TreeBASE meets NCBI, again

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. The mapping in and of itself isn't terribly exciting, but it's the starting point for some things I want to do regarding how to visualise the data in TreeBASE.

Because TreeBASE 2 has issued new identifiers for its taxa (see TreeBASE II makes me pull my hair out), and now contains its own mapping to the NCBI taxonomy, as a first pass I've taken their mapping and added it to http://iphylo.org/linkout. I've also added some obvious mappings that TreeBASE has missed. There are a lot more taxa which could be added, but this is a start.

The TreeBASE taxa that have a mapping each get their own page with a URL of the form http://iphylo.org/linkout/<TreeBase taxon identifier>, e.g. http://iphylo.org/linkout/TB2:Tl257333. This page simply gives the name of the taxon in TreeBASE and the corresponding NCBI taxon id. It uses a Semantic Mediawiki template to generate a statement that the TreeBASE and and NCBI taxa are a "close match". If you go to the corresponding page in the wiki for the NCBI taxon (e.g., http://iphylo.org/linkout/Ncbi:448631) you will see any corresponding TreeBASE taxa listed there. If a mapping is erroneous, we simply need to edit the TreeBASE taxon page in the wiki to fix it. Nice and simple.

At the time of writing the initial mapping is still being loaded (this can take a while). I'll update this post when the uploading has finished.

Some VIZBI 2011 links

Given that the Twitter stream tagged #vizbi will fade away soon, I've grabbed most of the links I tweeted during VIZBI 2011 and have put them here. This isn't intended as a comprehensive list, merely the things which caught my eye, and didn't flash by faster than I could tweet.

Books

• Visual Complexity: Mapping Patterns of Information
• Visual Thinking for Design

Movies

• DNA
• Malaria lifecycle Part 1
• Malaria lifecycle Part 2
• WEHI.TV

People

• Drew Berry
• Manuel Lima
• Tamara Munzner
• Fernada Viégas
• Martin Wattenberg

Software and websites

• Arena 3D
• BioBlender
• BLAST Atlas
• Cerebral v.2.0
• Chromograms
• CloVR
• Cytoscape
• EMAGE
• embedded Python Molecular Viewer (ePMV)
• Fleshmap
• GenomeView
• History Flow
• HivePlots
• ImageVis3D
• JProfileGrid
• Many Eyes
• Molecular Maya
• Molecular Movies
• PathBLAST
• Phyloviewer
• Powerwall
• Quartz Composition of DNA
• Scribl
• Sequence Surveyor
• Shape of Song
• Sybil
• Topiary Explorer
• Vrtual Worm
• Web Seer
• Whole Brain Catalog

VIZBI 2011

I've spent the last three days at VIZBI, a Workshop on Visualizing Biological Data, held at the Broad Institute in Boston (note that "Broad" rhymes with "Code"). A great conference in a special venue that includes the DNAtrium. Videos of the talks will be online "real soon now", look for the keynotes, which were full of great ideas and visualisations. To get a flavour of the meeting search for the hashtag #vizbi on Twitter (you can also see the tweet stream on the VIZBI home page). All the keynotes were great, but I personally found Tamara Munzer's the most enlightening. She drew on lots of research in visual perception to outline what works and what doesn't when presenting information visually. You can grab a PDF of her presentation here.

One aspect of the meeting which worked really well was the poster presentations. Poster sessions were held during coffee breaks, and after the last talk of the session but before the audience broke for coffee, each author of a poster got 90 seconds to introduce their poster (there were typically around 10 posters per break). This meant the poster authors got a chance to introduce themselves and their work to the workshop audience, and the audience could discover what posters were being displayed. Neat idea.

I gave a presentation on phylogenies, which I've put on slideshare. After explaining that I thought phylogeny visualisation was mostly a solved problem (as evidenced by the large number of tree viewers available), I continued the theme of why I don't think 3D works for phylogeny (except for geophylogenies), made the pitch for building a phylogeny viewer on the iPad, and finished with my recent work on Google Maps-style viewing very large trees.

Phylogeny VIZBI 2011

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