missing annotations

[Antonialock]

quite a large number of annotations are missing from this publication: http://pombase2.bioinformatics.nz/reference/PMID:10348908 https://curation.pombase.org/pombe/curs/8e27bf8723065210

e.g cellular component: nucleus & a large number of phenotypes

last time it was approved was back in 2015.

[Antonialock]

(FYI i just added 2 extensions to the nucleus term)

[kimrutherford]

Hi. I think you were looking at the wrong preview page. This looks OK: http://pombase2.bioinformatics.nz/reference/PMID:11129048

[Antonialock]

ah that looks better but it is stil missing this anntation:

  | prr1Δ | FYPO:0000280 | sterile

(that's what promted me to look at this paper...I was going to add that annotation, I thought I had missed it, but then I saw that it was present in the session).

[kimrutherford]

prr1Δ | FYPO:0000280 | sterile

I've look into that. Could it be that sterile isn't a cell phenotype and isn't a population phenotype so is not shown?

[Antonialock]

hmm, yeah...ste11 isn't showing sterile either

[Antonialock]

odd though...old site also sorts population/cell and it is showing there http://www.pombase.org/spombe/result/SPAC8C9.14#fission_yeast_phenotype-single_allele-cell_phenotype

[kimrutherford]

I checked Chado and the missing annotation is there. I checked the parents of "sterile" and it isn't a descendant of the "population phenotype" term (FYPO:0000003) and it's not a descendant of the cell phenotype terms (FYPO:0000002 and FYPO:0000652). So I think that explains it.

odd though...old site also sorts population/cell and it is showing there

I checked the code for the old site. On the old pages anything the isn't a descendant of the population phenotype term (FYPO:0000003) is put in the "cell phenotype" section of the page.

[mah11]

Kim's right, sterile and other mating phenotypes are neither cell nor population phenotypes in FYPO. I kind of think that's biologically reasonable - it takes two to tango (or mate), so it's not strictly a cell-level process. Technically two can count as a small "population" but I suspect that's not very intuitive; certainly I tend to think of the population phenotypes as the ones you assay by looking at a big population in a culture.

There are other terms that aren't classified as either cell or population - the molecular function phenotypes, developmental process phenotypes (mainly because of the ascus, which isn't a single cell), and a handful of oddballs that defy categorization.

I don't remember explicitly requesting that mating phenotypes go under cell phenotype for the legacy pombase display, but that appears to be what it does.

I wouldn't object to putting anything that's not a population phenotype under cell phenotype for the pombase page displays if it's easy for Kim to do. That would be better than kludging up the ontology itself.

[mah11]

wrong sodding button

[Antonialock]

that would work for me..

[Antonialock]

this rings a bell, I guess we must have had the same discussion eons ago :-)

[kimrutherford]

this rings a bell, I guess we must have had the same discussion eons ago :-)

Yep! #259

[kimrutherford]

I wouldn't object to putting anything that's not a population phenotype under cell phenotype for the pombase page displays if it's easy for Kim to do.

Currently the code expects to be configured with a list of high level terms for each category. So the quickest fix for "sterile" is to at another term to the config. like: FYPO:0000301 mating phenotype

If it helps I can do a query to find terms that still wouldn't appear in either category.

[mah11]

I found around sixty or so terms that don't fall under MF, cell or population phenotype, but I didn't check how many of those are under mating or developmental process.

[kimrutherford]

I found around sixty or so terms that don't fall under MF, cell or population phenotype,

I get 62 so that consistent.

Only 29 of those have annotation:

abnormal ascus development abnormal conjugation abnormal telomeric repeat sequence altered cytochrome absorption spectrum conjugation without glucose starvation conjugation without nitrogen starvation decreased concentration of M-factor in growth medium decreased concentration of P-factor in growth medium decreased pH of growth medium decreased queuosine level in tRNA h- specific sterility h+ specific sterility increased Argonaute-associated RNA length increased concentration of M-factor in growth medium increased concentration of P-factor in growth medium increased concentration of polysaccharide in growth medium increased poly(A) tail length normal ascus morphology normal conjugation normal conjugation frequency normal frequency of conjugation with h+ cells normal galactose:mannose ratio in glycoprotein glycan normal minichromosome loss normal monoacylglycerol phosphate chain length normal poly(A) tail length normal telomeric repeat sequence normal topoisomerase-DNA adduct level queuosine absent from tRNA sterile

If I filter out FYPO:0000301 mating phenotype too there are only 20:

abnormal ascus development abnormal telomeric repeat sequence altered cytochrome absorption spectrum decreased concentration of M-factor in growth medium decreased concentration of P-factor in growth medium decreased pH of growth medium decreased queuosine level in tRNA increased Argonaute-associated RNA length increased concentration of M-factor in growth medium increased concentration of P-factor in growth medium increased concentration of polysaccharide in growth medium increased poly(A) tail length normal ascus morphology normal galactose:mannose ratio in glycoprotein glycan normal minichromosome loss normal monoacylglycerol phosphate chain length normal poly(A) tail length normal telomeric repeat sequence normal topoisomerase-DNA adduct level queuosine absent from tRNA

[mah11]

I don't think it would be outrageous to lump those in with cell phenotypes for display.

[kimrutherford]

I don't think it would be outrageous to lump those in with cell phenotypes for display.

I'll do that.

I tried looking for a short list of high level IDs I can add to the configuration to cover those. Unfortunately there aren't many.

There are quite a few direct children of normal phenotype (FYPO:0000257). Like:

normal galactose:mannose ratio in glycoprotein glycan - FYPO:0004942
normal ascus morphology - FYPO:0005157

I'll add those IDs to the config.

There are a couple of direct children of "normal vegetative phenotype" - FYPO:0001312 Is it OK to put all descendants of FYPO:0001312 in with the cell phenotypes? There aren't many at the moment. An example is:

normal monoacylglycerol phosphate chain length - FYPO:0005582

These two have only abnormal phenotype as a direct parent so there isn't a higher level grouping term that covers them:

decreased queuosine level in tRNA - FYPO:0003427
abnormal poly(A) tail length - FYPO:0002929

"abnormal ascus development" is a descendant of "abnormal biological process" - FYPO:0005447 and of "biological process phenotype" - FYPO:0000300. Is there any problem with including either of those terms in the config for the cell phenotype section?

Apart from "normal vegetative phenotype" the only other high level term we can add is:

altered effect on growth medium - FYPO:0001155

which has a few child terms in the list.

[mah11]

Apart from "normal vegetative phenotype" the only other high level term we can add is:

altered effect on growth medium - FYPO:0001155

which has a few child terms in the list.

Let's display this one under population phenotype - it's not quite build-it-into-the-ontology quality either way, but ever so slightly less clunky as population.

Is it OK to put all descendants of FYPO:0001312 in with the cell phenotypes?

As long as none of the descendants are also descendants of population phenotype, it's OK, but otherwise not.

The rest, both normal and abnormal, might as well just get configured to show up with the cell phenotypes. They don't fit well anywhere; if they did they'd have more specific ancestry somewhere.

[kimrutherford]

The annotation to sterile is there now, but appears twice :-/

I'll fix that tomorrow or Monday.

[mah11]

erm, on some of the FYPO term pages it looks like everything is duplicated

examples: population - http://preview.pombase.org/term/FYPO:0002344 cell - http://preview.pombase.org/term/FYPO:0003486

[kimrutherford]

The annotation to sterile is there now, but appears twice :-/

The duplication is fixed now.