Biodiversity Informatics: key institutions and a few Research and on-going Projects in France

Gilles Boeuf, Laboratoire Arago, Université Pierre et Marie Curie/CNRS, Banyuls-sur-mer, Muséum national d’Histoire naturelle, Paris and Agropolis International,

Montpellier

Montpellier, TDWG Annual Conference, November 13th, 2009

© Santo, 2006

Collections and databases are essential in systematics and for the study of biodiversity. They have to be easily assessible and inter-operable on the international level. French Centres and Institutions already have very important collections and databases about specific diversity including microorganisms, fungi and plants, insects, shells, other invertebrates, fish, mammals, birds… and also in fossils for paleodiversity, including both plant and animal remains and human remains with asociated tools.

French Research is very active in such domains notably in agronomical Sciences, and mainly in Montpellier (INRA, CIRAD, IRD, USTL, CNRS, Agropolis International,…) and also in natural and human sciences, mainly in Paris (MNHN, UPMC, CNRS, IRD…).

French situationVery difficult to be exhaustive in front of

all the initiatives presented at e-biosphere 2009,

Strong interest to participate to LifeWatch in operating a national net for biodiversity,

Strong supporting of the different French Ministeries for a « très grande infrastructure de recherche » (very large research framework) in a next future.

Data bases « de-labelling » on standards specified by TDWG, for data inter-operability with GBIF and EDIT taxonomic platforms: a huge project in course with the digitisation of plants collection (10 M specimens !),

At the national level, technical platform for deposit and inter-operability between French partners (ie Sonnerat) and to prepare LifeWatch,

To evolve to an « e-Museum », positioned on an international context and be able to work in different ways with all the data concerning biodiversity, climate change, global warming, conservation and habitats, invasive species…

Muséum national d’Histoire naturelle

I Method and Software Development First attempt in 1994-1996 by J Lebbe and R

Vignes to create a French dynamics in the framework of « National net of Biosystematics », abandoned for the Human Genome project,

• Emergence of the LIS (Systematics and Computing Laboratory) in Paris, MNHN/UPMC and the AMAP in Montpellier (Botany and Bioinformatics of plant architecture), developing of tools for analysing/exploiting morphological data and traits and tools for identification, as already presented in this meeting,

• A recent trend consisting in modelling the dynamics of Biodiversity, from observation and specimen data in MNHN, grande génothèque.

LIS and AMAPCommon point, interest to descriptive

and morphoanatomical data, development of tools for identification,

Differences: LIS clearly transversal, non-dedicated to specific area and taxons, AMAP only on vegetals from taxonomy to ecology, great originality in modelling plant growth dynamics.

II Infrastructure and tools for end-usersFrance today is the fourth supplier in data to

GBIF ; supporting of both Ministeries and private Fondations to specimen databasing,

The INPN (National Inventory of the Natural Patrimony), managed by the MNHN, access to million data and several hundred thousands species from France and French territories, with mapping tools and distribution modelling tools. SINP will soon provide still more data, knowledge and facilities,

Data from National Botanical Conservatories,MNHN specimen database increases every

year with 200 000 new records,To more and more favourize the public access.

MNHN PolicyStandardization of data, inter operability of

databases,TDWG has been and is instrumental and so is

now EDIT, development of the EDIT common data model,

LifeWatch constitutes the next step: from a national point of view, to provide developments, today weak from our part, to the EU level, to make our infrastructural strengths available for EU.

Biodiversity Informatics in the Master MNHN/UPMC,

Lack of European and French financed calls for projects.

A few others…Marine sciences, « Marine stations » from the

UPMC and Marseille, IFREMER, IRD, MARBEF, Marine Genomics…

Paleodiversity and paleoenvironments, UPMC/MNHN, project Xper « provide a highly efficient and user-friendly environment to manage, share and collaborate in the e-taxonomy era »

Agroforestry, Cirad and Ca-SIF : a shared and standartized catalogue to provide information on forest ecosystem (French public forest research platform ECOFOR )

Two French Agencies, Agence Nationale de la Recherche,

Fondation de coopération de recherche sur la biodiversité.

European NetsGBIF, EDIT, important involvement,LifeWatch,MARBEF,Species 2000 (MNHN, Species 2000 Europa

and 4D4Life),PESI…

ConclusionsClear need for a better organization and a better visibility

of the national efforts,The landscape remains fragmented, need of a structuring

support for Biodiversity informatics, maybe to trigger in 2010, the Year for Biodiversity?

Need for amplified digitisation and inter operability,Huge databases and digitised collections are very useful to

understand the past, manage the present an try to forecast the future.

Inter-institutions cooperation, maintaining the specificities of everyone, at French and international levels.

Many thanks to my colleagues, D Barthélémy, T Bourgoin, M Thibon, S Tillier and R Vignes.