Biodiversity informatics & taxonomy

Biodiversity informatics & taxonomy

The Aellopus clavipes, the Natural History museum.

Research

I am interested in the challenges facing taxonomy and systematics and the role of the web in making the subject more efficient and fundable, and more closely aligned with its user communities.

Biodiversity informatics is part of the broader “Environmental eScience Revolution” and a special issue of the Transactions of the Royal Society A was published in 2009 with papers from a meeting held at the Royal Society in 2008 as well as papers from participants in NERC’s eScience programme.

Selected paper

  • Gurney, R., Badcock, N. Garnett, N & Godfray, H.C.J. (eds.) 2009 The Environmental eScience Revolution. Transactions of the Royal Society of London A

eMoncot

eMonocot is a global online biodiversity information resource for monocotyledons, which include grasses, orchids, sedges, palms, lilies and yams and represent 20% of flowering plants. When complete, you will be able to use eMonocot to identify Monocot plants anywhere in the world, understand their diversity and evolutionary relationships, and explore a wealth of information including descriptions, images, conservation, geographical and ecological data.

The project is being funded by the Natural Environment Research Council (NERC) via a consortium grant to the Royal Botanic Gardens, KewOxford University and the Natural History Museum. Keep up with the progress of the project by following @eMonocot.

Unitary taxonomies

In particular I have explored the idea of unitary taxonomies, websites where the complete taxonomy of a group of organisms is housed. Such a site would provide an environment in which taxonomic research can be conducted, and a one-stop-shop for accessing information about the group’s taxonomy. It would also include “wiki” functions to enable anyone to contribute information. The site would present a provisional consensus taxonomy for ease of use by non-experts, though also mount alternative taxonomic hypotheses for the more specialist user.

Selected publications

  • Godfray, H.C.J. 2002 Challenges for taxonomy.  Nature 417, 17-19 (Commentary; reply to correspondence arising: “Towards taxonomy’s ‘glorious revolution’”, Nature 420, 461; related editorial “Ignorance is not bliss” Nature 2004, 430, 385).  Read full PDF text
  • Godfray, H.C.J. & Knapp, S. 2004.  Introduction to Theme Issue, “Taxonomy for the 21st Century”.  Philosophical Transactions of the Royal Society, London B. 359, 559-570. Read full PDF text
  • Godfray, H.C.J. 2005 Taxonomy as information science.  Proceedings of the Californian Academy of Science 56, Suppl. I (16), 170–181
  • Scoble, M.J., Clark, B.R., Godfray, H.C.J., Kitching, I.J. &  Mayo, S.J. 2007 Revisionary taxonomy in a changing e-landscape.  Tijdschrift voor Entomologie, 150, 305–317.
  • Godfray, H.C.J. 2007 Linnaeus in the information age (Commentary).  Nature, 446, 259-260. Read full PDF text
  • Godfray, H.C.J., Clark, B.R., Kitching, I.J., Mayo, S.J. & Scoble, M.J. 2008 The web and the structure of taxonomy.  Systematic Biology  56: 943–955.
  • Mayo, S.J. & 18 co-authors 2008 E-taxonomy for flowering plants: alpha-taxonomy on the Web.  Kew Bulletin  63, 1-16.
  • Godfray, H.C.J., Mayo, S.J. & Scoble, M.J. 2008 Pragmatism and rigour can coexist in taxonomy. Evolutionary Biology, 35, 309-311.
  • Clark, B.R., Godfray, H.C.J., Kitching, I.J., Mayo, S.J. & Scoble, M.J. 2009 Taxonomy as eScience. Transactions of the Royal Society of London A 367,  953-966.

The CATE project

This is a project funded by NERC’s e-Science initiative to explore issues of moving taxonomy to the web. It does this by working with two exemplar groups, the hawkmoths (Sphingidae) and aroids (Araceae). It is led by the Natural History Museum, who are responsible for the hawkmoths, and includes the Royal Botanic Gardens Kew, who are responsible for the aroids, and Oxford who lead on the bioinformatics. Illustrated are the hawkmoth Aellopus clavipes and the aroid Arum creticum.

Full details can be found at the CATE website.  Ben Clark at Oxford worked on the CATE bioinformatics and programming.

Taxonomy

Though I am not currently spending much time on it I am interested in the taxonomy of leaf-mining flies (particularly Agromyzidae) and their parasitoids (particularly Braconidae: Opiinae and Alysiinae (Dacnusini) – picture is of Dacnusa sibirica from the Polish biocontrol company site www.biopartner.com.pl).

Selected publications