Hi Arek, Tom, as you know, I am sympathetic with Tom's complaints, as we have also had a great deal of pain with the biomart/R interface in Bioconductor.
We are _very keen_ on the versioning, this will be a big step forward, from the dark ages to the enlightenment. Cheers Wolfgang > > On 22 Jul 2006, at 13:35, [EMAIL PROTECTED] wrote: > >> >>> BioMart has been designed in such a way that, the buffer for such >>> changes is the dataset configuration file, >>> which describes what _currently_ available in the database and >>> guarantees that anything in this file can be used to construct a valid >>> query. >>> These file were designed precisely for this purpose that the query >>> logic can be decoupled from evolving data. >> >> Assuming that you always start from scratch that's great, the problem is >> that by its nature we store query specifications in the workflow. These >> specifications include filter and attribute names (how else could they do >> it?) and users expect that a query written against version x of >> database y >> shouldn't suddenly stop working. >> >> Our interface will pick up the new configuration sure, it's not hardcoded >> in our code, but that doesn't help a user who writes a workflow then >> comes >> back the next day to find that it randomly fails. You need to take the >> potential for stored queries into account. >> > > ok, in this case you may find helpful the versioning which is coming into > central server from 0.5 and this is something that originally bioconductor > community asked for. We'll be able to serve multiple versions of the > databases > and so the workflow with hardcoded filters and attributes from version > 39 will still be able > to run against v 39 and it is guaranteed to work 'forever' rather than > relying > on the most recent currently published version. > > The other thing that you maybe able to to find helpful (coming with 0.5) > is listings > of filters and attributes so you can do easy diff between the versions > and see > for yourself what has changed. > > BTW, the changes as described in your email are rare anyway and they > normally > do not occur, there were only associated with our 'big cleaning up' > activities as per my archive > email. The changes which you may account more frequently is the presence > or absence > of certain attributes (not re-naming) but they are usually only limited > to things like > xrefs, while everything remains stable. For this however you need to > take your plea > to Ensembl team as we only pick up things that they map for every > release and this > is something that we do not have any control over > > a. > > >> Tom >> >> > > > ------------------------------------------------------------------------------- > > Arek Kasprzyk > EMBL-European Bioinformatics Institute. > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > Tel: +44-(0)1223-494606 > Fax: +44-(0)1223-494468 > ------------------------------------------------------------------------------- > > > -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
