I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it has many similarity measurements. Or to be exact, there are actually many ontology similarity measurements. And I want to know which similarity measurement is best suited for my case (cell line ontologies similarities). There might be a couple of good ones that are good for cells ontologies. These are a set of similarity measurements that are available in Fastsemsim.

Semantic Similarity

  • SemSim.TermSemSim
  • SemSim.ObjSemSim
  • SemSim.ObjSetSemSim
  • SemSim.SetSemSim
  • Specific Semantic Similarity measures
  • SemSim.MixSemSim
  • SemSim.avgSemSim
  • SemSim.maxSemSim
  • SemSim.BMASemSim
  • SemSim.SemSimUtils

Source: https://fastsemsim.readthedocs.io/en/latest/library.html

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    $\begingroup$ If your question is about python libraries, it would probably fit better (and get more answers) on SE Bioinformatics. $\endgroup$ – David Jul 21 '19 at 19:32
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    $\begingroup$ Yes, as it's about algorithm selection SE Bioinformatics is likely better. Also, I think you are using "ontologies" to refer to the terms/classes, when the ontology is in fact the collection of such terms. E.g. CLO and Cellosaurus are ontologies, and they have terms representing particular cell lines. $\endgroup$ – cmungall Jul 22 '19 at 3:47

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