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Fix aging related trait definitions #239

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rays22 opened this issue Apr 27, 2023 · 0 comments
Open

Fix aging related trait definitions #239

rays22 opened this issue Apr 27, 2023 · 0 comments
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rays22 commented Apr 27, 2023

GO editors think that the process of aging GO:0007568 is a phenotype: [The reason for obsoletion is that this represents a phenotype.] (geneontology/go-announcements#502)
There are several traits, phenotypes and diseases that are related to the process of ageing/aging.
I would live happily without ageing, but I need to fix the definitions of some ageing-related OBA terms:

entity_attribute.tsv
2736:OBA:0003870                GO:0007568      aging   PATO:0002325    onset quality
3652:OBA:0005494                GO:0007568      aging   PATO:0000161    rate

Shall I create new PATO quality terms for these?

  1. aging onset quality
  2. aging rate

I can use the new PATO terms this way:

2736:OBA:0003870                NCBITaxon:131567      cellular organisms   PATO:???????    aging onset quality
3652:OBA:0005494                GO:NCBITaxon:131567      cellular organisms   PATO:???????    aging rate
@rays22 rays22 self-assigned this Apr 27, 2023
@rays22 rays22 converted this from a draft issue Apr 27, 2023
rays22 added a commit that referenced this issue Apr 27, 2023
@rays22
Temporarily remove terms using obsolete GO aging process
b931b8e 
This commit intends to provide a short term fix for the issues caused by the obsoletion of the process term [aging GO:0007568](geneontology/go-announcements#502).
Need to add back these terms once there are appropriate replacement terms for [GO:0007568](https://www.ebi.ac.uk/ols/ontologies/GO/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0007568). See related issue #239.
gouttegd added a commit to FlyBase/drosophila-phenotype-ontology that referenced this issue Apr 27, 2023
@gouttegd
Redefine 'abnormal aging' to remove dependency on GO:0007568.
216da10 
Since 'aging' (GO:0007568) is now obsolete in GO, and does not have a
proposed replacement AFAIK, we redefine our own 'abnormal aging' so that
it no longer depends on the obsoleted GO term. Likewise for the
subclasses 'increased speed of aging' and 'decreased speed of aging'.

There is a proposal to create an 'aging rate' quality in PATO
(obophenotype/bio-attribute-ontology#239) that
we could use to maintain a logical definition of 'abnormal aging', but
until that quality is available and with the FBcv release planned for
next week (and with it the refresh of the GO import, which will bring in
the obsoletion of GO:0007568), for now we remove the logical definition
entirely.

closes #168
@gouttegd gouttegd mentioned this issue Apr 27, 2023
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@rays22 rays22 mentioned this issue Apr 28, 2023
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