On 29 Jan 2001, Dave Matthews wrote:
> Such unbalanced situations almost always arise from loading sequences into
> a model like Keith's:
>> ?Sequence ...
> Species ?Species XREF Sequence
>> Which is a natural way to process input from Genbank/EMBL records. Of
> course the input could be balanced better by parsing otherwise, eschewing
> the XREF and loading the data from the other side:
>> Species : X
> Sequence Y
>> , but this would still require additional code to filter which Species
> should be excluded.
I think this is a good point Dave and I am probably guilty of always using
XREFs in our database when a conventional link may be more appropriate.
In most cases there is no real use in looking at a list of thousands of
objects, but would limiting the use of XREFs affect the way in which you
could query the data?
E.g. if I wanted to find out ATP genes in Arabidopsis or Brassica species
I could formulate a query like:
Find Species "Arabidopsis*" || "Brassica*"; Follow Protein; Gene_name =
Would I still be able to do this if I didn't have the XREFs between
Species and Protein (admittedly I could rework the query starting from
Gene_name, but there may be reasons where you want to query in this way) ?
~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and
~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer.
~ Nottingham Arabidopsis Stock Centre, University Park,
~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091