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geneontology / noctua-form-legacy

Simple annoton editor workbench for Noctua.
BSD 3-Clause "New" or "Revised" License
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External Search for existing annotations #41

Open tmushayahama opened 6 years ago

tmushayahama commented 6 years ago

This feature lets you quickly do an "external search" to Golr server for existing annotations for that particular GP and aspect. It works just like the Component Companion.

In Brief

Step 1 - Enter Gene Product

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Step 2 - Select 1 or more rows and Click Save

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Step 3 - Your fields are populated

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@thomaspd Can you explain in more details. @kltm @cmungall

cmungall commented 6 years ago

is this scheduled for 1.0?

thomaspd commented 6 years ago

I don’t think it’s in the requirements but it’s one of the first things curators ask for when they see Noctua. So as long as it doesn’t delay the 1.0 release date I think it would be good to include it.

From: Chris Mungall notifications@github.com Reply-To: geneontology/simple-annoton-editor reply@reply.github.com Date: Monday, March 12, 2018 at 2:59 PM To: geneontology/simple-annoton-editor simple-annoton-editor@noreply.github.com Cc: Paul Denis Thomas pdthomas@usc.edu, Mention mention@noreply.github.com Subject: Re: [geneontology/simple-annoton-editor] External Search for existing annotations (#41) Resent-From: pdthomas@usc.edu

is this scheduled for 1.0?

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thomaspd commented 6 years ago

The major use case is for curators trying to create a larger "pathway" or other model, using annotations that are already in the GO database. This was in the original spec Huaiyu and I drew up years ago, and multiple curation groups asked for this functionality during the Noctua demos at EBI and the Corvallis meeting. UCL was waiting for this functionality before creating larger models for SynGO.

tmushayahama commented 6 years ago

@cmungall @kltm from the earlier conversation about groups,

  1. Is there a way to attribute (providedBy) on each evidence node when a user is using annotations that are already in the GO database?
  2. If(1) then how do I easily get the uri from the group shorthand?
kltm commented 6 years ago

This sounds like: https://github.com/geneontology/noctua/issues/539#issue-297183549 https://github.com/geneontology/noctua/issues/458#issuecomment-369333576

I believe the current function companion technically accomplishes your 1 (and maybe 2), but I think we want to revisit if that is really what we want to do. As well, we should not have independent implementations of this translation.

vanaukenk commented 6 years ago

Also see: https://github.com/geneontology/simple-annoton-editor/issues/78