Cryptococcus NTR: capsule size and morphology phenotype

[dianeoinglis]

I do not see any existing terms for capsule morphology. Let me know if I missed them. Formally, the capsule is cell-associated and is external to the cell. An observation of increased or decreased capsule width does not necessarily include a measurement of 'capsule amount.' The synthesis of capsule components is an independent step from capsule formation.

altered capsule morphology phenotype altered capsule size phenotype increased capsule size phenotype decreased capsule size phenotype

Def: "An encapsulating structure phenotype relating to the size, shape, or appearance of the cell-associated extracellular capsule."

Ref issue #76

Thank you, Diane

[dsiegele]

Diane,

Reviewing this request and issue #76, I realize that the existing OMP terms for capsule phenotypes (see below) were supposed to be capsule morphology terms. (Their organization in the ontology is: capsule phenotype is_a cell envelope phenotype is_a cell morphology phenotype.) But when I responded to issue #76, I conflated capsule morphology and capsule formation. Now I need to correct my mistake and separate capsule morphology and capsule formation phenotypes but I don't want to make things worse by changing terms you have already used for annotation. Would you please let me know which of the existing terms you have used and how you used them? I will edit the definitions per your suggestions in issue #76.

Existing OMP terms: OMP:0000203 capsule phenotype .....OMP:0000211 absence of capsule .....OMP:0007133 altered capsule phenotype ..........OMP:0000050 decreased amount of capsule ..............OMP:0006102 abolished capsule formation ..........OMP:0000036 increased amount of capsule .....OMP:0000204 presence of capsule

I will add the new terms you requested above: altered capsule morphology phenotype altered capsule size phenotype increased capsule size phenotype decreased capsule size phenotype

Thank you,

Debby

[dsiegele]

Terms made: OMP:0007502 altered capsule morphology .....OMP:0007503 altered capsule size ..........OMP:0007505 decreased capsule size ..........OMP:0007504 increased capsule size

[dianeoinglis]

Hello Debby,

I think this is the information you requested.

Existing OMP:0000204 presence of capsuleused for “capsule formation: normal”

Existing OMP:0007133 altered capsule phenotype replaced APO “capsule formation: abnormal” which was used as a placeholder for the requested NTR “altered capsule morphology” for “asymmetric, partially detached capsule”and altered polysaccharide composition”

Existing OMP:0000050 decreased amount of capsule used for APO “capsule formation: decreased” (not accurate term for phenotype)

Existing OMP:0006102 abolished capsule formation used for “capsule formation: absent”

Existing OMP:0000036 increased amount of capsule used for APO “capsule formation increased” which is not ideal for “thicker capsule phenotype.” Waiting for NTR “increased capsule size”

Requested NTR “increased capsule size” to be used for observed “enlarged capsule” phenotype

Requested NTR: “altered capsule morphology phenotype” will be used for observed asymmetric, partially detached capsule”

Requested NTR: “decreased capsule size phenotype” will be used for observed “small capsule”

Thank you, Diane

[dsiegele]

Diane,

Thank you for the information on how you've used OMP terms to annotate Cryptococcus genomes. I added your information to a summary of the existing capsule terms in OMP.

I'd appreciate your feedback on my ideas for reorganizing the terms. ..... i) OMP:0006102 ! abolished capsule formation. Move this term to be a child of OMP:0007505 ! decreased capsule size and perhaps change the name to just 'abolished capsule' ..... ii) obsolete OMP:0000037 ! increased amount of capsule and OMP:0000050 ! decreased amount of capsule.

I will make a term for altered composition of capsule. Is this definition OK? An altered capsule morphology phenotype where the composition of the capsule is altered relative to a designated control.

Thank you,

Debby

2016-11-19 summary of capsule terms in OMP and their use for annotating Cryptococcus phenotypes

OMP:0000203 capsule phenotype .....OMP:0000204 presence of capsule used for APO “capsule formation: normal” .....OMP:0000211 absence of capsule

.....OMP:0007133 altered capsule phenotype used as a placeholder for the requested NTR “altered capsule morphology” for “asymmetric, partially detached capsule”and altered polysaccharide composition” ..........OMP:0000036 increased amount of capsule used for APO “capsule formation increased” which is not ideal for “thicker capsule phenotype.” Waiting for NTR “increased capsule size” ..........OMP:0000050 decreased amount of capsule used for APO “capsule formation: decreased” (not accurate term for phenotype) ...............OMP:0006102 abolished capsule formation used for APO “capsule formation: absent”

.....OMP:0007502 altered capsule morphology ..........OMP:0007503 altered capsule size ...............OMP:0007505 decreased capsule size will be used for observed “small capsule” ...............OMP:0007504 increased capsule size to be used for observed “enlarged capsule” phenotype