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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

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jtarraga
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Support pharmacogenomics

jtarraga and others added 30 commits May 4, 2023 08:22
@jtarraga
lib: implement PharmGKB downloader, #TASK-4325. #TASK-1111
0c5957c
@jtarraga
core: download PharmGKB variant and clinical annotation files, #TASK-…
726b4a0 
…4325. #TASK-1111
@jtarraga
lib: add the PharmGKBBuilder class, #TASK-4325. #TASK-1111
2ed9ed7
@jtarraga
lib: parse PharmGKB clinical annotation files, #TASK-4325. #TASK-1111
42c9911
@imedina
lib: improvements in pharmacogenomics
4080ad7
@imedina
lib: add phrama variant annotation to evidence
426d6de
@jtarraga
lib: parse PharmGKB study parameters file, #TASK-4325. #TASK-1111
b1f617c
@jtarraga
lib: parse PharmGKB label annotation file, #TASK-4325. #TASK-1111
5e0b5c1
@imedina
lib: pharmacogenomics minor improvements
475df23
@jtarraga
lib: parse PharmGKB guideline, phenotype and functional annotations, …
7de235b 
…#TASK-4325. #TASK-1111
@imedina
lib: fixes and improvements in PharmGKB builder
a12b2db
@jtarraga
lib: parse PharmGKB variants file to get the variant chromosome and p…
8f519bb 
…osition, #TASK-4325. #TASK-1111
@jtarraga
lib: create the pharmacogenomics JSON file after parsing the PharmGKB…
d33c183 
… files, #TASK-4325. #TASK-1111
@jtarraga
lib: update according to the biodata changes, #TASK-4325. #TASK-1111
595b28a
@imedina
Add new Pharmacogeonmics REST service
bf32a6f
@jtarraga
app: implement the command 'load' for pharmacogenomics, #TASK-4325. #…
4de3c35 
…TASK-1111
@jtarraga
Merge branch 'TASK-1111' of https://github.com/opencb/cellbase into T…
09e6fa6 
…ASK-1111
@jtarraga
server: implement pharmacogenomics web-services, #TASK-4325. #TASK-1111
87856d6
@imedina
lib: minor improvement in pharma clinical annotation data model
b7f7643
@imedina
server: minor improvements of REST API
94fe7a9
@jtarraga
lib: fix parse generic names and add junit test, #TASK-4325. #TASK-1111
c01d65f
@jtarraga
lib: add pharmacogenomics data to the variant annotation, #TASK-4325.…
22583c1 
… #TASK-1111
@imedina
lib: add field to pharmacogenomics variant annotation
029d7cc
@jtarraga
server: fix location filter in the pharmacogenomics webservice 'searc…
080d06e 
…h', #TASK-4325. #TASK-1111
@imedina
lib: filter mismatch alleles from pharmacogenomics annotation
be4dc90
@jtarraga
lib: select only the pharma clinical annotation matching the annotate…
80b9e40 
…d variant, #TASK-4325. #TASK-1111
@imedina
lib: check pharmacogenomics annotations have been found
3e019fb
@imedina
lib: add 'summary' to pharmacogenomics variant annotation
13a21fc
@jtarraga
lib: parse and add pharmacogenomics gene annotation, #TASK-4325. #TAS…
87cc78e 
…K-1111
@jtarraga
Merge branch 'TASK-1111' of https://github.com/opencb/cellbase into T…
36cbca4 
…ASK-1111
@jtarraga
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Task linked: TASK-1111 Add Pharmagenomics data to CellBase

@jtarraga jtarraga requested a review from imedina May 12, 2023 15:49
@jtarraga jtarraga changed the title TASK-1111 TASK-1111 Add Pharmagenomics data to CellBase May 12, 2023
imedina
imedina previously approved these changes May 17, 2023
View reviewed changes
imedina
imedina previously approved these changes May 17, 2023
View reviewed changes
@jtarraga jtarraga requested a review from imedina May 22, 2023 08:39
@jtarraga jtarraga merged commit 4374d16 into develop Jul 12, 2023
3 of 6 checks passed
@jtarraga jtarraga deleted the TASK-1111 branch July 12, 2023 10:44
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@imedina imedina imedina approved these changes

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@jtarraga @imedina