Re: [Treebase-devel] viz problem with trees for S11267

[Rutger V. <R....@re...>]

Yeah, I know, some of the studies are serialized incorrectly,
especially the ones with "mixed" data containing both DNA and
categorical data in the same matrix, or unusual state definitions in
some other way. This results in a character state set definition being
written out for every matrix column, and that takes up most of the
file. Another thing is that we're now using owl:sameAs statements to
specify the TreeBASE ID for every character.

There are a number of these issues, they're bugs, I'm recording them -
it's one of the things we should be fixing during Laurel's project. A
correctly formatted NeXML file is going to be bigger than the
equivalent NEXUS file, but perhaps like a factor of ten or so max,
depending on the amount of metadata (i.e. on the order of 1Mb for
S2012). That is a trade-off that is worth it because it will allow us
to export all the metadata in a single file. 13.7 Mb is obviously
wrong.

On Mon, Apr 18, 2011 at 1:03 PM, Roderic Page <r....@bi...> wrote:
> I've started trying again to harvest individual Nexml files, and it's still unbelievably slow. We're talking minutes for a study in some cases. The XML for S2012 took about 5 minutes to fetch and is 13.7 Mb in size(!). The NEXUS file is 164Kb.
>
> Need I say more...?
>
> Regards
>
> Rod
>
> On 15 Apr 2011, at 13:42, William Piel wrote:
>
>>
>> On Apr 15, 2011, at 4:14 AM, Roderic Page wrote:
>>
>>> For large studies the Nexml generation simply times out, so I gave up.
>>
>> If you still have some ID numbers for those big ones, I'd be happy to test it again. It may have been solved because of some recent changes.
>>
>> But, indeed, I'd like access to a dump too.
>>
>> bp
>>
>>
>>
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>
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> Roderic Page
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
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