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 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
