[ensembl-dev] Ensembl ID History Converter (IDmapper.pl) API Mapping Score Column

Andreas Kusalananda Kähäri ak4 at sanger.ac.uk
Mon Jun 11 09:53:02 BST 2012

Hi people,

Actually, I'd like to say about the stable ID mapping scores that it's
pointless to try to assign any significance to them when comparing
between releases since the various mapping strategies, penalties etc.
might have been tweaked.

Also note that we did not store the mapping scores to start with (thus
some of the the zeroes).  I seem to remember that we once we had our
stable ID mapping pipeline in place (it wasn't there from the start, but
I can't recall now when it came into being, probably around 2005 or so)
we might have tried to retroactively populate the stable_id_event table.

Some mappings might actually have been done manually by hand since then
and the score might have been set to 1 (hopefully) or zero depending on
who did it.


On Thu, Jun 07, 2012 at 07:17:05PM +0100, Kieron Taylor wrote:
> I'll catch this question for Andy.
> > Thanks Andy, that is great!
> >
> > Though I am a little confused about some results where the score is "0".
> > For example, with the example input included with the api (./IDmapper.pl
> > -s human -f idmapper.in), one of the results is:
> >
> > Old stable ID, New stable ID, Release, Mapping score
> > ENSG00000137361.1, ENSG00000137361.1, 3, 0
> The mapping score of zero actually implies that no alignment had to be
> run, so there is no score. This happens when the mapper discovers
> something exactly where it expects it to be, and skips the alignment.
> Scores of 1 are possible, but generally these are moppped up by the
> pre-alignment checks.
> Regards,
> Kieron
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Andreas Kusalananda Kähäri
Ensembl Gene Annotation Team


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