taskGNU Health - Tasks: task #16404, Update functionality in Health...

 
 

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task #16404: Update functionality in Health Genetics packages

Submitter:  Luis Falcon <meanmicio>
Submitted:  Sat 22 Jul 2023 09:30:50 PM UTC
   
 
Should Start On:  Sat 22 Jul 2023 12:00:00 AM UTC Should be Finished on:  Wed 22 Nov 2023 12:00:00 AM UTC
Category:  Data model Priority:  5 - Normal
Status:  Done Privacy:  Public
Assigned to:  meanmicio Percent Complete:  100%
Open/Closed:  Closed Release:  4.3.0
Module:  health_genetics Component:  Hospital Management

Jump to the original submission

Sun 06 Aug 2023 07:09:21 PM UTC, comment #9: 

health_genetics: Include URL to NCBI Reference SNP link  on natural variant. Make it clickable both in tree and form view.

https://hg.savannah.gnu.org/hgweb/health/rev/81d7c2eb2bea


Luis Falcon <meanmicio>
Group administrator
Mon 31 Jul 2023 08:47:51 PM UTC, comment #8: 

changeset:   6006:6bcb6ed503df
tag:         tip
user:        Luis Falcon <falcon@gnuhealth.org>
date:        Mon Jul 31 21:44:25 2023 +0100
summary:     health_genetics_uniprot: Update variants genotypes datafile (Task #16404)

changeset:   6003:a42ff8fc154f
user:        Luis Falcon <falcon@gnuhealth.org>
date:        Sun Jul 30 19:28:54 2023 +0100
summary:     health_genetics_uniprot: Update protein diseases datafile  (Task #16404)

changeset:   6002:31a1a6accb2b
user:        Luis Falcon <falcon@gnuhealth.org>
date:        Sun Jul 30 19:20:53 2023 +0100
summary:     health_genetics: Use xrefs in tree view to broaden search  (Task #16404)

changeset:   6001:19eaac7a9e63
user:        Luis Falcon <falcon@gnuhealth.org>
date:        Sun Jul 30 18:30:04 2023 +0100
summary:     health_genetics: Include MIM reference in protein diseases tree view  (Task #16404)

changeset:   6000:ac26acb4cf98
user:        Luis Falcon <falcon@gnuhealth.org>
date:        Sun Jul 30 11:40:33 2023 +0100
summary:     health_genetics: Rename dominance by inheritance_pattern  (Task #16404)

changeset:   5999:a014a117b9d7
user:        Luis Falcon <falcon@gnuhealth.org>
date:        Sun Jul 30 11:25:03 2023 +0100
summary:     Simplify protein-related views and terms  (Task #16404)

Luis Falcon <meanmicio>
Group administrator
Sun 30 Jul 2023 09:36:52 AM UTC, comment #7: 
Luis Falcon <meanmicio>
Group administrator
Sat 29 Jul 2023 07:23:02 PM UTC, comment #6: 

https://hg.savannah.gnu.org/hgweb/health/rev/8113f9148c16

Task #16404: Update functionality genetics packages

health_genetics:

  • Use human genes datafiles for grch38 and alternative loci
  • Include xrefs, protein and keywords in genetic diseases
  • Improve field descriptions
Luis Falcon <meanmicio>
Group administrator
Wed 26 Jul 2023 05:39:53 PM UTC, comment #5: 
  • Update and remove obsolete references of natural variants and phenotypes


    https://hg.savannah.gnu.org/hgweb/health/rev/8a94de111c42

  • Gene related proteins are now managed in main health_genetics package


   https://hg.savannah.gnu.org/hgweb/health/rev/6a87206acd60


Luis Falcon <meanmicio>
Group administrator
Wed 26 Jul 2023 12:21:38 AM UTC, comment #4: 
Luis Falcon <meanmicio>
Group administrator
Tue 25 Jul 2023 02:41:52 PM UTC, comment #3: 

https://hg.savannah.gnu.org/hgweb/health/rev/46fceee849f4

  • Include name aliases, omim, ensembl and refseq accession ids to gnuhealth.gene model.


  • Remove required and select from aliases attribute
Luis Falcon <meanmicio>
Group administrator
Sun 23 Jul 2023 06:25:50 PM UTC, comment #2: 

https://hg.savannah.gnu.org/hgweb/health/rev/6086a5d20fd7

  • Include hgnc_id
  • The primary key is now the HGNC identifier
  • Add symbol aliases
  • Include locus group and type
  • Update Gene form and tree view


Luis Falcon <meanmicio>
Group administrator
Sat 22 Jul 2023 09:39:30 PM UTC, comment #1: 

https://hg.savannah.gnu.org/hgweb/health/rev/1918c0c5d43d

  • Rename gnuhealth.disease.gene model to gnuhealth.gene
  • Rename disease_genes xml data files to human_genes
  • Update views and references in related modules


Luis Falcon <meanmicio>
Group administrator
Sat 22 Jul 2023 09:30:50 PM UTC, original submission:  

I'd like to update the genetics modules family (genetics, uniprot..) to be more generic and scalable.

This task will document the changes for the upcoming 4.4 release.


Luis Falcon <meanmicio>
Group administrator

 

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    Follow 9 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2023-12-23 meanmicio StatusReady For Test Done
        Open/ClosedOpen Closed
    2023-07-31 meanmicio StatusIn Progress Ready For Test
        Percent Complete80% 100%
    2023-07-29 meanmicio Percent Complete70% 80%
    2023-07-26 meanmicio Percent Complete60% 70%
    2023-07-26 meanmicio Percent Complete20% 60%
    2023-07-22 meanmicio Percent Complete0% 20%
    2023-07-22 meanmicio ReleaseNone 4.3.0

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