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89 issues in monarch-initiative/owlsim-v3

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#89

Explore many-to-many matches for profiles

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, in the situation ...

  • Opened by jmcmurry May 18, 2017
  • 3 comments
#88

Add option in services layer to include pairwise matches in all phenotypes

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 reduce ...

#87

Add prefix filter to service layer

Prefix filters were implemented with https://github.com/monarch-initiative/owlsim-v3/pull/76 but haven't made it to the service layer.

#86

For Hs configuration, add option for diseases and genes

We should add an option to add human gene-phenotype associations as well as disease-phenotype associations. Needed for https://github.com/NCATS-Tangerine/ncats-ingest/issues/25

#85

Factor in phenotype frequency

From R24 "We will develop algorithms that will weight feature frequencies and negative annotations using our Bayesian ontology-querying framework89, which we will extend from a purely HPO-based algorithm ...

  • Opened by jmcmurry May 5, 2017
  • 1 comment
#84

Docker image root ontology

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 to have more data, but it is slower ...

#83

Command error in repository Readme

The command to build docker just with human species data in readme is missing period symbol in the end. docker build --build-arg species=human -t owlsim-human should be docker build --build-arg species=human ...

#82

58 docker biolink update

We need to update our biolink instance before merging this PR.

#81

services: should be possible to match by individual IDs as well as class IDs

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

#80

Consider p value calculation for IC based sim calculations

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: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756558/. ...

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