Kent Shefchek

I wrote something similar here, https://github.com/monarch-initiative/mondo/issues/685 -- I think there are some disease "groups" that are really disease entities. For example cystic fibrosis is still a disease group in monarch...

Is the original request in scope or feasible to be included in mondo, or should we look for a workaround?

I think this would be useful for analysis and application views. Previously I have had to add extra checks (eg all OMIM identifiers are entities, for ex otherwise Angelman would...

what is the final word on distinguishing disease entity vs grouping class?

For example,[ I want to get all rare diseases in Mondo](https://github.com/monarch-initiative/mondo-rare-disease-analysis/blob/master/Mondo-Rare-Disease-Analysis.ipynb), I do a query to filter out any diseases with subclasses, this gives me Juvenile Huntington disease, but filters...

Is disease_grouping already a subset? This is essentially what I am asking for

> Perhaps for now a strategy where we annotate what are unambiguously disease groupings, and this can be a negative filter. You will still have classes that subsume one another....

The variant information is sometimes lacking, we attempt to resolve snps and indels to dbSNP, or make informative HGVS labels, but YMMV. Here are two example queries: https://solr.monarchinitiative.org/solr/golr/select/?q=*:*&wt=json&fq=subject_category:case&fq=object_category:variant&fq=is_defined_by:%22https://data.monarchinitiative.org/ttl/udp.ttl%22&rows=20&indent=on&fl=subject,object,object_label https://solr.monarchinitiative.org/solr/golr/select/?q=*:*&wt=json&fq=subject_category:case&fq=object_category:phenotype&rows=20&indent=on&fl=subject,object

I assume because the jars are not pushed to maven central, https://github.com/SciGraph/SciGraph/issues/192, this doesn't work without cloning the repo and building the jar locally. I'll update the wiki, thanks for...

Does the graph/neighbors/ work for non clique leaders? I think this has yet to be added: https://scigraph-ontology-dev.monarchinitiative.org/scigraph/graph/neighbors/Orphanet%3A353220?depth=1&blankNodes=false&relationshipType=subClassOf&direction=BOTH&entail=false I think these are related: https://github.com/SciGraph/SciGraph/issues/203, https://github.com/SciGraph/SciGraph/issues/135