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YuLab-SMU / GOSemSim

:golf: GO-terms Semantic Similarity Measures
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Filter Go terms by type of relationship #8

Open sfujio opened 8 years ago

sfujio commented 8 years ago

Hi, I need to calculate the similarirty between GO terms of a protein set, but I am interested only in the "is_a" type of relationship. I am a newbie in programming and haven´t quite yet figure out how the package handles the relation between the terms. I tried to understand by seeing the code of the functions but failed.

I would like to ask 1) if filtering for type of relationship between terms is possible, and 2) how is the information of the relationships is stored and obtained from GO.

Regarding point 2, maybe the package doesn´t need to know the type of relationship but at least it needs to know how the terms are related with each other in order to calculate some similarity measueres. I would like to know how is that information retrieved and handle.

Thank you for creating the package and for your time,

SF

GuangchuangYu commented 8 years ago

We used GO.db to query the GO term relationships.

Only calculate semantic similarity using is_a is not supported. GOSemSim only support filter out GO terms by dropCodes.