Chunlei Wu

Cannot start cerebro with the bundled JVM from ES v7.13

3

Tried to install the latest cerebro v0.9.4 in a docker container, together with ES v7.13, but got this error when start cerebro (no default-jdk installed, tried to use the bundled...

support for OpenAPI v3 extensions

13

As you may know, we currently host a copy of openapi-gui on our [SmartAPI](http://smart-api.info) project: http://smart-api.info/openapi-gui/. Thanks for making it available. SmartAPI defines a set of OpenAPI extensions to support...

Data source: OncoKB

3

http://oncokb.org/#/dataAccess need to get the permission first. similar to CIVIC and CGI.

update CADD data source

2

CADD has new version now, v1.6, at https://cadd.gs.washington.edu/download.

Currently we have a one-snapshot data from UniProt Variant, we can make it a complete MyVariant data source, by monitor the data release here: https://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/variants/ Load human variants only, but...

Evaluate and potentially switch to use ClinVar's new VCV xml dump file

1

VCV (variation in ClinVar) is a new variant-centric XML schema. More at https://pubmed.ncbi.nlm.nih.gov/31777943 MyVariant.info current imports data from ClinVar's original `ClinVarFullRelease_*.xml.gz` XML files (based on old RCV schema - no...

Data source: GWAS Central

1

https://help.gwascentral.org/data/download/

snpeff annotation switch to use GRCh37 and GRCh38 reference genomes

1

Currently, we use "hg19" and "hg38" reference genomes (from UCSC) to produce snpeff annotations. The result misses "gene_id" field (the value is the same as "gene_name"). We can switch to...

The exact VRS schema is here: https://vrs.ga4gh.org/en/1.1/schema.html

An example:  It does not impact the actual released data and what's reported in /metadata endpoint, so no user-side impact. But the incorrect number is reported in myvariant hub...