Hi Lori,
I agree with Michael. I for myself do not need the UNIGENE field. The
mot frequent columns that I use are:
ENTREZID, REFSEQ, ENSEMBL, SYMBOL, GENENAME, UNIPROT, gene_id and GO.
Best,
Tobias
Am 30.04.20 um 08:46 schrieb Stadler, Michael:
Hi Lori
Just my two-cents: I would not miss UNIGENE.
I am using org.db's mostly to annotate primary gene identifiers (ENTERZID,
ENSEMBL) with
additional human readable information (SYMBOL, GENENAME), and to map between
different
primary identifiers. I mostly use, in decreasing order of importance:
org.Hs.eg.db org.Mm.eg.db org.Rn.eg.db org.Ce.eg.db org.Dm.eg.db
org.Sc.sgd.db
And the most frequent columns that I use are (again, decreasing order of
importance):
ENTREZID ENSEMBL SYMBOL GENENAME UNIPROT GO
Maybe there is some indirect other usage that I am not aware of.
Best wishes,
Michael
-----Ursprüngliche Nachricht-----
Von: Bioc-devel <bioc-devel-boun...@r-project.org> Im Auftrag von Shepherd, Lori
Gesendet: Mittwoch, 29. April 2020 19:50
An: Bioc-devel@r-project.org
Betreff: [Bioc-devel] Removal of Information in OrgDb generated from NCBI --
Feedback needed.
Hello Bioconductor maintainers
The core team was made aware of an issue with one of the make orgDb functions
in AnnotationForge:
https://github.com/Bioconductor/AnnotationForge/issues/13
Investigating further, NCBI will no longer be updating the gene2unigene file.
The url has moved to an ARCHIVE directory and there is an explanation and
notice of retirement found here:
ftp://ftp.ncbi.nih.gov/repository/UniGene/README
We use this function in creating OrgDb's for the AnnotationHub as well as the
recommended way for users to make custom OrgDb's from NCBI.
Temporarily we are working on updating the url to the new location but we are
thinking of removing the gene2unigene data from the orgDbs. We would like to
ask the community especially those that utilize the orgDb objects frequently if
this data is still necessary and would the removal of UNIGENE cause a large
disruption to current packages/functions/utilization of objects?
Any feedback is greatly appreciated.
Thank you
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
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