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

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

I tried loading the JSON files I shared with you the other day in
couchdb and it turned out I would have to recompile it with more
memory or else it chokes. So the idea is that it's just the metadata
that goes into a database, and you like that to be couchdb as opposed
to a triple store, right? And you like the idea of distributed
editing, so does that mean you also like the idea of distributed
searching, along the plug-in idea? With the various projects you've
done to annotate/correct/taxon map treebase data, it would be great if
those could be plugged into a common, easy-to-use front end.

On Thu, Apr 14, 2011 at 5:04 PM, Roderic Page <r....@bi...> wrote:
> So I guess I'd do the following:
>
> 1. Separate data entry from data access. SQL may have a place for data entry, but that's it. And MySQL is fine, really.
>
> 2. The data access end is a document database like CouchDB which stores metadata (and trees) as JSON
>
> 3. Simple query API that more or less wraps CouchDB queries, search by taxon, identifier, geography, or full text.
>
> 4. Store data on disk in original format, as well as derived formats as Rutger suggests. Being able to grab dumps in various formats is handy, especially if the data can be reliably obtained.
>
> 5. Have a web interface that's simple, easy to use, supports search without asking user whether something is a number or not, use SVG for trees, enable users to log in using Facebook/Twitter/Mendeley
>
> 6. Devolve as much editing as possible to other places, e.g. Mendeley for bibliographic stuff
>
> 7. Never, ever mention RDF. Bonus points for not mentioning XML.
>
> My sense as an outside observer is that much of the current iteration of TreeBASE has been driven by technology (Postgresql, Tomcat, RDF, Java, XML), not usability. I understand the rationale for the choices (I think), but at the end of the date TreeBASE should be about the trees. It's not about publications, it's not about sequences, it's not really about data (OK, a little bit about data), it's about trees. I should be able to find my trees, find trees from a paper, find trees for a taxon, find trees from a given part of the world, find trees that use a given sequence, find trees that look like my trees.
>
> Read Michael Wolfe's answer to the question "Why is Dropbox more popular than other programs with similar functionality?" and you'll see where I'm coming from
>
> http://www.quora.com/Dropbox/Why-is-Dropbox-more-popular-than-other-programs-with-similar-functionality
>
> Regards
>
> Rod
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
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> University of Glasgow
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>
> Email: r....@bi...
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>
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
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