Category: Biodiversity Informatics

I put this talk together for a meeting just in case I needed to elaborate on a point in one of my reports. I never used it but post it here for the record. The Water Vole – Arvicola terrestris / amphibius? View more presentations from rogerhyam. The slides are pretty self explanatory….

I just wrote 500 words explaining the relationship between Taxonomy, Nomenclature and PESI for use in the PESI portal. Here they are: The process of creating a classification of life is split into two parts. Firstly experts decide which species exist. This process is called taxonomy. Secondly the experts work…

Sometimes two things cross your desk at the same time and they say more than either one of them would on their own. Firstly I was looking for a list of British birds and happened across the British Ornithologists’ Union (BOU) list of bird names and how they have changed…

I finally submitted deliverable D4.3 for the PESI project and in the great tradition of putting my outputs on my blog here is a PDF copy: Application and Adoption of Taxonomic Standards. This will be of interest to those involved in taxonomic and nomenclature projects as it shows our collective…

You can know the name of a bird in all the languages of the world, but when you’re finished, you’ll know absolutely nothing whatever about the bird… So let’s look at the bird and see what it’s doing — that’s what counts. I learned very early the difference between knowing…

Although there are standards for abbreviation of author names (notably Brummitt in botany) these are not always followed and often embellished. Furthermore it is believed that the added nomenclatural precision author names add is not worth the cost of their inclusion. If author names were included then every variation of…

At last month’s TDWG2009 conference I was on a panel for a brief discussion at the end of a session. There were around 200 people in the audience and handful of us up front as lambs for the slaughter. One of the questions from the floor concerned the automation of…

Keeping up with the nearly-year-old tradition of putting all outputs on my blog here are the latest two reports I have submitted as part of the PESI. Report on authoritative taxonomic standards from multiple sources suitable for deployment within European Research Area – resubmission with some clarifications. (PDF = PESI_D4.1_Standards_Report_v2.1.pdf )…

I have been wrestling for some time with how to handle taxonomic hierarchies when combining multiple classifications. This is partly motivated by a pressure to produce consensus hierarchies for navigation (a task that I think is probably not worth doing but which is beyond the scope of this post) and…

In this episode of our longest running soap opera Terry & Tina confuse Eric who takes off with Malcolm. “Cabinets” is a public service broadcast with the aim of promoting  community understanding of complex taxonomic issues. — Cue opening credits — The story so far:Terry is a taxonomist and he…

Several years ago I was involved in the developing the “TDWG Ontology”. Quite what the TDWG Ontology was/is remains an enigma for many. Around 2005/6 we tried to move away from modeling things in XML Schema and into some form of frame based modeling with well defined classes and properties…

Over the past few months I have been working on how to represent biological taxonomy and nomenclature using Description Logics. Here I combine these thoughts with a rather naive view of DNA Barcoding to suggest a new approach to taxonomy. Description Logic (DL) is an extension of frame based languages…

Last week I took part in a meeting at GBIF in Copenhagen to discuss the role GBIF could play in  Persistent Resolvable Identifiers (the technology formally known as GUIDs and often confused with UUIDs. Perhaps they should be called PRIs – pronounced ‘prize’ – just kidding.) This is the culmination…

Here is the first draft of a book chapter I have written for an upcoming Systematics Association volume. My intention with this work is to outline the current situation with regard to taxonomy and GUIDs for a slightly more general audience. It includes a walkthough of the difference between nomenclature…

I was writing a report on the role of nomenclators in PESI when I realized that (with a little tweaking and injection of dangerous opinions) one section would make a good blog post. In order to facilitate the accurate exchange of taxonomic information, both within the taxonomic community and more…

I just gave a talk at e-Biosphere ’09 . This was a 15 minute talk to possibly the largest audience I have ever addressed (400ish). Several people asked for copies of the slides so here it is as a PDF. Why you should care about data standards The thought of…

Tdwg Ontology 03.Key View more presentations from rogerhyam This talk has been put together for the LifeWatch WP5 workshop “Semantic Data Integration” taking place in IBED Nieuwe Achtergracht 166, 1018 WV Amsterdam between Monday 18 may 13:00 and Tuesday 19 may 15:00, 2009. Having discovered Slideshare I am wondering whether…

I recently took part in a very long discussion on LSIDs on the TDWG-TAG mailing list. This seems to have been a perpetual discussion over the past four years. On reflection I realised that over two posts I had produced a kind of personal position paper on LSIDs and that…

Back last year at TDWG2008 in Fremantle there was a Wild Ideas session where people could propose crazy things that might not be serious or urgent. I gave a presentation called SpeciesIndex?: A practical alternative to fantasy mashups. This was meant to be a bit of fun but actually went…

I have been wanting to push people in the direction of semantic technologies for quite a while now. Mainly this has taken the form of weaning them off the notion that well formed or valid XML is a generic solution to data interoperability rather than just a application level data…

With apologies to René Magritte. Imagine you are a judge in a small court and I am the accused. I have been caught stealing coconuts from the local supermarket. In my defense I say I did it to feed the last remaining flock of dodos that I have living in…

I have been doing some thinking about capturing images of herbarium specimens so as to facilitate the “taxonomic process” – whatever that might be. The trigger for writing this down was a quote from an excellent series of papers on digitisation of specimens: “Plant sheets are usually scanned at somewhere…

What’s the Problem? Imagine you are a biologist looking at a group of organisms. You may be interested in these organisms because they occupy similar ecological niches or the same geographical region or for any other number of reasons. In order to study these organisms you need to gather data…