as a grouping term if plant and non-plant vacuoles are real lexical differnces and that i) the replacement terms should all instead have vacuole as a synonym ii) Or it is actually OK to use sensu in this instance.

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4084":https://sourceforge.net/p/geneontology/ontology-requests/4084

[gocentral]

Logged In: YES user_id=735846 Originator: NO

Hi Val,

We'll take a look at this in our next sensu conference call. Shouldn't be long.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• priority: 5 --> 9
• assigned_to: nobody --> jenclark

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=473890 Originator: NO

I second Val, I find these terms a little confusing too.

I have some additional specific comments.

In this set of 3 terms:

vacuole, cell cycle-correlated morphology ; GO:0000324 .lumen of vacuole with cell cycle-correlated morphology ; GO:0000328 .membrane of vacuole with cell cycle-correlated morphology ; GO:0000329

I find the phrasing of the first one "vacuole, cell cycle-correlated morphology" confusing having the comma in the middle of it. I think the names of the other two term that are its children, where the name does NOT contain a comma read better and are more comprehensible. Maybe the comma could be taken out of the name for 324.

I notice that there is also a term called 'vacuole, cell cycle independent morphology ; GO:0000325'. Could we take the comma out of this name too? Also, this term does not have a hyphen, while its two child terms do. All the cell cycle-correlated terms have hyphens, so perhaps having hyphens in all of these terms would be most consistent.

In addition, I notice that these two terms: vacuole, cell cycle-correlated morphology ; GO:0000324 vacuole, cell cycle independent morphology ; GO:0000325

have parallel names, but do not have parallel positions within the DAG, in that 325 is a direct child of 'vacuole' while 324 (cell-cycle correlated) is not a direct child. Since the term 'vacuole, cell cycle-correlated morphology ; GO:0000324' is also a child of 'lytic vacuole', perhaps the names of this term and its two children should all include the word 'lytic'.

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=516865 Originator: YES

yipee, I spotted one to close!

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423 Originator: NO

yay!

fixed for SF 1949239

Original comment by: mah11

[gocentral]

• assigned_to: jenclark --> gomidori
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: --> PomBase

Original comment by: mah11