[Bioc-devel] FW: GO offspring consistency

[Jelle.Goeman at radboudumc.nl]

 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)
[1] FALSE

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

Best wishes,

Jelle
Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.