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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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(1d) Gene -> Pseudogene post-annotation #495

Closed nathandunn closed 8 years ago

nathandunn commented 9 years ago

We had discussed some ways to annotate pseudogenes. It seemed as though the major problem was that pseudogenes were either initially being annotated wrong (drag and drop default) or that further evidence changed the prediction.

Ideas: 1 - have users choose on the onset when dragging 2 - allow users to change the type from Gene -> Pseudogene -> Feature (RepeatRegion / TransposableElement).

If we choose 2, will likely execute SQL manually on backend and re-query the object. Both quick and complete. Will probably have to delete attributes (CDS, exons, transcripts etc.) depending on transformation.

nathandunn commented 9 years ago

FYI @mpoelchau @childers @selewis

selewis commented 9 years ago

On Thu, Jul 23, 2015 at 11:40 AM, Nathan Dunn notifications@github.com wrote:

We had discussed some ways to annotate pseudogenes. It seemed as though the major problem was that pseudogenes were either initially being annotated wrong (drag and drop default) or that further evidence changed the prediction.

Ideas: 1 - have users choose on the onset when dragging

1 is what we have now. It's awful (prone to errors or creating excessive

demands on the curators. Either way a bad situation)

2 - allow users to change the type from Gene -> Pseudogene -> Feature (RepeatRegion / TransposableElement)

Don't constrain it at all. Users should be able to switch from feature type A to feature type B as needed (and back again). The wee bit of complexity is that some features have a different 'depth' and the history will need to keep track of the prior depth.

Also wanted to add that in past discussions it's clear that 'pseudo' can be apply to different levels (pseudogene, pseudotranscript, pseudoexon). It seems to be synonymous with broken/non-functional. Don't think we need to go there yet, but bear it in mind.

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Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/495.

nathandunn commented 8 years ago

This is a duplicate / sub-case of #220 .