Dear BioC Team, The annotation utilities of BioC are great and enable very comfortable mapping!
I am currently wondering whether I am able to programmatically access which BioC currently supports. I am aware of the available.db0pkgs() from AnnotationForge, however what I am actually interested in are the corresponding org.<Species>.<IDType>.db packages. As far as I can currently tell, there is no easy map between the .db0 and the org.db packages, is it? In part, this is possible by mapping "human.db0" -> "human" -> "Homo sapiens" -> "Hs" -> org.Hs.eg.db; but there are exceptions to the 1. org.Xx format for species (e.g. org.Mmu, org.Sco, org.Tgondii) and 2. the default usage of entrez gene ids (.eg) even for popular model organisms such as yeast ("org.Sc.sgd.db") and arabidopsis ("org.At.tair.db") - for which there are surely good reasons, e.g. historical, however impairing programmatic + unified access. Now there are two options to resolve this: 1. passing this on to the user assuring the organism package is there and requiring him to provide his data based on corresponding IDs - which is not a good idea for end users not familiar with the BioC anno structure 2. giving end users a convenient unified way of inputting data such as: "give me your expression values for Entrez gene IDs" and I will do what needs to be done. This would hoever require me to hardcode such exceptions to a generic mapping, and this is apparently a bad idea as these mapping might change and new organisms are expected to come into the game. So how to resolve this - am I overseeing something? Thanks & Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel