owlsim-v3
owlsim-v3 copied to clipboard
monarch-initiative
Ontology Based Profile Matching
At the moment the root ontology of the docker image is monarch.owl, which is too inclusive when one just wants to generate data for Human for example. It doesn't hurt...
When presenting results I'm often asked for a p value to determine if a match is significant. @drseb has proposed a way to generate p values for similarity scores here:...
The match command takes a list of class IDs. Adding individual IDs throws an error. Instead individual IDs should be replaced with all instantiated direct classes
In owlsim2 there is an ability to filter on namespace. In Monarch we use this as a workaround to generate species specific queries. However, it may be useful to add...
This can be thought of as a simple boolean limit case of other matchers; e.g. jaccard with a floor function. although this is not anticipated to be useful for the...
The ways in which ontologies and annotations are loaded is confusing and not well documented. - everything can be combined into one OWL file, which works for us in monarch...
cc @cmcnamara87
Currently the route is `/match/{matcher}/...` which on the one hand is nice as new matchers can easily be slotted in. however, different matchers will have different parameterization, and may have...
1. Rename classes and matcher labels, e.g. NaiveBayesFixedWeightTwoStateProfileMatcher --> bernoulli naive bayes 2. Check grid values (ideally this could be split into a yaml file) 3. Verify behavior is the...