[Bioc-devel] Removal of Information in OrgDb generated from NCBI -- Feedback needed.

[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-bounces using r-project.org> Im Auftrag von Shepherd, Lori
Gesendet: Mittwoch, 29. April 2020 19:50
An: Bioc-devel using 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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