is there an R library to compute semantic similarity in SNOMED ontology?
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izem.rima • 0
@izemrima-24225
Last seen 9 months ago

Hello, I am interested in computing semantic similarity (any metric would do at this stage) of concepts in SNOMED ontology. Is there an R library that does that already?

I already found the following closely related packages

  • A perl package which calculates semantic similarity in SNOMED https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815481/ ... but I am unfortunately not a perl programmer.

  • An R library (gosemsim) that calculates semantic similarity for a different ontology (GO) than SNOMED.

    Pointing me in the right direction would be much appreciated, thank you!

goSemSim snomed semantic similarity • 241 views
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@vincent-j-carey-jr-4
Last seen 1 day ago
United States

https://cran.r-project.org/web/packages/ontologySimilarity/ provides measurements of semantic similarity for general ontologies. I am not clear that SNOMED can be readily incorporated into this framework however. I do not see an OWL or OBO representation and a look at the "known deficiencies" section of https://en.wikipedia.org/wiki/SNOMED_CT indicates that there may be some distance to go before SNOMED can be modeled with familiar ontology structures.

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