Kent Shefchek

After upgrading to gunicorn 20.0.0 biolink no longer renders the swagger api-docs page, https://api-dev.monarchinitiative.org/api with 'ReferenceError: SwaggerUIBundle is not defined' Nginx is showing: upstream prematurely closed connection while reading upstream...

We are often asked to generate gene sets based on filters, that amount to generating gene sets and performing set operations on them. We could theoretically introduce this functionality to...

Currently on the monarch ui we pull gene descriptions and pmid via the client/browser; however, this behavior is blocked by some browser setups and also results in us over pinging...

Steps to reproduce: Give bad url to ontobio yaml config, eg: owlsim2: url: "https://httpstat.us/404" timeout: 10 Start biolink with gunicorn, eg: gunicorn -k gevent --log-level=info --timeout 90 --worker-connections 5 --bind...

BioLink API "GET /bioentity/phenotype/{id}/anatomy/" Not Functioning

6

Original ticket by @Superraptor in [monarch-app](https://github.com/monarch-initiative/monarch-app/issues/1519) Hi! First, I'd like to say amazing work here, I'm a huge fan of the Monarch Initiative application and the API has been an...

The kgx validator currently requires CamelCase for node categories and snake case for edge types. It could be useful to optionally turn off this check, since some groups transferring knowledge...

For the normalization service it would be useful to load a TRAPI compliant graph into kgx, perform a clique merge, and output the graph in the TRAPI json format

Consider "modifies frequency or severity of condition" instead of "contributes to condition" for RO:0003304

2

Currently RO has the term "contributes to condition" which is a parent of: - contributes to frequency of disease - contributes to severity of condition - ameliorates condition - exacerbates...

Term request - frequency_in_condition

10

It would be useful to have a relationship to link an instance of a phenotype to the frequency seen in a cohort of patients diagnosed with a condition. This could...

uPheno OBO Purls forward to http://ontologies.berkeleybop.org/

3

Some uPheno OBO purls resolve to http://ontologies.berkeleybop.org/, for example http://purl.obolibrary.org/obo/GO_0022008PHENOTYPE Should these be resolving elsewhere, or is Monarch effectively the source for these IRIs? See https://github.com/monarch-initiative/dipper/issues/741