Computer-aided taxonomic identification

Objectives

The number of taxonomists and ecologists is dwindling the world over at an alarming rate. This has been acknowledged as one of the “taxonomic impediments” hindering the full implementation of the Convention on Biological Diversity (CBD). The CBD Secretariat has called for a global taxonomy initiative (GTI) to remove or reduce the knowledge gaps in our taxonomic system. This has led to the development of several projects on the “sound management of biological diversity” This research project, consisting of four phases of implementation is aimed at developing multimedia tools of taxa self-training and identification of species.

Materials and Methods

This project is based on the data collected by the Institute on mangroves, trees of the Western Ghats and pollen taxa. Various applications available online or as CD-ROMs, rely on a common tool for identification and self-training of taxonomists (IDAO) developed by CIRAD.

This software is based on the calculation of similarity coefficients which allows for data insufficiency, intra-specific variations as also errors of observation. Contrarily to dichotomous keys, the species here are not eliminated: only the percentage of similarity is modified. An identikit of the individual is internally programmed to react to every response of the user and this enables the non-specialist of botany to identify the species through illustrations.

The system also signals data deficiencies as well as errors of observation on the part of the user. Once the identification procedure is completed, the user is provided with a descriptive analysis of the species in which all technical terminology has been hyper-linked. The entire collection of documents (photographs, illustrations and descriptions) is available at all times. This system adapted to small PDA (Personal Digital Assistant) and UMPC (Ultra Mobile PC), has been implemented with the support of the European Commission for identifying crop weeds of the Indo-Gangetic plains(OSCAR project), trees of the Western Ghats (BIOTIK project), mangrove plants and and pollen grains.

Partners

• UMR AMAP, Botanique et Bioinformatique de l’Architecture des Plantes (UMR CIRAD-CNRS-INRA-Université Montpellier II).
• Programme "Management of cutivated ecosystems" of the CIRAD.
• Research Unit Communication and Innovation Studies University of Wageningen, The Netherlands.
• National Herbarium Nederland (NHN-Leiden), University of Leiden, The Netherlands
• Rice Wheat Consortium for Indo-Gangetic Plains.
• University of Andhra Pradesh in India
• University of Ruhuna in Sri Lanka
• Karnataka, Kerala and Tamil Nadu Forest Departments.
• National University of Laos, Lao PDR

Funding

• French Institute of Pondicherry
• European Commission under ASI@IT&C programme

Team

IFP

• Dr. B.R. Ramesh - Head of Botany Laboratory
• Dr. F. Borne – Head of Geomatics and Applied Informatics Lab.
• Dr. N. Ayyappan – Botanist
• Dr Vasanthy G - Palynologist
• D. Balasubramanian - Manager of Information Systems
• S. Aravajy – Botanist
• Mr. G. Jayapalan - Research Assistant
• Mr. K. Ramesh Kumar – Technician

UMR AMAP, Montpellier, France

• Dr. Pierre Grard, Project Leader - Botanist
• Dr. C. Edelin - Botanist
• Dr. J. Prosperi – Botanist
• Dr. P. Couteron – Plant Ecologist

University of Wageningen, The Netherlands

• Dr. Rico Lie – Anthropologist

National Herbarium Nertherlands, Leiden

• Dr. P.J.E. Kessler - Botanist
• Dr. C.E. Ridsdale - Botanist

National University of Laos

• Prof. Dr. Bouakhaykhone Svengsuksa

Rice Wheat Consortium

• Dr. R.K. Gupta –Director RWC – Agronomist

University of Andhra Pradesh

• Prof. A.V. Raman

University of Ruhuna in Sri Lanka

• Dr. Sanath Hettiarachchi - Head of Botany Department
• Dr. L.P. Jayatissa – Botanist

Main Outputs

Books and CD-ROMS

• Pollen grains of South Indian trees V.1.0 - A user-friendly multimedia identification software

G. Vasanthy, P. Grard. Research assistance G. Jayapalan. Collection Ecologie no.45, IFP, 2007. [CD-ROM]
Language : English.

An electronic pollen flora including digital and scanning electron micrographs and descriptions distinguishes itself by the graphic identification system of pollen without the plethora of terms; it enables many levels of users (in South India as well as in the tropics, subtropics and sub-temperate regions in India, Asia and other continents) to learn palynology by the "click of the mouse". The descriptive part furnishes palynological terms linked to the illustrated definitions and the bibliographic link for quick reference. Pollen Typification; and Taxonomical, Ecological and Distributional notes for the selected 147 genera (Mangroves: 11, Western Ghats: 129 and others: 7) are also given.

A microtaxonomic, research tool, (adapted from IDAO by CIRAD) will aid "users" interested in climate related past vegetational changes.

Keywords: pollen flora, computer-aided identification, trees, micro-characters

• Mangroves v1.0. A multimedia identification system of mangroves species of South-East India and Sri Lanka. [CD-ROM]

J. Prosperi … [et al.], Collection écologie n°44, Pondicherry-Montpellier, IFP/CIRAD, 2005.
Language: English. 300 Rs (11 €)

Mangroves is a graphical identification system of plant species, the only tool of its kind available on South-Asian Mangroves at present. The system, entirely graphic, enables non-specialists to make determinations with the help of just a small number of characters, chosen according to their availability for the particular plant to be identified. It meets the needs of amateur botanists, agronomists, forest officers and nature lovers with a keen sense of observation. The use of frequently observable vegetative characters has been favoured, as well as an extensive illustration of species.

The major part of the work presented in this CD-ROM was carried out in the framework of the European Commission funded project entitled “Assessment of mangroves degradation and resilience in the Indian subcontinent: The cases of Godavari Estuary and southwest Sri Lanka”.

Keywords: botany, computer-aided identification, mangroves, vegetative characters

An online version is also available.

• LE BOURGEOIS T., JEUFFRAULT E., GRARD P., CARRARA A., 2001. AdvenRun V.1.0, Principales mauvaises herbes de La Réunion . CIRAD / Ministère de l’Agriculture et de la Pêche.

Chapters in books

• GRARD P. & PORDIÉ L., 2003. Rethinking taxonomy in the age of technology: Perspectives and limitations of a new informatics tool for conservation in the Himalayas, In Aumeeruddy-Thomas Y., Karki M., Parajuli D. and Gurung K. (Eds), Wise practices in sustainably managing Himalayan medicinal plants, WWF.
• GRARD P., PROSPERI J., & DEPOMMIER D. 2002. New tools for capacity building in taxonomy and environment management: an application on mangrove species, In Traditional ecological knowledge, conservation of biodiversity and sustainable development. D. Depommier & P. S. Ramakrishnan Eds. Publication Département d’Ecologie, Institut Français de Pondichery, 41: 155-173pp.

Articles

• AYYAPPAN, N. & PARTHASARATHY. N., 2006. Prismatomeris tetrandra (Roxb.) K. Schum. Subsp. malayana (Ridley) J.T. Johansson- a new record to Indian tree flora, Journal of Economic and Taxonomic Botany, 29(4): 802-804.

• LIE R. & BALASUBRAMANIAN D., 2006. OSCAR-An exercise in ICT, Agriculture and Society, i4d magazine, www.i4donline.net : 29-30

Others

• GRARD P., 2002. “A multimedia approach to computer-aided identification for capacity building in taxonomy”. Poster & software presented at the "3ème réunion du Groupe de Travail sur la Taxonomie" organized by "Secrétariat de la Convention sur la Diversité Biologique" (preparation of Rio Summit+10), Pretoria, South Africa, 8-13 July 2002.