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[GO] Re: [MOBY] Re: GO Xref Abbs now served by MOBY

Mark Wilkinson markw at
Thu Feb 26 11:19:59 PST 2004

On Thu, 2004-02-26 at 08:57, Michael Ashburner (Genetics) wrote:

> A number of others have much missing data .. are those to be completed
> by you (i.e. Mark W) ?

Any that you find missing data are *mostly* from the BioMOBY additions
to the namespace list, since most of the fields in your flatfile are not
useful to us (in fact, they are in many cases exactly what we are trying
to replace through the MOBY project, e.g. example_url and example_id,
since these are not guaranteed to be static, so should be "discovered"
at run-time)

In some cases the parser may have made errors, as you have already
discovered.  These I will fix by hand.  In other cases, the flatfile
itself was ambiguous (using various terms to describe the same thing,
e.g. "example" and "example_id" were both used to give examples of an ID
number) -  couldn't possibly find all such cases by eye, so there may be
instances where the parser missed some such fields.

> Would be nice if Mark's output could preserve the alphabet order of
> records.


Midori - you don't need to edit both the flatfile and the database. 
Just edit the flatfile and I'll tweak the parser to read it properly,
including those cases where information appears on multiple lines (i
have a feeling that this file is not used by anyone in an automated way,
given it's "peculiarities"...)


Mark Wilkinson (mwilkinson at
University of British Columbia iCAPTURE Centre

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