[Bioc-devel] FW: GO offspring consistency

Jelle.Goeman at radboudumc.nl Jelle.Goeman at radboudumc.nl
Tue Dec 2 13:29:36 CET 2014

 Hi All,

When working with the GO.db package we ran into a seeming inconsistency in the GOBPOFFSPRING object. It seems there that a term's offspring may have offspring that is not offspring of the term itself. This seems inconsistent with the DAG structure of gene ontology.

> library(GO.db)
> xx <- as.list(GOBPOFFSPRING)
> setapt <- xx$"GO:0006915" #apoptosis
> subsetapt <- xx$"GO:0042981" #offspring of apoptosis
> "GO:0042981"%in%setapt
[1] TRUE
> all(subsetapt %in% setapt)

Is there something wrong or are we misunderstanding the GOBPOFFSPRING object?

Best wishes,

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