I stumbled across this tweet yesterday (no doubt when I should have been doing other things), and disappeared down a rabbit hole. Emerging, I think the trip was worth it. Markdown wikis Among the tools listed by @zackfan01 were Obsidian and Roam, neither of which I heard of before.
Following on from the previous post Rethinking annotating biodiversity data, here are some more thoughts on annotating biodiversity data. Annotations as sticky notes I get the sense that most people think of annotations as "sticky notes" that someone puts on data. In other words, the data is owned by somebody, and anyone who isn't the owner gets to make comments, which the owner is free to use or ignore as they see fit.
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.
I've just spent a frustrating few minutes trying to find a reference in BioStor. The reference in question is and comes from the Reptile Database page for the gecko Phyllodactylus gilberti HELLER, 1903. This is primary database for reptile taxonomy, and supplies the Catalogue of Life, which repeats this reference verbatim. Thing is, this reference doesn't exist! Page 39 of Proc. Biol. Soc.
Yesterday I fired off a stream of tweets, starting with: Various people commented on this, either on twitter or in emails, e.g.: So, to clarify, I'm not abandoning wikis. I'm just frustrated with the limitations of Semantic Mediawiki (SMW). Now, SMW is a great piece of software with some cool features.
I've made some progress on a wiki of phylogenies. Still much to do, but here are some samples of what I'm trying to do. First up, here's an example of a publication http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021: In addition to basic bibiographic details we have links to GenBank sequences and a phylogeny. The sequences are georeferenced, which enables us to generate a map.
Sadly I won't be at TDWG 2009, at least not in person. However, there is a session on wikis, which may contain this brief screencast of my iTaxon experiments. The screencast was made in haste, but tries to convey some of the ideas behind these experiments, especially the idea that by linking data together we can generate more interesting and rich views of objects such as scientific publications.
At the start of this week I took part in a biodiversity informatics workshop at the Naturhistoriska riksmuseets, organised by Kevin Holston. It was a fun experience, and Kevin was a great host, going out of his way to make sure myself and other contributors were looked after. I gave my usual pitch along the lines of "if you're not online you don't exist", and talked about iSpecies, identifiers, and wikis.
The e-Biosphere meeting in London June 1-3 has announced a The e-Biosphere 09 Informatics Challenge: The "real time" aspect of the challenge seems a bit forced.
I'm slowing trying to get phylogenies into the wiki that I'm playing with. Here's an early example, the TreeBASE tree T6002, from the study A Phylogenomic Study of Birds Reveals Their Evolutionary History. The tree is displayed using my tvwidget. Below are listed the OTUs in the tree in a crude table. The idea is that this table will contain a mapping between OTU labels and taxa.