Wednesday, January 31, 2007

When phylogenetic names would be useful

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To avoid being charged with being consistent (unlikely, I know), despite being underwhelmed by phylogenetic names in the context of TreeBASE...
10 comments:
Tuesday, January 30, 2007

Quixotic(?) tree of Life visualisation

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The Ant Room has a nice post on Visualizing the tree of life , with some cool links. And just to balance that, Donat Agosti drew my attentio...
1 comment:

Encyclopedia of Life

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Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the sc...

Phylocode

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Comments by David Marjanović elsewhere on this blog ( here and here ) about TreeBASE, classification and Phylocode have prompted me to wri...
4 comments:
Thursday, January 18, 2007

The joys of mapping names in TreeBASE

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Here's a fun example of how databases get out of sync, making them harder to link up. TreeBASE taxon T4628 is labelled Bolitoglossa somb...
Tuesday, January 16, 2007

A manifesto

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The funding of pPOD mentioned earlier today motivates me to write some notes on what I think "core database technologies for enabling ...
5 comments:

processing PhylOData (pPOD)

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Some good news! pPOD, a NSF-funded project on integrating data from AToL (A Tree of Life) projects has been funded. Val Tannen (right) is ...
Monday, January 08, 2007

chem-bla-ics: Including SMILES, CML and InChI in blogs

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Browsing Postgenomic.com eventually lead to Egon Willighagen's post about Including SMILES, CML and InChI in blogs , which talks about ...
Saturday, December 23, 2006

Unique Author Identification | Public Library of Science

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Very interesting post by Richard Cave on a PLoS blog concerning unique author identification . Here's the opening paragraph. I [Richard...
1 comment:
Saturday, December 02, 2006

Folksonomies - why philosophy is a bad thing

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The November 2006 issue of D-Lib magazine contains an article by Elaine Peterson entitled "Beneath the Metadata: Some Philosophical Pro...
6 comments:
Wednesday, November 29, 2006

Homonyms and uBio's data model (yet more on names)

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As part of the TreeBASE name mapping exercise, I've come across some interesting names, such as "Diplura". This is a homonym, ...
6 comments:
Friday, November 24, 2006

Demise of Phyloinformatics.org

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As noted on the Society of Systematic Biology (SSB) web site , the journal Phyloinformatics has disappeared. It only published eight papers...
Friday, November 17, 2006

More on names (and frogs)

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Molecular Phylogenetics and Evolution carries two articles debating the application of names to trees, which reflects tensions between two ...
Tuesday, November 14, 2006

Synonomy and kinds of name

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Just wanted to write this example down before I loose it. Browsing Bill Piel's trees in Google Earth , and was looking at Lee et al....
1 comment:
Monday, November 06, 2006

The politics and practice of accessibility in systematics

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Stumbled across New Infrastructures for Knowledge Production: Understanding E-science while writing about TAXACOM on the iSpecies blog . Th...
1 comment:
Sunday, October 15, 2006

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Mac Spoof: Upgrading Really should be doing some work, but nearly wet myself when I saw this...
1 comment:
Friday, September 22, 2006

PygmyBrowse demo

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I've now put a simple demo of the PygmyBrowse tree browser up here . It's a simple toy just to demo the idea.
2 comments:
Wednesday, September 20, 2006

PygmyBrowse

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I've previously bemoaned the lack of a decent way to display and navigate through phylogenies. Ryen White , a graduate of Glasgow'...
Tuesday, August 29, 2006

Collaborative data matrices using EditGrid

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EditGrid is an online collaborative spreadsheet tool that I stumbled across via Ogle Earth . It strikes me thjat this could be a way to cre...
2 comments:
Tuesday, August 08, 2006

Connotea and TreeBASE

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One of my (forever) ongoing projects is to map taxon names in TreeBASE to names in external databases (such as uBio ) as a way of checking t...
1 comment: