Re: [Treebase-devel] TreeBase NeXML export bug: ids of otu elements are not unique

[Rutger V. <rut...@gm...>]

For posterity and in the interest of completeness:

When TreeBASE reads such a NEXUS file with namespaced taxon labels
(TaxonLabel) it will scope the strings to the study, and will attempt to
give them normalized references to at least the level of a
commonly-occurring "variant" of a name (TaxonVariant), and ideally (most
commonly) a known, true Taxon.

Subsequently, references to these TaxonLabel objects are collected into
multiple TaxonLabelSet bins, which represent the encountered taxa blocks.

When NeXML is generated, the generic (not entirely thought-through)
approach has been to generate all XML identifiers from the primary keys in
the database. This might fail to generate unique XML IDs for otu elements
in studies where the same TaxonLabel occurs in multiple TaxonLabelSet bins
(which are serialized to multiple "otus" elements).

A possible fix would be to generate XML IDs for otu elements by combining
the TaxonLabel primary key with the TaxonLabelSet PK. Unfortunately, this
will be a bit messy to get right because the ID references (from tree node
to otu, from sequence to otu) need to generate the correct string as well.


On Thu, Jan 2, 2014 at 9:15 PM, Mark Holder <mth...@gm...> wrote:

> Hi,
> The example is the ID  Tl241048 in
>
> http://treebase.org/treebase-web/search/downloadAStudy.html?id=10000&format=nexml
>
> The nexus output has multiple taxa blocks and the taxon name
> Cardamine_alpina_DAE2_R325 (which is associated with the offending otu
> elements in the nexml form) occurs in multiple taxa blocks. In the
> (mesquitized) form of NEXUS that allows multiple TAXA blocks, the
> block TITLE acts like a namespace. So identical taxa labels are not a
> problem in NEXUS. But in nexml spec ids are supposed to be unique
> throughout the file.
>
> I suspect this difference in approaches to dealing with disambiguation
> may be the source of the bug.
>
>
> all the best,
> Mark
>
> --
> Mark Holder
>
> mth...@gm...
> mth...@ku...
> http://phylo.bio.ku.edu/mark-holder
>
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-- 

Dr. Rutger A. Vos
Bioinformaticist
Naturalis Biodiversity Center
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the
Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com