PMID:18758733 (outstanding: cell vs germ tube)

pombase / fypo

Fission Yeast Phenotype Ontology

Creative Commons Attribution 4.0 International

15 stars 6 forks source link

PMID:18758733 (outstanding: cell vs germ tube) #1927

Closed fypoadmin closed 9 years ago

fypoadmin commented 9 years ago

inviable after spore germination, without cell division, elongated cell

Original comment by: Antonialock

fypoadmin commented 9 years ago

Isn't this

FYPO:0002379 Ontology fission_yeast_phenotype Term name inviable after spore germination, without cell division, with elongated germ tube

or one of it's children? (I think I have been using (eventually the germ tube looks like a normal cell- but you can usually still make out the spore body) v

Original comment by: ValWood

fypoadmin commented 9 years ago

I really wouldn't know the difference

Original comment by: Antonialock

fypoadmin commented 9 years ago

which figure?

val

Original comment by: ValWood

fypoadmin commented 9 years ago

ah they don't show the micrograph for this one "microscopic inspection of haploid cells brearing gle1::ura4 revealed that the spores did not germinate, or germinated but stopped growth at elongated abnormal cells".

Original comment by: Antonialock

fypoadmin commented 9 years ago

I think its the same as

Term name inviable after spore germination, without cell division, with elongated germ tube ...or at least related too....sometimes the germ tube ends up looking like a normal cell if it widens enough. I don't know if we would still call this a germ tube, but it was originally the germ tube. Maybe there is a subtle difference? if so siblings?

Original comment by: ValWood

fypoadmin commented 9 years ago

More generally, are there any criteria to determine when something has stopped being the germ tube and matured into the actual cell? I have no idea myself ...

If so, we could put them in the text defs for these terms to make it clearer when to use which term (and why we would have separate terms).

If not, it's hard to argue that there should be separate terms. It also feels not entirely satisfying to have "cell" and "germ tube" phrases as synonyms, but I'm not sure what else we could do if we can't clearly define the difference between wonky cell and wonky germ tube.

Original comment by: mah11

fypoadmin commented 9 years ago

I don’t know the answer to this. I asked Jacky about it last time I saw her. I remember her saying that sometimes the conjugations tube ends up looking like a normal cell. Definitely in the swollen multinucleate ones it no longer looks like a germ tube. Maybe we could put this one at pending and ask Jacky when she comes in the New Year.

Original comment by: ValWood

fypoadmin commented 9 years ago

summary: PMID:18758733 --> PMID:18758733 (outstanding: cell vs germ tube)

Original comment by: mah11

fypoadmin commented 9 years ago

note to self: if they're different, and we add a new term, update spp2-8 fypo:2379 from PMID:11027257 to the new one

Original comment by: mah11

fypoadmin commented 9 years ago

chatting with Val & Jacky -- we think cell and germ tube are the same, or near enough, to stick with one term. I'll add a synonym.

Original comment by: mah11

fypoadmin commented 9 years ago

status: open --> closed-works-for-me

Original comment by: mah11

fypoadmin commented 9 years ago

synonyms added

Original comment by: mah11