Postagens de Rogue Scholar

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Publicados in iPhylo

So it looks like TreeBASE is in trouble, it's legacy Java code a victim of security issues. Perhaps this is a chance to rethink TreeBASE, assuming that a repository of published phylogenies is still considered a worthwhile thing to have (and I think that question is open). Here's what I think could be done.

Publicados in iPhylo

I'm continuing to play with the new version of iSpecies, seeing just how far one can get by simply grabbing JSON from various sources and mashing them up. Since the Open Tree of Life is pretty unresolved ("OMG it's full of stars") I've started to grab trees from TreeBASE and add those.

Publicados in iPhylo

Bryan Drew and colleagues have published a piece in PLoS Biology bemoaning the lack of databased phylogenies: This is an old problem (see for example "Towards a Taxonomically Intelligent Phylogenetic Database" doi:10.1038/npre.2007.1028.1), but alas the solution proposed by Drew et al. is also old:In my opinion, as soon as you start demanding people do something you've lost the argument, and you're relying on power ("you don't get to publish

Publicados in iPhylo

In response to Rutger Vos's question I've started to add GBIF taxon ids to the iPhylo Linkout website. If you've not come across iPhylo Linkout, it's a Semantic Mediawiki-based site were I maintain links between the NCBI taxonomy and other resources, such as Wikipedia and the BBC Nature Wildlife finder. For more background seePage, R. D. M. (2011). Linking NCBI to Wikipedia: a wiki-based approach. PLoS Currents, 3, RRN1228.

Publicados in iPhylo

One of the things I find frustrating about TreeBASE is that there's no easy way to get an overview of what it contains. What is it's taxonomic coverage like? Is it dominated by plants and fungi, or are there lots of animal trees as well?

Publicados in iPhylo

Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: doi:10.1186/1471-2105-8-158). Today I find myself releasing yet another mapping, as part of my NCBI to Wikipedia project. By embedding the mapping in a wiki, it can be edited, so the kinds of problems I encountered with TbMap, recounted here, here, and here.

Publicados in iPhylo

Being in an unusually constructive mood, I've spent the last couple of days playing with the TreeBASE II API, in an effort to find out how hard it would be to replace TreeBASE's frankly ghastly interface.After some hair pulling and bad language I've got something to work. It's very crude, but gives a glimpse at what can be done.