Alex H. Wagner, PhD

Update documentation for ClinVar ID

3

Address the validation mentioned for ClinVar entries in #759.

We had a discussion during the documentation sprint today about the use of the terms _summary_ (e.g. variant summary, gene summary) and _statement_ (e.g. evidence statement) in CIViC. Assertions currently...

Currently, we use obsolete SO terms in our Variant Type(s) field, which validates any entry against those terms. Consequently, when attempting to enter a newer term (e.g. `SO:0001606 - amino_acid_substitution`),...

Currently all of the listed entities return detailed information in batches from advanced search endpoints. However, the only way to get `suggested_changes` is still through the `GET :entity_id/suggested_changes` endpoints, returning...

Check Validation of Variant Origin

1

I ran across 3 evidence items lacking a `variant origin` designation. Somehow these got past our form validation. May be worth validating at both the client and server to prevent...

I was just reviewing the code for CIViC actionability scores, and it looks like it relies entirely on evidence level and rating... but doesn't account for conflicting evidence at all....

Under Review button

2

It would be cool if a revision or submission could be "checked out" by an editor, perhaps to notify other editors or authors that a statement is under review. Since...

The civic database is checked for "version" on deploy, as a holdover from an earlier method for importing data into the database. This should be addressed in the puppet deploy...

Checking for text directly transferred from source material

2

We may want to implement some sort of check for lengthy substrings in submitted evidence items that match the source text (if available to the server). It may help in...

Copied from genome/civic-meeting#22: _From Discussion:_ > Have a mechanism where an expert can suggest other experts to work on a specific gene or variant. Optionally specify a missing gene or...