Sep 14, 10:18 PM
TOAD Modelling
A basic query to ask in biogeography is ‘what species lives here?’. There are a lot of data resources to answer that question. I come up with at least four different types of data resources. First, there are direct records of observations of species, one online example being the citizen science effort eBird which allows birdwatchers to record on the Web what birds they’ve seen. There are coarse-scale range maps, an example being the map in this species account on the mountain lion. There are species lists collected over a substantial period of time, such as lists from parks and nature reserves. Finally, there are probabilistic distribution models generated by tools such as openModeller.
We have just started work on a Semantic Web application that will return information in RDF on species status and distribution for a selected geographic area. The aim of the application is to provide a framework for amalgamating the four types of data sources above into some sort of uniform species list. (I’m calling this TOAD data, for Taxon Observation And Distribution. A TOAD ontology may be in the not-too-distant future.)
I think the basic data granule here comes down to who-where-what-when? That is, a combination of data source by geographic region by taxonomic entity by time period. For now the idea is to concatenate the who-where-what-when parameters into a single URI, thus designating it as a resource over which one can return an RDF description. Variants of this URI pattern will return information such as species lists for a particular region (either according to one data source or across all data sources handled by the system), sets of observation data for a particular species, or metadata for a data source.
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One of my on-going projects is to put together species lists for my area (Sitka, Alaska).
So far I have been utilizing all the resources I have found, and I would be interested in any others. However, due to the relatively remote and rugged nature of this area, along with the effects of topography, the ocean (Sitka is on an island), and past ice ages, it’s probably a little more difficult to connect the dots, so to speak, based on observations from the broader region. Despite that, it’s still interesting see what things are predicted to be here as ultimately I would like to find and document (photographically) most of our local species.
I am wondering if there is a (relatively easy) way for me to make the observations/information/lists I compile accessible to broader efforts such as you are describing here.
— Matt Goff · Sep 15, 02:38 AM · #
Your project is exactly the sort of effort that we’re trying to facilitate with our research. For now, there are a couple things to explore in terms of making your observations more widely available. First, there are a decent number of citizen science efforts that allow people to input natural history data over the web. eBird which I mentioned above is probably the biggest of these, and a good list of some of the others is found here at Burning Silo.
Second, I’ll mention our own efforts in developing tools to aid in ‘semantic ecoblogging’, on view in the blog FieldMarking. In particular, we have just developed a Firefox plugin for capturing data on species observations as reported on a blog. We’d love to have feedback on how well this tool might work for you.
— Allan Hollander · Sep 15, 09:59 AM · #
The timing of this blog is perfect for me. The next two features I’m looking to add to the Mushroom Observer website are expanded geographic information and tagging/RDF descriptions.
I’m relatively new to RDF and have never used it for describing species or natural history observations (unless you count the one little test I did with the previous version of Spotter). I’d love to get some pointers to good working examples as well as existing ontologies I might use or expand on. Any recommendations on how best to hook up to mapping systems would be great as well.
— Nathan Wilson · Sep 17, 10:02 PM · #
There are lots of possibilities for mapping systems that could be integrated into your site. For lightweight mapping, I would suggest Google Maps or the open source OpenLayers.
Looking briefly at the data in Mushroom Observer, it seems that much of the data only has text locations. You will need to geocode these before you could map them. Two things that might help with the geocoding are the tools from the Biogeomancer Project and the open web-based APIs from MetaCarta.
In terms of ontologies to use, the Spotter observation ontology is one place to start, and it is straightforward to look at the RDF that Spotter generates. The TOAD ontology I mention above is still at the brainstorming stage. I also have a biodiversity resource ontology that could be used to describe species lists, tthough I would need to put up an example of this.
— Allan Hollander · Sep 19, 06:06 PM · #