Bioinformatics:Intelligence for

Biodiversity Policies and Decision Making

CONABIOThe Mexican National

Commission for the Knowledge and Use of Biodiversity

• Is an inter-ministerial commission, created in 1992. Its main objective is to promote and coordinate actions oriented to the knowledge and sustainable use of Mexico’s biological richness; specially those conducted to obtain, organize, analyze and spread information about this richness (National Biodiversity Information System, SNIB).

• Composed by the following Ministries: Environment, Agriculture, Health, Social Development, Education, Tourism, Economy, Energy, Foreign Service and Treasury.

• Presided ex officio by the President of Mexico; its Technical Secretary is the Minister of the Environment.

What is CONABIO?

 

Mission 

To promote, coordinate, support and carry out activities aimed at improving our understanding of biological diversity, as well as at its conservation and sustainable use for the benefit of society.

VisionIn Conabio, our goal is to become an organization that:

• Contributes significantly to decision making and to the establishment of policies regarding the conservation and sustainable use of biodiversity, providing data, information and knowledge obtained through the support of its generation and integration.• Is a leader and innovator in biodiversity informatics, efficient processes and maintains high quality products and services.• Is a mandatory point of reference for biodiversity issues in Mexico.

Biodiversity data is essential for a variety of “decision makers”

• Government officers at federal, state and municipal levels.

• Scientists, experts, consultants.

• Farmers, foresters, peasant and indigenous communities.

• NGOs and the general public.

THEIR NEEDS ARE HIGHLY VARIED AND ALSO THEIR QUESTIONS

To answer questions from those users

• We need precise and detailed information at diverse time and space scales, from the local to the global and from day-to-day to long term information.

• Such data is available only for very few species, communities or ecosystems, or at very broad scales.

Many relevant problems require answers to “whereabouts” questions

• “Whereabouts” questions refer to the presence of entities in places:– Which species are to be found in a given place.– Where can I find a given species.

• Despite their apparent simplicity, these questions are often fundamental and very relevant in both applied and basic science.

Whereabouts questions can be answered using the data in scientific collections

Georeference Taxoreference

• Specimens provide connections to geographically structured information and indexed information to the Latin binomial.

• The world’s scientific collections have about 3 billion specimens. Only 2-3% are electronically accessible !!

How is a Biodiversity Information System constructed?

* Specimen databases* Catalogues and authority files* Species databases* Remote sensing capabilities and electronic

cartography* Statistical and analytical tools* Expert networks, ………….

The datalayer

The informationlayer

The knowledgelayer

Specimen dataAuthority files

Geospatial dataSpecies attributes data

Updating

MetadataStatistical tools

Extrapolation toolsVisualizationOrganization

Web-based applications

ConservationInvasive speciesBioprospecting

BiosafetyRestoration

DBMGIS

TCP/IPXML

Accumulation curvesBioclimatic modelsComplementarity

Hot-spot detection

Specimen databases

• Data is obtained either doing field work or computerizing existing collections

• Requires complex processes to maintain data quality

• Keeping the data updated is a major problem

Price per georeferenced specimen: about 3 US dlls.

Localities of plant specimens in different herbaria

TEX (University of Texas, Austin) UADY (Universidad de Yucatán)

ARIZ (University of Arizona) CIIDIR (Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional de Durango)

XAL (Instituto de Ecología de Xalapa) CAS (California Academy of Sciences)

MEXU (Universidad Nacional Autónomade México)

CICY (Centro de Investigaciones Científicas de Yucatán)

Localities of plant specimens in different herbaria

The Virtual Herbarium of Mexico1,008,000 registers from 79 Herbaria, mainly in Mexico and the United States, plus other 25 countries

All data together...

Data repatriation program of Mexican specimens in foreign collections

Total of specimens = 353,373Consistency = 92.3% Source: 25 SNIB data bases

Mexico13%

Europe2%

Canada3%

ND 18%

USA64%

National museums (14)Foreign museums (40)

Repatriation of data on Mexican birds

Quality control of biotic inventories

Objectives of quality control of taxonomic-biogeographical information:

• To establish a protocol to asset the biological information consistency.

• To establish a method for quality control in databases using automatic or semi-automatic routines of data verification.

• To develop tools to analyze databases and to identify errors and inconsistencies in its data.

.

Data bases quality control

Omission. Absence of information

Capture. Type mistakesCorrect name spelling: Correct name spelling: Megalomma bioculatumMegalomma bioculatum

Género  Especie  No. de registros 

Megaloma  boiculatum  12 Megaloma  Sp. A 8

Descripcion Género Especie NoRegistros

Características de Peces Muhlenbergia diversiglumis 168

Plant specimen associated to fishes catalog

Out of context data entry in taxon name

Data contextual errors

Redundancy

IdNombreLocalidad Nombre

707 Cascada Misolha, 20 km S Palenque, Tenejapa km 95

5833 Cascada Misol-Há, Chis.

2524 Mesa de la Avena, 15 mi SW de Colonia Juárez

2525 Mesa de la Avina, 15 mi SW Col Juárez

2608 Mimbres, 2.4 km W, 50 km Ciudad de Durango-Mazatlán

6318 Mimbres, 2.4 km W, Carretera Durango-Mazatlán, 50 km

Georreferenciación-Catálogo de localidades

Same locality, different ways of writing it

Conventional

Convention in Collect number field for no data available is: 9999, ND or NA.

Convention to this data field is: high, rare, scarce.

HomogenizeSpecies described by the same author but typed with different spelling

Incorrect information (inconsistencies)

Taxon names in more than one higher taxonomic category. Example: Genus Fosterella in Bromeliaceae and Haemodoraceae families

Catalogues and authority files

• Files that document correct nomenclature and hierarchy, according to some accepted author.

• They are INDISPENSABLE, but:– Expensive– Difficult to obtain and update.

• ITIS, Species 2000, local files or regional.• CONABIO has 66 catalogues, for about 70,000

names.

Growth of the databases

0100200300400500600700800

0

1,000,000

2,000,000

3,000,000

4,000,000

5,000,000

6,000,000bases de datos taxonómicasbiogeográficas bases de datos ecológico-genéticasfichas de especies

Registros curatorialesgeorreferidos

The Biodiversity World Information Network (REMIB): Worldwide users

It is conformed by 32 nodes in six different countries: Mexico, Costa Rica, Spain, Peru, the UK and the US. It links 121 collections and more than 6.4 million data from 170 countries.

REMIB’s engine

CONABIO developed a software to access distributed taxonomic databases called Mallos©

and gregalis© after the species Mallos gregalis, a social spider endemic to México.This species occurs in mountainous areas of central Mexico and its nests, which are occupied and enlarged by successive generations may reach several square meters and contain up to 20,000 spiders.

The Mallos© gregalis©

• Mallos© is the engine of the gateway of REMIB, it allows WWW users to obtain biodiversity data directly from the databases of the collections owned or under control of its nodes, by contacting gregalis©, which controls the query and sends back the data.

• Technology is based on the use of TCP/IP sockets constructing “pipe-lined” processing, where processing of received chunks can begin before the complete data has arrived.

Mallos©

• The information query parameters travel encrypted; the query is sent through the net.

• The nodes receive the query (which is interpreted considering the model and DBMS of the resident database) and send back the answer in an unformatted data.

gregalis©

• gregalis© uses a database independent interface – DBI which is a database access module. It defines a set of methods, variables and conventions that provide a consistent database interface independent of the actual database being used.

• In simple language, the DBI interface allows users to access multiple databases types transparently. So, if you are connecting to an Access, Oracle, Informix, mSQL, Sybase or whatever database, you don´t need to know the underlying mechanics of the 3GL layer.

Species databases• Documented information about:

– Morphology– Ecology– Legal status– Images– Literature

• CONABIO has databases about reforestation, invasive species, CITES-listed and endangered species. We are starting a transgenics database.

Biotica®, a data manager developed by CONABIO

SNIB uses specially developed software

..

Remote sensing capabilities and electronic cartography

• National cartography at scales of 1:4,000,000, 1:1,000,000 y 1:250,000; Local a 1:50,000. Extreme and average temperatures, rainfall, radiation, soil, vegetation, biogeography and elevation.

• National territory images: Landsat MSS, TM y ETM for 1973, 1993 and 2000. AVHRR and MODIS daily.

Satellite images available in CONABIO

Landsat MSS, TM y ETM 925Spot 903DMSP-OLS 350AVHRR 12,777MODIS 6,512

TOTAL 21,467

Images reception systems for satellites NOAA (AVHRR) and Terra & Aqua (MODIS)

Detection of forest fires through satellite imagery

CONABIO detects daily through remote sensing technology, those hot spots in the country where there is a very high probability of wildfires.

This information is available to the public daily in Internet through CONABIO’s web page. Additionally, CONABIO sends the information electronically to authorities in charge of combating forest fires, so they carry out the needed actions.

Goal: Contribute to the early forest fires detection

1998

Post fire session assessment with DMSP (military) satellite images

1999

The program begun with AVHRR and daily publishing on the WEB

2000

Automatization (programs)

20052001 2003 ...2002

Two types of satellite images AVHRR and MODIS

Reduce the response time (2 hrs)

Program calibration

Index of propagation risk

Daily information

Hot spotsDaily image

MDT and vegetation Dynamic maps

Metadata

Images

On-line cartography

CONABIO has 279 maps available through www.conabio.gob.mx, users can unload 132 of them.

Statistical and analytical tools

Since specimen data is geographically highly biased, one needs tools to:

– Assess completeness and bias of the data.– Extrapolate to obtain probabilistic

distributions, richness estimates, etc.  

#S

#S

#S#S#S#S

#S#S#S#S

#S

#S

#S

#S

#S#S#S#S#S#S

#S#S#S

#S#S

#S#S#S

#S

#S#S#S

#S#S#S#S

#S

#S

#S#S#S#S

#S

#S

#S

#S

#S#S

#S

#S#S

#S

#S

#S

#S#S

#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S#S

#S#S#S#S#S#S#S

#S

#S#S

#S#S#S#S#S

#S

#S#S#S#S#S

#S

#S

#S

#S

#S#S#S#S#S#S#S#S#S#S#S#S

#S#S#S#S#S#S#S#S#S #S

#S#S

#S #S

#S#S#S#S#S

#S

#S

#S

#S#S

#S

#S#S #S

#S#S #S#S #S#S #S#S#S#S#S

Use of analytical tools

•Domain

•GARP

•FloraMap

•Bayesian Tools

•Bioclim

A completeness index of the recollect effort

• The incident-based coverage estimator (ICE) (Colwell –

http://viceroy.eeb.uconn.edu/Estimates), can be used as the

asymptote• Calculate a C index to

measure the biological inventory completeness

j

ice

iceiceice

notfrfreqice

Qlasdeiacionvar

deeCoeficient

CQ

C

SSS

2

21

10 iceS

ObservadasEspeciesC

museos nacionalesmuseos extranjeros

Mexican birds data

Completeness index of the recollect effort (observed/predicted) C = 0.98

Rectangles of 1.9x106 km2

Yellows C < 0.6Pale oranges 0.61 < C < 0.8Dark oranges 0.81 < C < 1

Rectangles of 4.8x105 km2

Rectangles of 4.8 x 104 km2

Rectangles of 1.2 x 105 km2

White C < 0.3Yellows 0.31 < C < 0.6Pale oranges 0.61 < C < 0.8Dark oranges 0.81 < C < 1

Rectangles of 7.5 x 103 km2

Rectangles of 1.8 x 103 km2

White C < 0.3Yellows 0.31 < C < 0.6Pale oranges 0.61 < C < 0.8Dark oranges 0.81 < C < 1

Rectangles of 4.5 x 102 km2

White C < 0.3Yellows 0.31 < C < 0.6Pale oranges 0.61 < C < 0.8Dark oranges 0.81 < C < 1

Expert networks

• Help of experts is required to obtain, update and interpret the data. Often, the experts are from abroad.

• The experts networks are an essential component of the SNIB.

...

CONABIO’s services and products for environmental decision making

Invasive species

Cactoblastis cactorum

Climate surface obtained byFloramap (12 layers)

Platyopuntia localities MNHSD, IBUNAM, ENCB, MOBOT, NMNH, UAH

North American Platyopuntia richness Obtained by “adding” 96 GARPS

Red isolines: High similarity to climate in the original cactoblastis cactorum sites.

Blue regions: Richness of species of Platyopuntia.

Vulnerable areas to Cactoblastis according to statistical and analytical tools

Detection & evaluation of public health problems

Low probability Med. probability

High probability

Peromyscus maniculatus

The case of Hantavirus

#S#S#S#S #S#S #S#S #S#S

#S#S #S#S #S#S #S#S#S #S#S#S

#S #S#S#S#S#S #S#S #S#S#S#S #S#S #S#S#S

#S#S #S#S#S #S#S#S#S #S #S#S#S#S#S #S#S#S#S#S#S#S #S#S#S #S#S #S#S #S#S#S#S#S#S#S#S#S#S#S#S#S#S #S#S#S#S

#S#S

Risk-assessment of introductions of transgenic crops to their wild relatives

Cd. Obregón

Tecomán, Col.

Comarca Lagunera

Planicie Huasteca

Gossypium barbadense

Which is the potential area of distribution of a species?

Rhynchopsittapachyrrincha

Species predicted distribution from museum specimen data

Montes Azules

Calakmul

Laguna de Términos

Pantanos de Centla

GUATEMALA

MEXICO

Wildfires, March 18th, 2003

Early detection of forest fires program through satellite imagery

Provides an important tool for environmental decision making in issues related to management, protection and conservation.

Regional prioritizations

Provides detailed information about listed species in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), to facilitate the identification of these species to customs authorities, as well as technical personnel and society.

CITESIdentification Guide

How much does society use CONABIO’s data?

Monthly visits to CONABIO’s web site

Currently CONABIO’s web site receives an average of 30,000 hits per day

0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

Monthly records provided to users through Remib

Log

Scal

e

1,000.00

10,000.00

100,000.00

1,000,000.00

10,000,000.00

CONABIO: a successful story

Fulvio Eccardi

“...Mexico's National Commission for the Knowledge and Use of Biodiversity provides a shining example of what can be achieved.... it

has built what many Western scientists acknowledge is one of the most powerful

biodiversity management systems around.”

Nature, 1998

“… the good news is that CONABIO’s concept is now, in effect, being replicated worldwide through the Global Biodiversity Information Facility (GBIF)…”

BioScience, 2004

“...those countries better positioned in bioinformatics will have a strategic scientific and commercial advantage…”

R. M. May. Chief Science Advisor to the British Government

CONABIO is considered among the three best institutions of its kind. It has, nevertheless much more to do in the future, among these:

• Development of basic bioinformatics• Development of bioinformatic products, oriented to specific users• Support to applied research• Support to a greater number of users