Malachi Griffith

Add associated conditions from phenotypes section of Entrez gene

2

It would be great to be able to pull `associated condition` information from Entrez via mygene.info. For example, for BRAF (https://www.ncbi.nlm.nih.gov/gene/673): Under phenotypes they list conditions from the genetic testing...

OpenCRAVAT integration

1

OpenCRAVAT has these really beautiful variant reports that among other things provide results from a whole collection of variant effect predictors (FATHMM, MutPred, PROVEAN, etc.). See example here: https://run.opencravat.org/webapps/variantreport/index.html?chrom=chr11&pos=48123823&ref_base=A&alt_base=C This...

CIViC bot task to update fusion names to use new delimiter convention

2

To adhere to new guidelines for naming of RNA fusion variants we would like CIViC bot to propose suggested changes for the attached variants. [variants-2022-02-17.xlsx](https://github.com/griffithlab/civic-client/files/8100137/variants-2022-02-17.xlsx) For each variant in this...

Update info from MyGene.info

6

Two points. 1. Can we improve the formatting of the gene aliases we get from MyGene.info. Currently looks like this: 2. It would be useful to add info from Entrez...

Allow oncogenic evidence and assertions

8

After lengthy discussion it was decided that to support documenting of oncogenic evidence (distinct from biochemical functional evidence) we should do the following: 1.) For functional evidence. Add a new...

Allow entry of variant coordinates via ClinGen Allele Registry

1

We currently enter coordinates and ref/var sequences and then try to map to ClinGen Allele Registry. I would be if we could actually enter a valid Allele Registry ID and...

Implement variant sets to support genotypes and other combinations of variants

2

Currently we have several issues that could be resolved by supporting a notion of variant sets. 1. A combination of variants that co-occur in a single individual or tumor. This...

Establish formal backups of the CIViC database

1

@acoffman raised this important point. We should do this before we completely abandon the CIViC spreadsheet.

Develop a variant and gene 'clinical relevance score' that can be used to sort variant and gene browse grids

3

Currently when looking at the browse variant or gene pages we can sort by number of evidence items. This is nice, but it is possible for a gene/variant to have...

Just a note to think about this: http://www.ontobee.org/ "Ontobee: A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee...