Sunday, January 27, 2008


Annotating images with user-created overlays is a must for defining morphological characters, or enhancing ontologies. This seems to be a relatively tricky thing to do over the web. Inputdraw is a SWF widget that is free for noncommercial use. It allows you to save overlays drawn on images into forms, the data are then saved as SVG text. The OpenCollections software also mentions an annotation system that is in the works, though the bottom line there is that its not quite ready prime time. At a recent Morphbank meeting someone (apologies for not remembering who) mentioned that another solution might involve using the Google Maps API to create polylines or points on custom "maps", which would in fact be your images. The Beginning Google Maps Applications with Rails and Ajax book is a decent starting point for implementing this approach. Note that you would need .gif or .png formatted images if you attempt this. I used the Beginning Google Maps book to finally implement maps "natively" within mx (we still have hooks to BerkeleyMapper, which is a great service), but not without several hours of frustration. While the book is quite clearly written the code provided in Chapter 3 is incomplete or erroneous in several very frustrating ways, so make sure to download the updated code from the website if you have the book.

As I add new tables to mx I'm starting to add fewer and fewer columns, with the idea that tagging can be used as the primary means of extending the basic objects. Tagging essentially allows you to extend your records to as many fields as you want, and is therefor a very simple way to provide extensibility. A new book on the tagging phenomenon by Gene Smith looks to be a must read, I think I'll order mine now.

Finally, while somewhat older news, I keep thinking about social annotation with respect to taxonomy, and also things like scoring phylogenetic characters. How might things discussed in this Google talk from Luis von Ahn be applied to systematics research? Within taxonomy one approach could be to simply photograph many specimens and then allow the general public to point out the similarities and difference. These could then be vetted by the "experts" as a starting point. This approach, albeit with a greatly simplified "taxonomy" and character set, is being used at GalaxyZoo. In the GalaxyZoo example the galaxies have already been classified by computer algorithms into various types, so there is an excellent comparative dataset for testing things like the trustworthiness of the public contributions. Games like those discussed by von Ahn could also be used in developing hypotheses of character homology. In systematics we present homology hypotheses that are then further tested using phylogenetic analysis. What if part of this testing requires that the definition of these hypotheses be agreed upon by two or more experts, using games like those discussed by von Ahn? In theory this agreement is already required, to some degree, as implemented in the review process that occurs prior to publication. It could, however, be made more explicit (and fun?). Given the right framework for playing these games there would be many beneficial spin offs including obvious things like annotated ontologies of morphological characters.

Sunday, January 13, 2008

FigTree v1.1

Andrew Rambaut has posted a message to the beast-users listserv, he's just released a new version of FigTree. Among other things this new version allows you to re-root trees (something I bugged him for a while back, as I'm sure others did as well). Perhaps even better, the source code has been released. With these new features, and now that others can conceivably add new bells and whistles, I suspect FigTree will remain the premier tree rendering software for some time.