[Bioc-devel] supported organisms

[Ludwig Geistlinger]

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.Geistlinger at bio.ifi.lmu.de