[BioC] Many missing GO terms from GOHyperG call using mgu74av2

Seth Falcon sfalcon at fhcrc.org
Wed Jun 29 21:27:30 CEST 2005

Hi Francois,

On 29 Jun 2005, fpepin at cs.mcgill.ca wrote:
> How often are the metadata packages being rebuilt right now? What
> decides when they're being rebuilt?

Presently, the metadata packages are rebuilt approximately every six
months as part of the six mongth release cycle of BioConductor (and

> Is there a reason why that wouldn't be a good idea? I personally
> like having the latest annotations. I can see a problem trying to
> reproduce a given analysis, but old annotations can be kept around
> for a while.

In the past, the packages have been updated more frequently.  Clearly,
it is nice to have the most up-to-date annotations available.  

Unfortunately, the structure of the data sources (the inputs to
building the annotation packages) change rapidly.  It is often the
case that running a new annotation package build is a non-trivial task:
we have to figure out how and why an XML DTD changes or a field in
a csv file is missing, etc.

In the past, the structural changes in the data have led to matching
changes in the annotation packages and this leads to incompatibilities
with existing, released BioC packages.  

So it is for the above reasons, that we felt it best to stay with a
build of the metadata for an entire release.

We *do* plan to update the annotation packages and utilize the devel
arm of the data repository to host updated builds in-between
releases.  But our ability to do so is limited to the person-hours we
have available to dedicate to the task.  

Best Wishes,

+ seth

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