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Make sure diseases in the omit-list.txt are excluded from the db build #351

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damiansm opened this issue Sep 30, 2019 · 0 comments
Open

Make sure diseases in the omit-list.txt are excluded from the db build #351

damiansm opened this issue Sep 30, 2019 · 0 comments

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@damiansm
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HPO team have a curated set of OMIM disease IDs with gene associations they suggest omitting as they are susceptibility genes etc

Investigation revealed there are some 138 diseases in the https://github.com/monarch-initiative/hpo-annotation-data/blob/master/rare-diseases/annotated/omit-list.txt file that are included in phenotype-annotation.tab and, hence, our database.

Easiest solution will to be to switch our db build to use http://compbio.charite.de/jenkins/job/hpo.annotations.2018/lastSuccessfulBuild/artifact/misc_2018/phenotype.hpoa and this already has them excluded
@damiansm damiansm mentioned this issue Sep 30, 2019
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julesjacobsen added a commit that referenced this issue Aug 21, 2023
@julesjacobsen
Change for #351, #373, #379 - update exomiser-phenotype-data to take …
9d23ea4 
…annotations from phenotype.hpoa

Update application.properties and ResourceConfigurationProperties to remove unused fields.
Update DiseaseInheritanceCacheReader and DiseasePhenotypeReader to parse phenotype.hpoa file
Update DiseaseResourceConfig to use hpoa resource
julesjacobsen added a commit that referenced this issue Aug 21, 2023
@julesjacobsen
Change for #351, #373, #379 - update exomiser-phenotype-data to take …
92b1f57 
…annotations from phenotype.hpoa

Update application.properties and ResourceConfigurationProperties to remove unused fields.
Update DiseaseInheritanceCacheReader and DiseasePhenotypeReader to parse phenotype.hpoa file
Update DiseaseResourceConfig to use hpoa resource
julesjacobsen added a commit that referenced this issue Sep 15, 2023
@julesjacobsen
Change for #351, #373, #379 - update exomiser-phenotype-data to take …
37c5f7b 
…annotations from phenotype.hpoa

Update application.properties and ResourceConfigurationProperties to remove unused fields.
Update DiseaseInheritanceCacheReader and DiseasePhenotypeReader to parse phenotype.hpoa file
Update DiseaseResourceConfig to use hpoa resource
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@damiansm