NTR: normal resting structure and anatomical structure grouping terms

[CuzickA]

Terms for 'sclerotia' are needed for https://github.com/PHI-base/curation/issues/120 and https://github.com/PHI-base/curation/issues/192

For https://github.com/PHI-base/curation/issues/192 we need 'normal sclerotia production' and for https://github.com/PHI-base/curation/issues/120 we need altered sclerotia production 'increased number of sclerotia' and 'decreased number of sclerotia'.

These terms are not straight forward so I undertook a thread of email discussion with @martin2urban to figure out the best term name and positioning of the term in PHIPO. The example we discussed was for https://github.com/PHI-base/curation/issues/192 'normal sclerotia production'. I will document our discussion in the comments below.

@ValWood, we would appreciate your input on the reasoning that we have used below

[CuzickA]

Initial email where I thought sclerotia may fit under reproductive phenotype

Email response from Martin

Examples for resting structures known in fungi:

• Sclerotium: A compact, hardened mass of fungal tissue that allows the fungus to survive adverse conditions and serve as a reservoir of nutrients.
• Chlamydospore: A thick-walled spore formed by certain fungi that functions as a survival structure during unfavorable conditions.
• Teliospore: A specialized spore produced by fungi of the order Ustilaginales (smut fungi) that plays a role in the life cycle and dissemination of the fungus.
• Stromata: Compact structures made up of fungal tissue that can serve as a resting stage for certain fungal species and as sites for spore production.
• Hibernating mycelium: A dormant mycelium formed by some fungi that remains inactive during unfavorable conditions until conditions become more favorable for growth.

Telia (singular: telium) are structures found in certain species of fungi, particularly those belonging to the order Ustilaginales, commonly known as smut fungi. Telia are often visible as dark, swollen, or galled areas on the host plant. Teliospores are typically formed inside structures called telia, which are dark, swollen, or galled structures found on the host plant. The teliospores are thick-walled and compact, allowing them to withstand harsh environmental conditions and persist for extended periods. They are often dormant and have a resting stage, enabling the fungus to survive unfavorable conditions such as cold temperatures or periods of drought.Teliospores play a crucial role in the life cycle of smut fungi. Under favorable conditions, teliospores germinate and give rise to basidiospores or sporidia, which are capable of infecting host plants and initiating a new cycle of infection and reproduction. In summary, teliospores are specialized spores produced by smut fungi that allow the fungus to survive harsh environments and serve as a means of dissemination to new host plants, contributing to the overall reproductive cycle of these fungi.

Discussion We decided to use the phrase 'resting structure' to cover the set of examples above, which could be added in as synonyms.

[CuzickA]

My follow up question

'Do you think we could add in the word ‘reproduction’? So the new term would be ‘Normal reproductive resting structure’?'

Answer

According to Merlin AI: No, resting structures are not reproductive structures. Resting structures are structures that are present in an organism but are not involved in reproduction. Examples of resting structures include leaves, branches, and roots. Reproductive structures, on the other hand, are structures that are involved in the production of offspring, such as flowers, fruits, and seeds.

I think it is a reasonable answer. The primary function of resting structures is not reproduction. (see more beneath)

Chlamydospores are not primarily considered reproductive structures in fungi. While chlamydospores can potentially contribute to the dispersal and propagation of fungi under certain circumstances, their main function is to provide a means of survival and stress resistance rather than direct reproduction. Chlamydospores are formed in response to adverse conditions and serve as a means for fungi to remain dormant until more favorable conditions arise. Once conditions improve, chlamydospores can germinate and give rise to actively growing hyphae, which can then produce reproductive structures, such as spores, to facilitate sexual or asexual reproduction. However, it is important to note that the primary purpose of chlamydospores is not reproduction, but rather survival and persistence.

[CuzickA]

My next query is where to place this term in PHIPO as it cannot go under 'reproductive phenotype'

Placing the term under 'individual organism phenotype' does not seem appropriate as a resting structure refers to a specific anatomical structure within an individual organism, typically a tissue or organ that is in a state of relaxation or dormancy. It is not a whole individual organism.

[CuzickA]

Suggestions for checking @ValWood please

Physical quality phenotype (def: A phenotype that affects any physical object quality, such as morphology, number, location, etc., of an individual, tissue, cell, or cellular component.) -abnormal anatomical structure physical quality phenotype (def: A physical anatomical structure phenotype in which the amount, distribution, morphology, or other physical characteristic of a cell part, cell, or tissue, or individual is abnormal in the vegetative growth phase of the life cycle.) --NTR: increased number of resting structures (def: A single species phenotype where the frequency of occurrence of resting structures is increased.) --NTR: decreased number of resting structures (def: A single species phenotype where the frequency of occurrence of resting structures is decreased.) -NTR: normal anatomical structure physical quality phenotype (def: A physical anatomical structure phenotype in which the amount, distribution, morphology, or other physical characteristic of a cell part, cell, or tissue, or individual is normal in the vegetative growth phase of the life cycle (i.e. indistinguishable from wild type.) --NTR: normal number of resting structures OR presence of resting structures (def: A single species phenotype where the number of resting structures is normal (i.e. indistinguishable from wild type). OR A single species phenotype where the production of resting structures is normal)

[ValWood]

That seems to work. I would call them anatomical structure phenotypes,.

This also seems to mirror the Fungal Anatomy Ontology https://ontobee.org/ontology/FAO?iri=http://purl.obolibrary.org/obo/FAO_0001008

[CuzickA]

Thanks @ValWood , I can add the FAO as a cross-ref

Do you mean to remove 'physical quality' from 'abnormal anatomical structure physical quality phenotype' and 'NTR: normal anatomical structure physical quality phenotype'?

so that its

physical quality phenotype -anatomical structure phenotype --abnormal anatomical structure phenotype --normal anatomical structure phenotype --normal organism morphology

[ValWood]

I meant anatomical structure physical quality phenotype

[CuzickA]

Thanks @ValWood

So it would be

physical quality phenotype -NTR: anatomical structure physical quality phenotype (def: A phenotype that affects any anatomical structure physical quality, such as morphology, number, location, etc.) --abnormal anatomical structure physical quality phenotype ---NTR: increased number of resting structures ---NTR: decreased number of resting structures --NTR: normal anatomical structure physical quality phenotype ---NTR: normal number of resting structures --normal organism morphology

[ValWood]

Yes

[CuzickA]

For new term requests, please provide the following information:

Preferred term label

anatomical structure physical quality phenotype

Synonyms

Textual definition

A phenotype that affects any anatomical structure physical quality, such as morphology, number, location, etc.

Suggested parent term

physical quality phenotype (PHIPO:0001220)

fc5a4f3

[CuzickA]

Preferred term label increased number of resting structures

related synonym increased number of sclerotia

Textual definition A single species phenotype where the frequency of occurrence of resting structures is increased.

Suggested parent term abnormal anatomical structure physical quality phenotype (PHIPO:0001221)

42b19eb

[CuzickA]

Preferred term label decreased number of resting structures

related synonym decreased number of sclerotia

Textual definition A single species phenotype where the frequency of occurrence of resting structures is decreased.

Suggested parent term abnormal anatomical structure physical quality phenotype (PHIPO:0001221)

79bf754

[CuzickA]

Preferred term label normal anatomical structure physical quality phenotype

Textual definition A physical anatomical structure phenotype in which the amount, distribution, morphology, or other physical characteristic of a cell part, cell, or tissue, or individual is normal in the vegetative growth phase of the life cycle (i.e. indistinguishable from wild type.)

Suggested parent term anatomical structure physical quality phenotype (PHIPO:0001373)

1cdc754

[CuzickA]

Preferred term label normal number of resting structures

related synonym normal number of sclerotia

Textual definition A single species phenotype where the number of resting structures is normal (i.e. indistinguishable from wild type).

Suggested parent term normal anatomical structure physical quality phenotype (PHIPO:0001376)

834c761

[CuzickA]

Move 'normal filament morphology (PHIPO:0001206) under 'normal anatomical structure physical quality phenotype (PHIPO:0001376)' 8533648

Move 'abnormal anatomical structure physical quality phenotype (PHIPO:0001221)' under 'anatomical structure physical quality phenotype (PHIPO:0001373)' c2d6eb3

Now looks like this

Closing ticket as completed