Move 'hyphal terms' under 'hyphal growth phenotype'

[CuzickA]

The key issue is that hyphae are part of a multicellular individual. Therefore they should not be cellular processes, but individual processes. Population growth= number of individuals Cell growth is increases in cell size (single cell) Individual growth is either increase of cell size of all cells in an individual, or an increase in number of cells in an individual.

[CuzickA]

Move 'abnormal hyphae formation' and 'normal hyphal formation' under hyphal growth phenotype

now looks like this 620fe7a

[CuzickA]

Edit def d8e50a6 abnormal hyphae formation ->abnormal hyphal formation from A single species cellular process phenotype in which hyphae formation is abnormal. to An individual species growth phenotype in which hyphae formation is abnormal.

[CuzickA]

Next edit defs for decreased rate of germination tube formation A single species cellular process phenotype in which the rate, or speed, of germ tube formation is decreased.

decreased rate of hyphae formation-> hyphal A single species cellular process phenotype in which the rate, or speed, of hyphae formation is decreased.

increased number of hyphal septa A single species cellular process phenotype in which the number of septa produced during hyphae formation is increased.

[CuzickA]

@ValWood 1) Did we say we were leaving the 'filamentous colony phenoypes' where they were but changing the labels to 'hyphal'?

2) Are the 'cell morphology ohenotypes' moving under 'hyphal growth phenotype?

[ValWood]

1. I thought that we decided that the hyphal colony shape could all be interpreted as aspects of hyphal growth phenotypes, if so they should become related synonyms. I think we said we would only have colony morphology terms for the couple of yeast form phenotypes.

2. The ones related to growth would be synonyms of some hyphal growth phenotype (definitely the size ones).

hyper branching and sinusoidal filament can go under morphology, but not under cell morphology

Does that make sense?

[CuzickA]

Thanks @ValWood For the hyphal colony size terms I propose...

101764f

PHIPO:0001209 hyphal colony size phenotype will merge (and become related synonym) into PHIPO:0001214 hyphal growth phenotype

PHIPO:0001054 abnormal size of filamentous colony will merge (and become related synonym) into PHIPO:0001215 abnormal hyphal growth 7f510c1 32d9ca0 ad791e2

NTR: abnormal hyphal growth deb0ce2

PHIPO:0000205 decreased aerial height of filamentous colony is moved under parent 'PHIPO:0001212 decreased hyphal growth' 4bbeccd

PHIPO:0001146 decreased size of filamentous colony will merge (and become related synonym) into PHIPO:0001212 decreased hyphal growth 4bbeccd

PHIPO:0001066 normal size of filamentous colony will merge (and become related synonym) into PHIPO:0001210 normal hyphal growth e08e0c8

PHIPO:0000196 normal aerial height of filamentous colony is moved under parent 'PHIPO:0001210 normal hyphal growth' eed92f1

PHIPO:0001210 normal hyphal growth remove parent PHIPO:0001209 hyphal colony size phenotype e08e0c8

Val- please could you sanity check for me?

[CuzickA]

Remove parent 'colony morphology' from 'hyphal growth phenotype' 409ab1b

[CuzickA]

PHIPO:0000273 filamentous colony shape phenotype merge into PHIPO:0001214 hyphal growth phenotype (related synonym) 1730798

PHIPO:0000958 'abnormal shape of hyphal colony' merge into PHIPO:0001097 'abnormal hyphal formation' ff4df31

PHIPO:0000278 normal hyphal colony shape merge into PHIPO:0001211 'normal hyphal formation' 889ba93

[CuzickA]

PHIPO:0001208 colony morphology phenotype edit to unicellular colony morphology phenotype

old def A single species population phenotype affecting the morphology of a colony. new def A single species population phenotype affecting the morphology of a colony of unicellular individuals.

Comment: Note that colony morphology terms are not used in PHIPO to annotate filamentous-form colonies because these phenotypes can be related to specific growth terms for hyphal colony morphology please search for PHIPO:0001214 (Hyphal growth phenotype). For unicellular colony morphology at the usual resolution it is usually not possible to make any statement about an individual. For dimorphic pathogens these terms are suitable for yeast-form colony phenotypes.

Add 'unicellular' to all these term names and update defs.

437f7ad Done now looks like

[CuzickA]

PHIPO:0000963 normal population growth during dimorphic hyphal-form @jseager7 Please could you pull out any sessions where this term has been used? Thanks

[jseager7]

@CuzickA The only usage of 'normal population growth during dimorphic hyphal-form' term is in PMID:29020037 (as of 30 November).

[CuzickA]

Edit def for PHIPO:0001214 hyphal growth phenotype

to An individual species growth phenotype which affects the size, extent or rate of directional growth of an individual organism. 269d802

[CuzickA]

Add comment Although this phenotype is for an individual it can be inferred from a population in a colony.

to normal aerial height of filamentous colony normal hyphal growth abnormal hyphal growth decreased hyphal growth abolished hyphal growth decreased aerial height of filamentous colony 8460115

[CuzickA]

Questions still to address 1) Where do these terms belong ? (comment above in ticket that they do not belong under cell morphology) 2) Do we need hyphal formation and hyphal growth? 3)Need to consider terms 4) see new ticket on restructuring population growth terms into 'unicellular' and moving terms out and directly under 'single species' for terms that can be used for both individuals and populations eg increased reistance to chemical

[ValWood]

We won't have primary termns with these names will we?

normal aerial height of filamentous colony decreased aerial height of filamentous colony

won't these need to become related synonyms of normal aerial height of filament etc?

[CuzickA]

I could change the term labels to normal aerial height of filamentous colony ->normal aerial height of filament

In the past we thought we could combine 'aerial filament height' with 'filament length' but we had one paper where there was a change in the aerial height of the filament but not the radial length of the filament on the plate (or maybe the other way around I cant quite remember ;-)). Do we need to keep these terms separate? it is quite common to look at aerial height of fungal colonies so it may be useful to have both.

[ValWood]

I think it is OK to annotate

normal aerial height of filamentous colony to normal aerial height of filament

we want to move away from colony terms for describing anything other than yeast-type growth (normal aerial height of filamentous colony would be a related synonym do people will find it)

Although observed in a different way it's really showing the same thing isn't it?

[CuzickA]

so is it ok to have both normal aerial height of filament and normal filament length (for radial growth on plate)?

[ValWood]

normal aerial height of filament and normal filament length (for radial growth on plate)?

I feel that they can probably both exist. should height be a descendant of length? I guess things can be higher and not longer (depending on 'waviness?' ) so maybe not?

[CuzickA]

PHIPO:0000196 normal aerial height of filamentous colony ->normal aerial height of filament

Old def A single species hyphal colony shape phenotype where the aerial height of the filamentous colony is normal (indistinguishable from wild type).

New def An individual species growth phenotype in which the aerial height of an individual hypha is normal (indistinguishable from wild type).

0cb30ed

[CuzickA]

PHIPO:0000295 decreased aerial height of filamentous colony -> decreased aerial height of filament

old def A single species hyphal colony morphology phenotype where the aerial height of the filaments is decreased affecting colony shape.

new def An individual species growth phenotype in which the aerial height of an individual hypha is decreased.

d3d33e7

[CuzickA]

Should the terms under 'cell morphology phenotype' all move to 'morphology phenotype'

note that 'morphology phenotype' and children do not have any definitions.

[CuzickA]

Next: 1) check defs for hyphal growth terms see below 2) look at morphology phenotype AND cell morphology phenotype see #297

[CuzickA]

Edit defs and move terms in PHIPO:0001214 'hyphal growth phenotype' branch 6b3d382

[CuzickA]

merge PHIPO:0001211 normal hyphal formation into PHIPO:0001210 normal hyphal growth 7c5b3e9 2b83e70 cc1099b 4994bf4

[CuzickA]

merge PHIPO:0001087 'abnormal hyphal formation' into PHIPO:0001215 'abnormal hyphal growth' 0547e38

[CuzickA]

I think all tasks are completed here now so closing this ticket.

[jseager7]

@CuzickA I've fixed a problem in one of the commits above, where PHIPO:0001052 'hyper-smooth unicellular colony shape' had been merged into PHIPO:0001215 'abnormal hyphal growth', instead of PHIPO:0001054 'abnormal size of filamentous colony' as intended. This might be the cause of the problem that was causing 'decreased hyphal growth' to be blocked for annotation.

Here's the fix: ec3200c517464391e979e2408bdaa48b826815b5

[CuzickA]

Well spotted! Thank you @jseager7