Tuesday, June 17, 2008

Godfray et al. 2007

Godfray, H.C.J., B.R. Clark, I.J. Kitching, S.J. Mayo, and M.J. Scoble. 2007. The web and the structure of taxonomy. Syst. Biol. 56(6): 943-955.

The main thesis of this paper is "an easily accessible taxonomic knowledge base is critically important for all biodiversity-related sciences". Yes, I agree with this but isn't an easily accessible knowledge base about anything quite handy? In this paper, the authors "review different ways in which taxonomy has already made use of the Web or may do so in the future". This paper made me think about how much work taxonomists are doing on their free time, for free, putting information on the web so that other people can have it at a click's moment. I understand that it is great to share all of our knowledge and have open access to everything, but I guess some days I feel like our capitalist society is crushing me and must..make....money.....

Notes on the paper:

-they talk about the 'second' bioinformatics crisis being solved by making genomic sequence and other data available on the Web and developing data handling and mining tools for accessibility and analyses. So I'm wondering, do people think that crisis is over? How can we gauge when a crisis is over? Hmm..

-"a major part of being a specialist in a group is the ability to navigate [through publications scattered throughout the literature] and to understand the location of different sources of information and specimens (Scoble, 2004)". SO TRUE!

-"the absence of an up-to-date and accessible taxonomy is a serious shortcoming to an expanding user base...".

-the authors are for a 'current consensus' taxonomy with option to see competing hypotheses if user is so inclined. I can imagine some authors of taxonomic web pages with a tiny little click button at the bottom of their page with teeny tiny words "for alternative hypotheses, click here".

-the authors talk briefly about taxonomic resetting and how doing this, people could be missing out on some important "nuggets of information". Well I guess if everything was on the specific webpage for a taxonomic group, you would never have to dig through that old literature. It would be so great! I can definitely see this as a wiki sort of deal.

Types of taxonomy on the web:

1. Fundamental data
-collection lists
-specimen digital images (2- and 3-dimensions)
-specimen locality data
-catalogues of previous taxon hypotheses
-literature (pdf's)

2. Collection-level metadata
-e.g. number of specimens of a given species within a particular museum

3. Data used in phylogenetic studies
-raw sequence databases
-aligned sequence files
-character matrices
-tree databases (treebase)

4. Raw data synthesis (better called species name lists)
-Species 2000 project

5. Tools
-source of software (database, phylogenetic)
-online keys
-Globally Unique Identifier (GUI)/LifeScience Identifiers (LSID's)

6. Web Publication

7. Wikis
-e.g. Wikispecies, Citizendium

8. Mash-Ups - Federating data
-a web page produced by automatically searching the web for all information available on a certain taxa
-e.g. iSpecies

9. Unitary taxonomies
-all resources relevant to the systematics of a particular group would be present at a single site (Godfray 2002)
-definitely a lot of advantages and disadvantages to this proposal

The authors then discuss the Cate Project (Creating A Taxonomic E-scienc), which is a website with software resources used to allow new taxonomic hypotheses to be advanced within the site. It is basically a test of the unitary taxonomy idea.

They conclude by stating that a web-based, unitary taxonomy is the way to avoid possible future schisms in the field of taxonomy.