synonym FYPO:0002303

[fypoadmin]

ID FYPO:0002303 Ontology fission_yeast_phenotype Term name inviable mononucleate monoseptate vegetative cell

in the paper I am reading right now PMID:7798319 they call this phenotype displaced nucleus the septum (dns), add for searching?

Original comment by: Antonialock

[fypoadmin]

should this be "displaced nucleus with septum"

if the nucleus is displaced, it should be a child of mislocalized nucleus during vegetative growth"

I read "interphase nucleus to be situated in one half of the septated cell"

this one is a bit weird- I guess because the nucleus is in the correct place for one nucleus in a cell which has undergone mitosis- but because mitosis is aberrant there is only a single nuclei (is that right), so maybe it isn't displaced.

One for M when she gets back...

Original comment by: ValWood

[fypoadmin]

The quick and easy (but perhaps also quick 'n' dirty) way to handle this would be to add "displaced nucleus with septum" as a related synonym for FYPO:0002303, but not change the parentage, def, etc. That way anyone who encounters the "dns" description would know which term is the best match, but we don't mess about with the descriptions we've worked out based on more data (and we get to dodge the question of whether the nucleus is really in the right or wrong place in a situation that's got a lot else wrong with it ;) ).

Synonym added; will close this if that's OK with you.

Original comment by: mah11

[fypoadmin]

to me it sounds good

Original comment by: Antonialock

[fypoadmin]

yep sounds like a good compromise!

Original comment by: ValWood

[fypoadmin]

yay!

Original comment by: mah11

[fypoadmin]

• labels: --> other ontology change
• status: open --> closed-accepted

Original comment by: mah11

[fypoadmin]

I don't think this synonym is in?

Original comment by: Antonialock

[fypoadmin]

it is ...

Original comment by: mah11

[fypoadmin]

I can't see dns or displaced nucleus with septum

Original comment by: Antonialock

[fypoadmin]

I didn't include 'dns' but 'displaced nucleus with septum' is in the files

Original comment by: mah11

[fypoadmin]

hm, maybe one for Kim then

Original comment by: Antonialock

[fypoadmin]

• assigned_to: Midori Harris --> Kim Rutherford

Original comment by: Antonialock

[fypoadmin]

I've had a look at this.

The "displaced nucleus with septum" synonym is in Canto but is not showing up in the search because it is a RELATED synonym. Currently the synonyms are weighted so that RELATED and BROAD synonyms don't show up near the top of the list of matches. The EXACT synonyms and the term names have the highest weights, NARROW synonyms are slightly lower and RELATED and BROAD are a lot lower.

I think we talked about whether to include the RELATED and BROAD synonyms in the search at all and then decided to include them with a low weight. They are currently very low weight as I wasn't sure what to use. I was too conservative. They have something like 1% of the weight of the EXACT synonyms (although Lucene is a bit of a scary black box in this regard).

I'll tweak the scoring so that RELATED and BROAD are more likely to show up. I'll try giving them a quarter of the weight of NARROW synonyms.

Original comment by: kimrutherford

[fypoadmin]

OK the change in weighting sounds good. We can go back if we get too many spurious.

Couldn't displaced nucleus the septum (dns) be exact for this phenotype ...I think they are equivalent?

Val

Original comment by: ValWood

[fypoadmin]

I didn't make them exact because the wordings describe things at different scales: the term name, 'inviable mononucleate monoseptate vegetative cell', describes a whole cell, whereas 'displaced nucleus with septum' only describes some of the cell parts (and omits the inviability).

Original comment by: mah11