Can we limit XREFs? Please? (re: xace crash)

Keith Bradnam keith at thale.life.nottingham.ac.uk
Mon Jan 29 10:53:53 EST 2001

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 

More information about the Acedb mailing list

Send comments to us at biosci-help [At] net.bio.net