[Taxacom] Visualizing Biodiversity

Roderic Page r.page at bio.gla.ac.uk
Wed Aug 31 06:26:12 CDT 2011

As a follow up, about this time last year I put together another visualisation of EOL's tree, modelled on a iPhone display. Might be a useful approach if space is an issue.

Another way to tackle the quest for a visualisation is to make the data available via an API so programmers could play with it. For example, if you could model it on EOL's API (but simplified to remove stuff that's unique to EOL).

Basically, all you need is to be able to return the following information for a node in your classification:

1. node id
2. node label (e.g., "Animalia")
3. total number terminal nodes (e.g., how many species)
4. list of immediate child nodes (e.g., phyla if current node is a kingdom) by id, each with information on 1-3 above

Technical digression: serve data in JSON format and support callback parameters and developers will love you for it.

If you did this, then it would be straightforward for anyone with a visualisation to play with the classification, but without needing a complete copy of the classification on their own machines.



On 31 Aug 2011, at 05:08, <Tony.Rees at csiro.au> <Tony.Rees at csiro.au> wrote:

> Dear Taxacomers,
> In my efforts to produce a listing of all genera I end up with, among other things, summary data on higher levels of my taxonomic hierarchy plus the number of child taxa each contains (current example by phylum: http://www.marine.csiro.au/mirrorsearch/ir_search.list_phylum). I realise that this tabular approach is pretty much as unexciting as it gets so was wondering about an improved visual manner to present this type of information, preferably in the form  of a navigable hierarchy as per the present hyperlinks.
> One example I have come across which seems really neat is Kris Urie's EOL Tree Viewer (aka "VOLE" - Viewer of life on EOL), for example starting point see http://kurie.github.com/EOL-tree-viewer/#COL, however I was wondering whether taxacomers have more suggestions or personal favourites worth looking at. Of course I would also have to work out how to load in my data, but that's a detail maybe.
> All suggestions / examples welcome (and may even be used on my site if I can figure out how to implement one or more of them). (Also I have a feeling that Rod Page may have some experience in this area). Of course it would also be nice if someone could take this on as a pet project for free, however I would never dream of asking such a thing (for comparison / light relief see http://www.27bslash6.com/p2p.html).
> Regards - Tony
> Tony Rees
> Manager, Divisional Data Centre,
> CSIRO Marine and Atmospheric Research,
> GPO Box 1538,
> Hobart, Tasmania 7001, Australia
> Ph: 0362 325318 (Int: +61 362 325318)
> Fax: 0362 325000 (Int: +61 362 325000)
> e-mail: Tony.Rees at csiro.au
> Manager, OBIS Australia regional node, http://www.obis.org.au/
> Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
> Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566
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Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r.page at bio.gla.ac.uk
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