Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#1133 closed enhancement (fixed)

Experimental factors - inherit annotations

Reported by: base Owned by: Nicklas Nordborg
Priority: minor Milestone: BASE 2.9
Component: web Version: 2.8.2
Keywords: Cc:

Description

I have in BASE2 created a new annotation at the Biosource level. When I want to use this annotation as an experimental factor in an experiment, i must manually edit it to be inherited under under the 'inherited annotations' tab. This has to be done one by one for each raw bioassay included within the experiment - and thus very laborious if the experiment holds many raw bioassays (in my case more than 200). I suggest that annotations defined as experimental factors in an experiment should be automatically inherited to their raw bioassays - as they were in in BASE 1.

Change History (7)

comment:1 Changed 12 years ago by Nicklas Nordborg

It is not trivial to automatically inherit annotations. There must be some kind of manual interaction, since a raw bioassay may have multiple parents of the same type with different annotation values. Suggestions for a user interface for this are welcome.

Maybe it would work to just inherit all annotations that we can find, and then use the "Experiment overview", which generate warnings if multiple inherited annotations are found, to manually remove the annotations that are not wanted.

comment:2 Changed 12 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

I'll have a go at this. I am thinking of something like a "Auto inherit" button for each row in the experimental factors tables on the experiment view page. When clicking on the button BASE will try to automatically find and inherit annotations of the specified experimental factor to all raw bioassays that:

  • Doesn't already has a value for that experimental factor
  • The logged in user has write permission

comment:3 Changed 12 years ago by Nicklas Nordborg

Duplicates needs to be manually removed.

comment:4 Changed 12 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [4630]) Fixes #1133: Experimental factors - inherit annotations

comment:5 Changed 12 years ago by Nicklas Nordborg

Component: corepluginsweb
Milestone: BASE 2.9
Priority: majorminor

comment:6 Changed 12 years ago by Nicklas Nordborg

(In [4651]) References #1133: Experimental factors - inherit annotations

Closing an unclosed tag (>).

comment:7 Changed 12 years ago by Nicklas Nordborg

(In [4652]) References #1133: Experimental factors - inherit annotations

Changed instructions to use the automatic function instead of the manual procedure.

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