Hobart

Seminar Abstract

Friday 24 April 2009, 11.30am (Tas time)
CSIRO Auditorium, Hobart

Tony Rees
Divisional Data Centre
CSIRO Marine and Atmospheric Research
Hobart

OBIS, IRMNG and TAXAMATCH: Biodiversity Informatics Tools from the CMAR Data Centre

The Divisional Data Centre at CSIRO Marine and Atmospheric Research has been involved in Biodiversity Informatics (loosely: the application of computing solutions to the study of biodiversity and biogeography) since 1998-9, when it undertook the redevelopment and extension of the Division’s CAAB database and web information system for marine species in Australia (www.cmar.csiro.au/caab). Since that time, key features of CAAB have been ported to OBIS, the Ocean Biogeographic Information System based at Rutgers University, N.J. (www.iobis.org), and two additional related systems have been developed: IRMNG, the Interim Register of Marine and Nonmarine Genera (www.obis.org.au/irmng/), and TAXAMATCH, a fuzzy matching algorithm for species scientific names (www.cmar.csiro.au/datacentre/taxamatch.htm).

OBIS is a web-based “data aggregator” for information on the distribution of marine organisms, with currently over 500 source databases from around the world queryable via a single web portal. Species distributions can also be rapidly visualized by a variety of mapping tools, or the data downloaded to a user’s computer for further analysis and visualization as required. The prototype for the current (generation 2) version of OBIS was constructed at CMAR and ported to the OBIS international portal in the USA in 2004 (An Australian node of OBIS, OBIS Australia, is also maintained by CMAR at www.obis.org.au).

IRMNG is a collation of existing resources of genus names for animals, plants, bacteria and viruses with the intention of flagging marine from nonmarine, and extant from fossil, names, so that (in principle at least) it can be used as a filter for automatically extracting “marine, extant” organisms (by scientific name) from mixed lists (such as those in museum databases, GBIF, and elsewhere). As well as currently containing over 200,000 genus names (to be >400,000 in IRMNG version 2), IRMNG also contains species names for a considerable subset of Australian and New Zealand taxa as acquired from relevant published and unpublished compilations.

TAXAMATCH is a novel approach to rapidly detecting candidate near match scientific names from a reference database, to any supplied input name (genus name, or genus+species). It outperforms other potential approaches in detecting virtually all “true” near matches while rejecting most false hits, with a comparatively brief execution (e.g. 1 second or better against a reference database of over 1.4 million species names).

Both IRMNG and TAXAMATCH have potential applicability outside of CMAR as well as in tandem with existing CMAR systems, and have attracted some interest from large scale biodiversity informatics initiatives such as GBIF (the Global Biodiversity information Facility) and the ALA (Atlas of Living Australia) project. This talk will review the essential features and potential use cases for the above systems, as well as give some insight into the history of their development and potential for additional functionality in the future.

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Location:
CSIRO = Marine Laboratories Auditorium, Castray Esplanade, Hobart

For further information, or to schedule a seminar, contact:
To schedule a seminar, contact:
Clothilde Langlais, (Oceanographic seminars) CSIRO Marine and Atmospheric Research (03) 6232 5399
Natalie Kelly, (Biology/Modelling seminars) CSIRO Marine and Atmospheric Research 0438 452 483
Jillian Enraght-Moony, (seminar administrator) CSIRO Marine and Atmospheric Research (03) 6232 5320
Communications Manager, Antarctic Climate and Ecosystems CRC (03) 6226 2265
Margaret Hazelwood, Institute of Antarctic and Southern Ocean Studies (IASOS) University of Tasmania (03) 6226 2971

Last updated 21/07/09