I am interested in gene ontology enrichment and/or depletion analysis in D. melanogaster. Therefore I implemented an package in R that does the job, also because I really want to learn R. For the direct annotation of Entrez ids to GO terms I used the org.Dm.eg.db package. By accident I discovered that also Genes with an NOT qualifier are annotated (roughly 3% of the fly genome) to a certain GO category making them indistinguishable from genes that are truely associated with a GO category. Did I overlook something or is there something to it?
I did test all NOT qualified GOIDS in Dm (before I just checked inviduals by eye) and it seems to me that in the majority of cases the NOT qualifier is respected in the Org.Dm.eg.db package.
Here is a link to an R data object containing https://drive.google.com/file/d/0B2cadPb0HTwbZW5sZWFxMUZOLUU/view?usp=sharing the basis of the test:
one file containing entrez Ids associated with GOIDs (created using org.Dm.eg.db)
the other file containing entrez ids associated with GOID categories from which they are explicitly excluded by the "NOT" qualifier (these mappings should not appear in the org.Dm.eg.db package)
org.Dm.eg.db_3.4.0 was used and the latest annotation file from http://www.geneontology.org/page/download-annotations