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TASK-1111 Add Pharmagenomics data to CellBase #653

Merged
merged 45 commits into from
Jul 12, 2023
Merged

TASK-1111 Add Pharmagenomics data to CellBase #653

merged 45 commits into from
Jul 12, 2023

Commits on May 4, 2023

  1. lib: implement PharmGKB downloader, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 4, 2023
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  2. core: download PharmGKB variant and clinical annotation files, #TASK-… 

    …4325. #TASK-1111
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    jtarraga committed May 4, 2023
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  3. lib: add the PharmGKBBuilder class, #TASK-4325. #TASK-1111

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    jtarraga committed May 4, 2023
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Commits on May 5, 2023

  1. lib: parse PharmGKB clinical annotation files, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 5, 2023
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Commits on May 8, 2023

  1. lib: improvements in pharmacogenomics

    @imedina
    imedina committed May 8, 2023
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  2. lib: add phrama variant annotation to evidence

    @imedina
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  3. lib: parse PharmGKB study parameters file, #TASK-4325. #TASK-1111

    @jtarraga
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  4. lib: parse PharmGKB label annotation file, #TASK-4325. #TASK-1111

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  5. lib: pharmacogenomics minor improvements

    @imedina
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  6. lib: parse PharmGKB guideline, phenotype and functional annotations, … 

    …#TASK-4325. #TASK-1111
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    jtarraga committed May 8, 2023
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Commits on May 9, 2023

  1. lib: fixes and improvements in PharmGKB builder

    @imedina
    imedina committed May 9, 2023
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  2. lib: parse PharmGKB variants file to get the variant chromosome and p… 

    …osition, #TASK-4325. #TASK-1111
    @jtarraga
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  3. lib: create the pharmacogenomics JSON file after parsing the PharmGKB… 

    … files, #TASK-4325. #TASK-1111
    @jtarraga
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  4. lib: update according to the biodata changes, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 9, 2023
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  5. Add new Pharmacogeonmics REST service

    @imedina
    imedina committed May 9, 2023
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  6. app: implement the command 'load' for pharmacogenomics, #TASK-4325. #… 

    …TASK-1111
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  7. Merge branch 'TASK-1111' of https://github.com/opencb/cellbase into T… 

    …ASK-1111
    @jtarraga
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  8. server: implement pharmacogenomics web-services, #TASK-4325. #TASK-1111

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  9. lib: minor improvement in pharma clinical annotation data model

    @imedina
    imedina committed May 9, 2023
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Commits on May 10, 2023

  1. server: minor improvements of REST API

    @imedina
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  2. lib: fix parse generic names and add junit test, #TASK-4325. #TASK-1111

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  3. lib: add pharmacogenomics data to the variant annotation, #TASK-4325.… 

    … #TASK-1111
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  4. lib: add field to pharmacogenomics variant annotation

    @imedina
    imedina committed May 10, 2023
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  5. server: fix location filter in the pharmacogenomics webservice 'searc… 

    …h', #TASK-4325. #TASK-1111
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    jtarraga committed May 10, 2023
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Commits on May 11, 2023

  1. lib: filter mismatch alleles from pharmacogenomics annotation

    @imedina
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  2. lib: select only the pharma clinical annotation matching the annotate… 

    …d variant, #TASK-4325. #TASK-1111
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  3. lib: check pharmacogenomics annotations have been found

    @imedina
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  4. lib: add 'summary' to pharmacogenomics variant annotation

    @imedina
    imedina committed May 11, 2023
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Commits on May 12, 2023

  1. lib: parse and add pharmacogenomics gene annotation, #TASK-4325. #TAS… 

    …K-1111
    @jtarraga
    jtarraga committed May 12, 2023
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  2. Merge branch 'TASK-1111' of https://github.com/opencb/cellbase into T… 

    …ASK-1111
    @jtarraga
    jtarraga committed May 12, 2023
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  3. lib: fix data models changes

    @imedina
    imedina committed May 12, 2023
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  4. lib: update according to biodata changes, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 12, 2023
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  5. Resolve conflicts, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 12, 2023
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  6. lib: minor pharma fixes and improvements

    @imedina
    imedina committed May 12, 2023
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  7. lib: update according to the biodata changes, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 12, 2023
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Commits on May 17, 2023

  1. Merge branch 'develop' into TASK-1111

    @imedina
    imedina committed May 17, 2023
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Commits on May 22, 2023

  1. server: add more filters in pharma/query and improve includes when an… 

    …notating variants, #TASK-4325. #TASK-1111
    @jtarraga
    jtarraga committed May 22, 2023
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  2. Merge branch 'TASK-1111' of https://github.com/opencb/cellbase into T… 

    …ASK-1111
    @jtarraga
    jtarraga committed May 22, 2023
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  3. Merge branch 'develop' into TASK-1111

    @jtarraga
    jtarraga committed May 22, 2023
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  4. Fix some issues after merging develop, #TASK-4325. #TASK-1111

    @jtarraga
    jtarraga committed May 22, 2023
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Commits on May 25, 2023

  1. server: improve pharma endpoints and update according to biodata chan… 

    …ges, #TASK-4325. #TASK-1111
    @jtarraga
    jtarraga committed May 25, 2023
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Commits on May 29, 2023

  1. lib: take into account haplotypes, and update according to biodata ch… 

    …anges, #TASK-4325. #TASK-1111
    @jtarraga
    jtarraga committed May 29, 2023
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Commits on Jun 9, 2023

  1. Merge branch 'develop' into TASK-1111

    @imedina
    imedina committed Jun 9, 2023
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Commits on Jul 12, 2023

  1. Merge branch 'develop' into TASK-1111

    @jtarraga
    jtarraga committed Jul 12, 2023
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  2. Merge branch 'TASK-1111' of https://github.com/opencb/cellbase into T… 

    …ASK-1111
    @jtarraga
    jtarraga committed Jul 12, 2023
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