After a short trip to meet Walter Jetz at Yale, I'm back in Boulder, have seen Paul Simon in Broomfield, CO and Wikipedia Loves Libraries! at Norlin last week, and am making a start at putting together my research ideas. Fun times ahoy!
But first, I'm still working through my notes from TDWG 2011. Here's a first installment of my treasure trove from day two; obviously, many awesome presentations and parallel talks were missed, probably because I was too busy enjoying them to take down notes. All errors are mine, and when you spot them, please do let me know in the comments!
- Islandora (p. aye-lan-do-ra) is a slick, open-source digital asset management system based on the popular Drupal CMS. Islandora was developed by the University of Prince Edward Island's Robertson Library. Islandora's goal is to steward digital assets in the long term, with an emphasis on long term stability, and to manage the entire research life cycle. Interestingly, the developers of Islandora provide paid support for their software through a private company, DiscoveryGarden, which I can think can be a valuable way of supporting scientific software development and maintenance. The presentation and demo (which I unfortunately missed, because of parallel sessions) was given by Mark Leggott, Islandora's Lead.
- If you want to play around with Islandora, their Sandbox instance is automatically reset regularly.
- The Field Book Project at the Smithsonian aims "to create one online location for scholars and others to visit when searching for field books and other field research materials". Sounds interesting! Unfortunately, I missed their presentation at TDWG; I'm hoping the So You Think You Can Digitize blog will cover them soon.
- FishNet 2 has a pretty slick interface, allowing search by a number of common fields or by drawing polygons on a map. Search results allow taxonomic checklists to be quickly assembled and downloaded as a CSV, among other features. You can definitely see the basis for a really fantastic data exploration tool here, and - being part of VertNet - definitely opens the possibility of a really first-rate data exploration tool for all those vertebrate records. And yes, there's an API as well. A good idea: FishNet 2 saves all search queries, so that developers can analyze what users are looking for.
- If you want to play around with this, try IRIS Couch, a CouchDB hosting service.
- Adrian Thomas Hine at the NHM Department of Entomology had an interesting talk on Species-level Metadata collection in museum; his argument in a nutshell being that even assembling species-level (rather than specimen-level data) could be valuable for research. He argued that this was also more sustainable, since maintaining this species-level index was a daily job for curators, and would answer a key question: what does a museum actually have?
- Cam Webb is working on modeling botanical data for the semantic web, based on DarwinCore.
- Filtered Push is a way to push annotations around between online repositories. My understanding of this tool is: if an analysis tool finds a specimen entry from GBIF suspicious, the dream is to allow the tool to "push" an annotation to GBIF, which GBIF can in turn "push" to the distributing museum for examination and verification by a curator. In this way, data can be improved across the interconnected databases we are now building.
- Ontobrowser, an "interactive ontology navigator and ontology-based image retrieval system", is a pretty good way of navigating Morphster, a "demonstration prototype of a service-oriented architecture enabling and supporting morphologically based phylogenetic studies". Try it out on the Hymenoptera!
- Chris Freeland talked about BHL's new Darwin Library Collection, "a digital edition and virtual reconstruction of the surviving books owned by Charles Darwin". They used detailed notes from di Gregorio and Gill, Charles Darwin's marginalia vol. 1 to map Darwin's own comments in his own hand onto books already scanned for the BHL, or - in some cases - Darwin's own annotated copies scanned directly into the BHL. Chris gave us a fantastic example of the latter, where Darwin wryly commented on Charles Lyell's thoughts on intraspecific variation that "if this were true, adios theory".
- Donald Hobern talked about annotation and ALAu. There were a lot of useful technical details about ALAu's implementation of annotations, but there are also some really interesting side projects being developed. The Online Zoological Collections of Australian Museums is a collection of animal data from museum across Australia, using the TAPIR protocol to aggregate the data from museum repositories. Identify Life, meanwhile, is a database of identification keys. Their Key to All Life project hopes to build one single gigantic identification key - for everything. How awesome is that? Give it a whirl yourself!
- Bob Morris introduced the Annotation Ontology, and stressed the importance of linking to the proof of what you're saying.
Part two will be out as soon as I can get around to it. Also: getting more and more excited for Life and Literature, just a week away tomorrow. It'll be great to see familiar faces from TDWG so soon after TDWG 2011 New Orleans!