Roger Hyam

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 of the LGTG (a.k.a. the Less Than Greater Than group). Thanks are due to Éamonn O Tauma and the team at the GBIF Secretariat for being wonderful hosts and to my fellow participants for being such good company.

This was a two and half day meeting that involved a group of us working on a document full of recommendations (to be published in the next month or so). As part of my contribution I came up with a slightly more detailed plan for how GBIF would interact with data suppliers and consumers. For a brief time this formed part of the final document but was then cut because it was too detailed. It may still make it back into the appendix but may also drop out completely so I thought I would present it here for posterity.

These are more or less just a series of notes and diagrams but they should be understandable to anyone involved in the field. I use the term GUID as this was before we changed to calling them persistent identifiers.

Note that what I present here is what I presented to the group and does not necessarily reflect the views of the group which will officially be published later.

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Tring the Fox

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 and taxonomy and an explanation of why nomenclature “sucks” – I don’t actually use the ‘s’ word in the chapter.

There are probably still some typos and there may be some factual errors – if so I’d really like to hear about them so I can get them ironed out before the book goes to press.

Taxa, Taxon Names and Globally Unique Identifiers in Perspective. (PDF ~ 332kb)

Enjoy!

Back story: I was asked to contribute to a new Systematics Association volume “Descriptive Taxonomy: The Foundation of Biodiversity Research” to be published by Cambridge University Press in the autumn. I have written my chapter and it has been accepted but not edited. I am an advocate of open access to scientific publications and it became clear that this publication was not going to be available on the web let alone on an open access basis so I asked CUP if I could publish it through Nature Precedings and they said “No” – but they positively encourage authors to publish drafts of their work on their own websites. This is a good compromise as it keeps my moral superiority intact and enables me to move at a reasonable speed but also allows CUP to have a business model producing those things they put in libraries…. what were the called? ah books!

I would advocate that anyone else who is writing contributions to CUP books take advantage of this arrangement and prepublish their material on their own website thus making it as widely and freely available as possible.

Edit: I just updated the PDF to include a few comments I have received.  You can still read the Old Version (PDF ~ 332kb) if you like

Gathering Storm

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 widely in the biological and environmental sciences, the e-infrastructure needs to provide  two dictionary functions for scientific names of organisms i.e.

1. A recognized list of the names used. To establish that any two studies are actually using the same names whilst accounting for spelling variants and homonyms as well as to facilitate consistency in spelling and presentation.
2. A mapping between the names and descriptions of the taxa they are used for. To establish that any two studies are using the names in the same sense or compatible senses.

If the ICBN and ICZN codes required all names to be registered in a single or limited number of places then this would effectively fulfil the first function. Unfortunately neither the ICBN or ICZN codes require names to be registered. Neither do they require names to be published in a particular list of journals. They merely set out the conditions for effective publication. The  publications in which new names appear could be published anywhere and deposited in any library. There is no requirement for them to be peer reviewed. Continue reading »