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microbialphenotypes / OMP-ontology

This repository contains the editors's working copy of OMP and public release files.
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Cryptococcus NTR: chitin deposition phenotype #100

Open Achchuthan opened 8 years ago

Achchuthan commented 8 years ago

NTR 1) chitin deposition phenotype xref: CHEBI:17029 " chitin"

APO cross-refs: id: APO:0000199 name: chitin deposition namespace: observable alt_id: YPO:0000199 def: "The pattern of chitin deposition in the cell wall." [SGD:mcc] subset: AspGD subset: CGD subset: CryptoGD subset: SGD is_a: APO:0000053 ! cell wall morphology

2) altered chitin deposition (is_a chitin deposition phenotype) 3) increased chitin deposition (is_a altered chitin deposition) 4) decreased chitin deposition (is_a altered chitin deposition) 5) abolished chitin deposition (is_a decreased chitin deposition)

dianeoinglis commented 8 years ago

These terms are ready to be created, especially:

altered chitin deposition increased chitin deposition decreased chitin deposition

Thanks, Diane

dianeoinglis commented 8 years ago

Pending term creation

dsiegele commented 7 years ago

I created the following terms. Please send feedback on definitions. Thank you!

OMP:0007624 presence of chitin in cell wall (is_a presence of cell wall) def: A presence of cell wall phenotype where the cell wall of a microbe contains chitin (CHEBI:17029).

OMP:0007625 absence of chitin in cell wall (is_a presence of cell wall) def: A presence of cell wall phenotype where the cell wall of a microbe doesn't contain chitin (CHEBI:17029).

OMP:0007626 altered cell wall chitin level (is_a altered cell wall morphology) def: An altered cell wall morphology phenotype where the amount of chitin (CHEBI:17029) measured in the cell wall of a microbe is altered relative to a designated control.

OMP:0007627 increased cell wall chitin level (is_a altered cell wall chitin level) def: An altered cell wall chitin level phenotype where the amount of chitin measured in the cell wall is increased relative to a designated control.

OMP:0007628 decreased cell wall chitin level (is_a altered cell wall chitin level) def: An altered cell wall chitin level phenotype where the amount of chitin measured in the cell wall is decreased relative to a designated control.

OMP:0007629 abolished cell wall chitin level (is_a decreased cell wall chitin level) def: A decreased cell wall chitin level phenotype where the amount of chitin in the cell wall is abolished.

dsiegele commented 7 years ago

When working on these terms I discovered that OMP:0007277 ‘cell wall phenotype’ and OMP:0005233 ‘cell wall morphology phenotype’ have the same definition. This is a relic of an early stage of the ontology where there was some interleaving of biological process phenotypes and cellular component phenotypes. I think the best way to deal with this is to obsolete one of the terms. Renamed OMP:0007277 ‘cell wall morphology phenotype’ and made it obsolete. Indicated OMP:0005233 as the replacement term.