clin-geneset-etl

Populate Redis table with scala

Redis docker-compose

Installation

on a swarm cluster or on a local environment Create a network instance with

docker network create -d overlay --attachable proxy Then Run

docker-compose up

To access the Redis instance on another console

Run:

docker exec -ti redis_redis_1 /bin/sh
redis-cli
> ping
the redis should answer PONG

To clean Redis run the following command on the cli:

flushall

to check for an alias and get ensembl id for that gene:

smembers gene:HYST2477

To get data for 1 ensembl id

smembers id:ENSG00000121410

To run etl

To compile and build runtime:

mvn clean install

Step 1 geneInfo

To execute etl with geneInfo (populate Redis with the geneInfo file (gene alias and gene info):

java -jar target/geneset-etl-1.0-SNAPSHOT-jar-with-dependencies.jar geneInfo Homo_sapiens.gene_info.txt

Step 2 HPO

To execute etl with hpo (populate Redis with the HPO file (Gene to HPO panel)

java -jar target/geneset-etl-1.0-SNAPSHOT-jar-with-dependencies.jar hpo ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt

Step 3 Orphanet

To execute etl with orphanets (populate Redis with the orphanets xml file (ensembl to orphanet panel)

java -jar target/geneset-etl-1.0-SNAPSHOT-jar-with-dependencies.jar orpha en_product6.xml

Step 4 Radboudumc

To execute etl with radboudumc (populate Redis with the radboudumc genes panels files in pdf (Gene to Radboudumc panel)

java -jar target/geneset-etl-1.0-SNAPSHOT-jar-with-dependencies.jar rad RAD_Files _DG217.pdf

Step 5 Omim

To execute etl with Omim (populate Redis with the omim genes maps file in txt (Gene -> Omim Phenotype + transmission mode)

java -jar target/geneset-etl-1.0-SNAPSHOT-jar-with-dependencies.jar omim genemap2.txt

Source of Data

NCBI

ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

HPO - Human Phenotype Ontology

http://compbio.charite.de/jenkins/job/hpo.annotations.monthly/lastSuccessfulBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt

Orphanet

RARE DISEASES WITH THEIR ASSOCIATED GENES:

http://www.orphadata.org/cgi-bin/index.php

Radboudumc

• Download all genes panels in PDF format https://www.radboudumc.nl/en/patientenzorg/onderzoeken/exome-sequencing-diagnostics/information-for-referrers/exome-panels

note1: (Feb 2020) 3 new panels were added : Liver, SHHM, Hereditary Bone Marrow Failure

note2: on Rad website, when we click on Muscle disorders, the Intelectual disorders shown instead... So, I'm running with a copy of 216 instead...

Omim (May 2020)

https://omim.org

• Download all the 4 Omim databases files:
  • mim2gene.txt
  • mimTitles.txt
  • genemap2.txt
  • morbidmap.tx