NTR pigmentation defect

[fypoadmin]

Hi Midori,

I need some form of term describing red colonies when cells are deprived of adenine (I can't really think of a single short summary of the term...the description could be something along the lines of accumulation of cellular red pigment in adenine limited conditions)

thanks Antonia

Original comment by: Antonialock

[fypoadmin]

and also a term for reduced pigmentation of colonies when cells are grown with limited adenine.

Original comment by: Antonialock

[fypoadmin]

is this adenine biosynthesis pathway, or just a selectable marker?

Val

Original comment by: ValWood

[fypoadmin]

Yeah. The authors were interested in the process that turn colonies red so they used an ade6 mutant as the basis of a mutational screen to look for double-mutants that did not form red colonies (or reduced red colonies).

Original comment by: Antonialock

[fypoadmin]

to clarify: "yeah" was in response to 'adenine biosynthesis pathway"

Original comment by: Antonialock

[fypoadmin]

I wonder if you need the condition in the phenotype term here? maybe the red cellular pigment accumulation is sufficient and the condition can be adenine limitation I think I'm basing this on the fact that there wont be many "differentia" required for this particular phenotype as there aren't other way of making a red pigment ?

How do you do x-ps for colours, does PATO have them? GO has GO:0043482 cellular pigment accumulation

Original comment by: ValWood

[fypoadmin]

The best thing I've come up with so far would be phenotype terms for normal/abnormal (and increased/decreased if useful) cellular pigment accumulation using GO:0043482 in the xp.

(Note - There's a little part of me that's worried that the ade mutant pigment accumulation isn't "normal" enough (because of the ade6 or ade7 mutation involved) for the GO term, but I can quietly ignore that.)

PATO does have terms for colors, but I don't think I'll use them for this term. What I would need for a more specific term would be a ChEBI term for the substance that is accumulating. I'm not sure it's characterized quite well enough for that, though. I've found descriptions that say the pigment is derived from a couple of pathway intermediates and transported to the vacuole as glutathione conjugates, but not much about structure.

Are there any other pigments that accumulate in pombe? If not, we wouldn't really need any other pigment-accumulation terms, and the fact that we don't have a differentia for the specific pigment in the ade mutants is no big deal.

I agree that the adenine level can go in conditions.

m

Original comment by: mah11

[fypoadmin]

did you settle on anything on this request?

I guess you are right in that the pigmentation defect isn't normal....

would it be possible to have one term for pigmented vacuoles and then a second term for 'double(/multiple) mutant phenotype where vacuole pigmentation is absent, although it is observed in one of the single mutant phenotypes' or similar (extremely inelegant I know)

Original comment by: Antonialock

[fypoadmin]

I was wondering whether the "increased cellular pigment accumulation" approach, with adenine level as a condition, would work for you. If so, I can add those terms; I'll include a comment to the effect that the "normal" occurrence is "not at all, or at least not enough to detect".

> would it be possible to have one term for pigmented vacuoles and then a
> second term for 'double(/multiple) mutant phenotype where vacuole
> pigmentation is absent ...

No, because whether a cell is a single/double/triple/etc. mutant is an aspect of its genotype, and we shouldn't mix genotype information into the phenotype ontology. I think you'd just annotate the double mutant to "normal cellular pigment accumulation" (or maybe increased but with lower expressivity than the single mutant).

Original comment by: mah11

[fypoadmin]

yeah I think that makes more sense than either other option

Original comment by: Antonialock

[fypoadmin]

cellular pigment accumulation phenotype FYPO:0000739 normal cellular pigment accumulation FYPO:0000740 increased cellular pigment accumulation FYPO:0000741

Note: for the xps, I've had to use GO:0033059, 'cellular pigmentation', instead of GO:0043482 'cellular pigment accumulation'. Although the name of GO:0043482 seems closer to the phenotype description, the term has 'cellular response to stimulus' as a parent, and I don't think that quite fits the phenotype.

I also just added the one term for "increased", since as far as we know, accumulating pigment is always abnormal.

cheers, m

(as usual, will close when terms are available in the curation tool)

Original comment by: mah11

[fypoadmin]

• status: open --> open-accepted

Original comment by: mah11

[fypoadmin]

to be honest it doesn't entirely make sense that a stimuli is only denoted by somethings presence, not somethings absence

Original comment by: Antonialock

[fypoadmin]

I guess so, but the GO:0043482 text definition includes "in response to some external stimulus", so I still think it's safer to use the other GO term for these phenotype xps -- if there's a stimulus with the ade6 pigment thing, it's internal, right?

Original comment by: mah11

[fypoadmin]

reopening this,

I have found another mutant showing pigmentation defects in response to a stimuli (presence of a substance rather than absence as in the case of the adenine mutants.

The mutant is hmt2- and colonies are yellow when Cd is present, brown in the presence of Cu and grey in the presence of Pb or Bi

Original comment by: Antonialock

[fypoadmin]

• status: open-accepted --> open

Original comment by: Antonialock

[fypoadmin]

Hey, I found this in PATO:

degree of pigmentation PATO:0002247 [i] pigmented PATO:0002248 -- [i] decreased pigmentation PATO:0002251 -- [i] increased pigmentation PATO:0002250 [i] unpigmented PATO:0002249

So I could change the xps to use these instead of GO process terms, and then we wouldn't have to worry about internal vs. external stimulus, or whether the process is normal. I'd also change some term names a bit:

FYPO:0000739 --> cellular pigmentation phenotype FYPO:0000740 --> normal cellular pigmentation (synonym:unpigmented cells, since normal cells don't accumulate pigment) FYPO:0000741 --> increased cellular pigmentation

There are also a bunch of PATO terms for specific colors. For the different-colored mutants, I think I'd prefer to put them in extensions on annotations to the rejigged FYPO:739-741, tho I'm not sure I can explain why. We could add child terms instead.

Original comment by: mah11

[fypoadmin]

Apologies if my thinking is flawed and I'm talking total gibberish!

I don't think colour should be expressed as a relation because relations link two things to produce an outcome such that:

A + B = C where A and B are linked by a relation to produce phenotype C In this case: mutant + Cd = yellow colony

Therefore yellow can't be added as a relation to the FYPO term cellular pigmentation phenotype, but should be added as a child instead

---

In order to use a relation then I think the FYPO term needs to = yellow colony because then Cd can be used as a relation

i.e. FYPO:XXX yellow colonies (a cellular pigmentation phenotype where colonies appear yellow) allele=deletion Extension=in_presence_of(Cd)

Original comment by: Antonialock

[fypoadmin]

I'm not sure I totally follow, but ...

- Cd isn't a relation, it's a substance

- presence of Cd is a condition, not a relation or an extension

- FYPO:0000741 increased pigmentation (extension:has_color=PATO:0000324)

is semantically equivalent to

id: FYPO:new name: increased yellow pigmentation intersection_of: FYPO:0000741 ! increased_pigmentation intersection_of: has_color PATO:0000324

and you could use the condition=(in presence of cadmium) with the annotation either way

(PATO:0000324 is 'yellow')

Original comment by: mah11

[fypoadmin]

At least I'm getting a feel for when I'm garbling!

been doing it this way now:

- FYPO:0000741 increased pigmentation

• extension:has_color=PATO:0000324
• • condition

Original comment by: Antonialock

[fypoadmin]

should be OK for the moment, and if you do it consistently, it'll only be a small amount of pain to change if we decide to do it differently

Original comment by: mah11

[fypoadmin]

I think I found a relation in RO that we could use ... I'll ask Chris when I pester him about relations generally. It's 'is_bearer_of'.

Original comment by: mah11

[fypoadmin]

OK, Chris recommends using is_bearer_of for now, and we'll keep thinking about whether there's a better way to do these annotations.

I'll close this, and one of us can open a new item if and when we're ready to convert the annotations to another format/syntax.

Original comment by: mah11

[fypoadmin]

• status: open --> closed-accepted

Original comment by: mah11

[fypoadmin]

umm, so should I change

• extension:has_color=PATO:0000324 to
• extension:is_bearer_of(PATO:0000324)

or leave it for now?

Original comment by: Antonialock

[fypoadmin]

Hmm. I think it should be changed, but don't know if it's better for you to do it manually or for Kim to automate it as part of loading. Best ask him ...

Original comment by: mah11

[fypoadmin]

ah I just saw the email pointing to this: https://sourceforge.net/apps/trac/pombase/wiki/ListOfRelations

Shouldn't be very many to fix, I can do it.

Original comment by: Antonialock