Dear team of Bioconductor,
The GO annotation of fungal species outside of 20 model organisms is outdated and a lot of genes miss GO annotation comparing to ensemble biomartr.
> bitr(x, 'SYMBOL', c("PMID", "GO", "ONTOLOGY"), botrytis)
'select()' returned 1:many mapping between keys and columns
SYMBOL PMID GO ONTOLOGY
1 BCIN_01g03900 21876677 <NA> <NA>
2 BCIN_01g03900 23104368 <NA> <NA>
3 BCIN_01g03900 26913498 <NA> <NA>
4 BCIN_01g03910 21876677 <NA> <NA>
5 BCIN_01g03910 23104368 <NA> <NA>
6 BCIN_01g03910 26913498 <NA> <NA>
7 BCIN_01g06850 21876677 GO:0016491 MF
8 BCIN_01g06850 23104368 GO:0016491 MF
9 BCIN_01g06850 26913498 GO:0016491 MF
11 BCIN_01g09430 21876677 GO:0005576 CC
12 BCIN_01g09430 21876677 GO:0050525 MF
Could you please update the annotation of this organism in OrgDb at your earliest convenience? Thank you very much for this work and wish you and your lovely team a lovely summer, autumn, winter and spring!
Best,
Bettina
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You are being unnecessarily mysterious with your question/request. What OrgDb might this be? We could hypothetically try to guess what you have mapped to
botyris
, but wouldn't it be easier if you were to tell us in the first place? Also please note that Bioconductor works on a semi-annual release cycle (which is coming up in mid May or so), and all of the annotation packages are updated only at the release. If you want an updated package, there are functions in theAnnotationForge
package that you can use to do so.Yes, I mapped to botrytis using Annotationhub and sorry for unclear explanation. However, it seems that it has been a long time the GO and Ontology are not updated in this unpopular organism. As I am not expertized in coding, I have no idea how to build an updated annotation package with AnnotationForge. It is good to know the updated version will be released in May. But can you please tell me will the annotation of this organism outside of 20 popular species also be updated?
Thank you very much for the information.