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Virtual Cell Framework
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Expand search to include annotations #223

Open ACowan0105 opened 2 years ago

ACowan0105 commented 2 years ago

Also a note to copy annotations from reactions to global parameters, needs clarification from Michael

jcschaff commented 8 months ago

It is unclear which search we are talking about:

  1. within database panel: search is currently client-side and can search through the loaded metadata stored with the list BioModelInfo objects to which the user has access. It would be inefficient to include all metadata with all biomodelinfo objejcts.
  2. server-side search??: would need to do database work to do this in a relational database. It may be more fruitful to use something like ElasticSearch instead (maybe @vcellmike and @jcschaff can discuss)
danv61 commented 8 months ago

@jcschaff @vcellmike I think it's about the search / filtering feature available in all the upper right corner tables of vcell. I'm not sure if it's about search within the user defined cross references, the text annotations, or both. Either way, I also think it would be time intensive, but I'm not sure how bad. Could be easy to implement for just one table (say, species) and see just how bad it is.

vcellmike commented 8 months ago

Server-side search (e.g. ElasticSearch) is the way to go, as it can be used with the web, not just the client.

Client-side search works on metadata that is manually added to the Publications table. It would be great to add PubMed and doi to searchable metadata if they are added through VCell annotations panel. Right now no annotations are searchable. It would be enough to add at least top-level annotations to metadata, if it's easy.

From: Jim Schaff @.> Sent: Monday, November 6, 2023 12:06 PM To: virtualcell/vcell @.> Cc: Blinov,Michael @.>; Mention @.> Subject: Re: [virtualcell/vcell] Expand search to include annotations (Issue #223)

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It is unclear which search we are talking about:

  1. within database panel: search is currently client-side and can search through the loaded metadata stored with the list BioModelInfo objects to which the user has access. It would be inefficient to include all metadata with all biomodelinfo objejcts.
  2. server-side search??: would need to do database work to do this in a relational database. It may be more fruitful to use something like ElasticSearch instead (maybe @vcellmikehttps://urldefense.com/v3/__https://github.com/vcellmike__;!!Cn_UX_p3!mtSWKfA2NXRDm5dg2jr676Jd60zR9Nm92SwJ1AWEkbSwnCJAC91DdOKTjyqbRGaIwSPIz0eVaSlULdL9BGiwNAVd$ and @jcschaffhttps://urldefense.com/v3/__https://github.com/jcschaff__;!!Cn_UX_p3!mtSWKfA2NXRDm5dg2jr676Jd60zR9Nm92SwJ1AWEkbSwnCJAC91DdOKTjyqbRGaIwSPIz0eVaSlULdL9BP9V5NM4$ can discuss)

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