Those annotations are in the session and in Chado. I guess the session must have been APPROVED when the last Chado load was done. Did you reactivate it?
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The annotations from APPROVED sessions get loaded into Chado, but they stay in the session. All annotations added in a session get called "new". That makes sense until you approve them. Perhaps they should be called "Approved" annotations once the session is approved? It's still going to be confusing if you re-activate a session.
Once we stop re-loading Chado at each release this problem will go away. APPROVED sessions will be loaded into Chado then marked as EXPORTED. Once a session is EXPORTED it won't be able to be edited.
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To be fair, do we need to make the distinction between "what is loaded at the moment" and "what will be loaded next load"?
If it is less confusing, just show 2 things:
- "what will be loaded from this session" (all the annotations made using canto) &
- "what is loaded from the embl files" (legacy stuff)
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I think labelling as APPROVED AND EXPORTED would help.
However, my problem with this session is that it has not yet been approved. I have not finished annotating it. This is why I was confused to see existing and new although I asked the question the wrong way around. I only expected to see 'new' and not 'existing'.
Probably a consequence of the migration? Perhaps you needed to treat in progress sessions as completed sessions to do the migration and so now, they show as both 'existing' and 'new' even though they have not been through approval?
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I don't think so. The "existing" section only shows stuff from Chado. If you're seeing annotation from the current session in the existing sections then the session must have been in the "APPROVED" state when Chado was loaded. Is it a session you reactivated?
This shouldn't happen to community curators.
If it is less confusing, just show 2 things:
- "what will be loaded from this session" (all the annotations made using canto) &
- "what is loaded from the embl files" (legacy stuff)
I agree about the first point, but the second should probably be "anything in Chado that isn't from Canto". Does that make sense?
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Lets not worry about this right now. It isn't a big issue, and won't be for the community as they won't often see reopened sessions. I think ideally longer term it would be good if we did not need to see existing annotations twice but lets revisit this when everything else is done.
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Can you give me an example? I just checked and all of the annotations shown as new are in the database.
Here,
curs/4794f2ac68f1b5ba
existing annotations
spo7 GO:0034399 nuclear periphery [exists_during] meiosis II IDA
spo7 GO:0035974 meiotic spindle pole body [exists_during] meiotic metaphase II IDA
also show as "new annotations"
I think this is just "how it is", probably its only confusing to me as I am opening old sessions.
Those annotations are in the session and in Chado. I guess the session must have been APPROVED when the last Chado load was done. Did you reactivate it?
Yes, I reactivated the session.
I guess I only expect them to appear as "existing" because they are not new annotations.
Why do they appear as both "new" and "eixisting"?
The annotations from APPROVED sessions get loaded into Chado, but they stay in the session. All annotations added in a session get called "new". That makes sense until you approve them. Perhaps they should be called "Approved" annotations once the session is approved? It's still going to be confusing if you re-activate a session.
Once we stop re-loading Chado at each release this problem will go away. APPROVED sessions will be loaded into Chado then marked as EXPORTED. Once a session is EXPORTED it won't be able to be edited.
Antonia asked
To be fair, do we need to make the distinction between "what is loaded at the moment" and "what will be loaded next load"?
If it is less confusing, just show 2 things:
- "what will be loaded from this session" (all the annotations made using canto) &
- "what is loaded from the embl files" (legacy stuff)
I think labelling as APPROVED AND EXPORTED would help.
However, my problem with this session is that it has not yet been approved. I have not finished annotating it. This is why I was confused to see existing and new although I asked the question the wrong way around. I only expected to see 'new' and not 'existing'.
Probably a consequence of the migration? Perhaps you needed to treat in progress sessions as completed sessions to do the migration and so now, they show as both 'existing' and 'new' even though they have not been through approval?
I don't think so. The "existing" section only shows stuff from Chado. If you're seeing annotation from the current session in the existing sections then the session must have been in the "APPROVED" state when Chado was loaded. Is it a session you reactivated?
This shouldn't happen to community curators.
I agree about the first point, but the second should probably be "anything in Chado that isn't from Canto". Does that make sense?
Yeah that makes sense.
Yeah I was getting really confused. I think it is all OK. This is how it has always been....
Lets adress this one later...it seems low priority. We can discuss on a call?
See also: https://sourceforge.net/p/pombase/curation-tool/839/
Perhaps we could rename the "existing" annotation section to: "Other annotation for PMID:01242424 in PomBase:"? Is that more obvious?
Lets not worry about this right now. It isn't a big issue, and won't be for the community as they won't often see reopened sessions. I think ideally longer term it would be good if we did not need to see existing annotations twice but lets revisit this when everything else is done.
Diff: