Make difficult sensu terms organism specific-meeting action

[gocentral]

This SF takes item removes this item from the princeton outstanding action items

I) vacuole, cell cycle-correlated morphology -> fiungal -type vacuole

any others.....

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4975":https://sourceforge.net/p/geneontology/ontology-requests/4975

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I've renamed the vacuole terms so that 'vacuole, cell cycle independent morphology' changes to 'plant-type vacuole' and 'vacuole, cell cycle-correlated morphology' becomes 'fungal-type vacuole' (in all cases, the "old" names are exact synonyms, and the 'sensu' synonyms are unchanged).

The vacuole terms seemed to be the worst, but I've spotted a few other possibilities: current name | suggested name | example GO IDs

• 1-2nm peptidoglycan-based cell wall | Gram-negative-type cell wall | GO:0009276, GO:0043164
• 20-80nm peptidoglycan-based cell wall | Gram-positive-type cell wall | GO:0009275
• cellulose and pectin-containing cell wall | plant-type cell wall | GO:0009505 and children

It would be nice to use 'nematode-type cuticle' for collagen and cuticulin-based cuticle extracellular matrix (GO:0060102 and children), but protein-based cuticle development (GO:00007592 and children) has 'sensu Protostomia and Nematoda' synonyms. Might be best to leave the cuticle terms as they are. Thoughts?

These two are nasty: GO:0002459 adaptive immune response based on somatic recombination of immune receptors built from leucine-rich repeat domains GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains

... but the 'sensu' synonyms are almost as intimidating, so I'm not sure it's worth changing them. There are some others where changing names wouldn't be much of an improvement.

I suggest just doing the three cell wall terms I listed above, and unless anyone notices any more howlers in the next week or so, close this item and open new ones if we decide on any more term name changes.

m

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> 224410
• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=735846 Originator: NO

Hi,

'sensu Protostomia and Nematoda' was our name for invertebrates since there was no 'invertebrata' in the taxonomy hierarchy, but if we going non-latin maybe you could just use plain 'invertebrate'?

The cell wall changes look excellent to me.

I've a feeling that David doesn't like the word 'type' in term names but I'm sure he will chip in.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=579762 Originator: NO

For the Gram neg and pos suggestions, I think these should be Gram-negative-bacterium-type cell wall and Gram-positive-bacterium-type cell wall. Multi-hyphenation problems aside, I think these are more correct.

Tanya (who could have hyphenated her last name when she got married but Reichert-Berardini doesn't really roll off the tongue now, does it?)

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=631592 Originator: NO

Actually, I do like the -type in the term names. Since terms represent types, this makes good sense to me.

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=436423 Originator: NO

OK, I'll give it the rest of this week; on Monday (or as soon thereafter as I can manage ...), I'll do the 3 sets of changes I said I'd do, plus any that come in here by then. (I'll add -bacterium- as Tanya recommended.) Any additional changes can be requested through the usual new-SF-item channels.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

changes done as proposed; closing

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11