Transcript Biodiversity Informatics: key institutions, research and

© Santo, 2006
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
 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 situation
 Very 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.
Muséum national d’Histoire naturelle
 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…
 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 AMAP
 Common point, interest to descriptive and
morphoanatomical data, development of
tools for identification,
 Differences: LIS clearly transversal, nondedicated 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-users
France 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 Policy
 Standardization 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 Nets
 GBIF,
 EDIT, important involvement,
 LifeWatch,
 MARBEF,
 Species 2000 (MNHN, Species 2000 Europa and
4D4Life),
 PESI…
Conclusions
 Clear need for a better organization and a better visibility
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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.