owlsim-v3
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monarch-initiative
Ontology Based Profile Matching
Use k least frequent annotations in a probabilistic calculation, where we sum probabilities for each interpretation of the k classes (ie search space of 2^k) cc @drseb
We'd like an algorithm that orders a list of phenotypes in a way that minimizes the sum of the sim distances between adjacent terms, with an option to co-sort two...
In this notebook: https://github.com/NCATS-Tangerine/cq-notebooks/blob/master/Orange_QB2_Other_CQs/Drug_Repurpose_By_Pheno/drug_repurposing.ipynb I input the phenotypes for Amyotrophic lateral sclerosis type 1, expecting other subtypes would show high similarity; however, many related diseases are receiving somewhat low scores....
It would be interesting to test out the profile matching when ALL pairwise phenotype matches (N Factorial matches above a threshold) are factored into the overall profile match score. Eg,...
It looks like currently it just returns the score for the profile-profile matches (whether performing search or profile pairwise comparison). This makes sense for search queries with many results to...
Prefix filters were implemented with https://github.com/monarch-initiative/owlsim-v3/pull/76 but haven't made it to the service layer.
Currently it's hard to know what is 'behind' a service. We want to add this for users, and our own debugging. dropwizard has some out the box healthchecks we can...
This will avoid this kind of code: ``` // Verify that matcher is negation aware if negated IDs are used if (!negatedIds.isEmpty() && !NegationAwareProfileMatcher.class.isAssignableFrom(matcher.getClass())) { throw new NonNegatedMatcherException(matcherName); } ```
The route '/ontolomatch/MP/HP' should return a set of best matches in MP for HP (note this is less than the full all-by-all table). Currently this gives a gateway timeout. Paging...