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monarch-initiative / owlsim-v3

Ontology Based Profile Matching
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Implement bayesian frequency awareness #56

Open cmungall opened 7 years ago

cmungall commented 7 years ago

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

cmungall commented 7 years ago

TODO

drseb commented 7 years ago

Frequency: http://compbio.charite.de/hpoweb/showterm?id=HP:0040279

This is aligned with Orphanet

jmcmurry commented 7 years ago

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 to a cross-species inference algorithm accounting for species differences. Our probabilistic framework also provides a natural framework for integrating quantitative data; existing phenotype ontologies provide ready-made ‘bins’ for quantitative phenotypes, such as ‘increased body weight’ or ‘abnormal femur size’. Terms such as these are used both in the model organism literature, and by the curators of model organism databases. Sometimes this is a judgment call on the part of a researcher, but in the case of many phenotyping pipelines, normal and abnormal ranges of measurements are defined as part of the protocol. We will use these protocols and the data gather from phenotyping pipelines to learn and interpolate normal ranges for a variety of phenotypes. This will allow us to combine both qualitatively assigned abnormal ranges with quantitative data. We will also improve our capacity for differential diagnostics as well as for novel disease gene discovery by including these new advanced scoring metrics within our website as well as in our tools such as Exomiser."

pnrobinson commented 6 years ago

@jmcmurry As far as I know, little is on the ground, but I think that some of the new algorithms will do something in this area. Can we put this down as a focus area for the second half of the grant?

jmcmurry commented 6 years ago

We can, but to the extent we can have a documented plan for this, it would help us all.