NTR: level of Man9GlcNAc / Man8GlcNAc

pombase / fypo

Fission Yeast Phenotype Ontology

Creative Commons Attribution 4.0 International

14 stars 6 forks source link

NTR: level of Man9GlcNAc / Man8GlcNAc #223

Closed fypoadmin closed 9 years ago

fypoadmin commented 12 years ago

NTRs please for:

parent terms: FYPO:0000991 decreased level of substance in cell FYPO:0000990 increased level of substance in cell FYPO:0001076 normal level of substance in cell (possibly FYPO:0001077 normal polysaccharide level??) could also add parent: altered level of glycan in cell

children: decreased level of Man8GlcNAc normal level of Man8GlcNAc increased level of Man9GlcNAc normal level of Man9GlcNAc

there may be more to follow...

Original comment by: Antonialock

fypoadmin commented 12 years ago

(no more to follow...)

Original comment by: Antonialock

fypoadmin commented 12 years ago

new terms normal Man8GlcNAc level FYPO:0001142 normal Man9GlcNAc level FYPO:0001143 decreased Man8GlcNAc level FYPO:0001144 increased Man9GlcNAc level FYPO:0001145

notes:

Argh, it was confusing how they went back and forth between GlcNAc and GlcNAc2;
I put the new terms under the polysaccharide terms because the CHEBI term corresponding to Man9GlcNAc2 has a path to polysaccharide;
There's no xp for FYPO:0001142 because of the multiple isoforms of Man8GlcNAc.

Original comment by: mah11

fypoadmin commented 12 years ago

status: open --> open-accepted

Original comment by: mah11

fypoadmin commented 12 years ago

ah yeah, I should have mentioned this. My interpretation was that in a cellular context they talk about GlcNAc2, whereas in an experimental context they talk about GlcNAc, because they add endo H to the assay see http://en.wikipedia.org/wiki/Endo\_H . Perhaps GlcNAc2 would be more correct if that is what is actually inside the cell? Although they measure GlcNAc in the assay....

Original comment by: Antonialock

fypoadmin commented 12 years ago

Thanks -- in that case, what I did is OK: I made exact synonyms using GlcNAc2, even though they're technically not the same substance, because for the purposes of observing and interpreting phenotypes they mean the same thing. Whew. I'll add comments too.

Original comment by: mah11

fypoadmin commented 12 years ago

terms in tool; comments will be along in next update

Original comment by: mah11

fypoadmin commented 12 years ago

status: open-accepted --> closed-accepted

Original comment by: mah11