Brazilian Cerrado ontology network and qualitative models: a case study

application of geolinked data approach to Ecology

Adriano Souza

University of Brasilia, Brazil

2013

This presentation

• Introduction

• Background and state of the art

• Research question

• Hypothesis

• The proposal

• Work in progress

• What is next…

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Ecoinformatics

“Ecologists have recognized the need for integrated data

systems to support cross-disciplinary collaboration to

understand the basic ecological principles that govern the

biosphere.”

Green et al. (2005)

A field of research and development focused on the interface

between ecology, computer science, and information technology.

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AI Technologies can be useful to theoretical development in Ecology:

• To organize knowledge bases compatible with computers,

including qualitative and quantitative knowledge;

• To perform fast assessment of assumptions, hypotheses and

other ideas in a theoretical context;

• To determine the consequences and the logical consistency of

long and complex paths of ecological reasoning.

Rykiel (1989)

Maybe the most immediate impact of AI Technologies will be on

the way ecologists organize, develop and implement models.

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Why models are necessary?

• To build and use models contribute to…

• Understand the structure of systems;

• Predict the behavior of systems;

• Control variables in order to obtain specific results.

• They are used in:

• Scientific research;

• Decision making and management;

• Education and training.

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Ecological models

To build ecological models is a complex task because...

1. Ecological models are heterogeneous, including both qualitative

and quantitative knowledge;

2.It is hard to collect data and perform experiments;

3.The available data is incomplete, inaccurate, uncertain and

many times expressed in qualitative terms;

4.The theoretical foundations and the laws (or first principles) are

still under development.

• New approaches to ecological modeling are required!

Qualitative

Reasoning6 of 41

Qualitative Reasoning (QR)

The use of QR models can contribute to clarify many aspects

and to improve the understanding of causal reasoning chains

involving environmental factors and changes in populations

and communities.

Salles & Bredeweg (2006)

It is an area of artificial intelligence that creates

representations for continuous aspects of the world to

support reasoning with little information

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Qualitative Ecological Models

Are promising because

• Allow to build and run simulations with incomplete knowledge;

• Allow to create a rich vocabulary about a variety of systems;

• Explicit representation of causality which gives support to

explanation of systems from its structure;

• Contribute to improve comprehension about complex systems

and fosters the decision making process.

Advantages over numerical models

• Inaccurate prediction, but CORRECT

• Easy exploitation of alternatives

• Automatic interpretation

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Qualitative Reasoning

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Semantic Web

Ecology

• DataOne

• OBOE

• JournalMap

• Domain Ontologys

QR

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What all savannas have in common?

“Savanna occurs over a vast range of conditions that have little in common except for their inability to support rapid tree growth.”

(Hoffman et al., 2012)

Source: Challenges and opportunities in remote sensing of global savannas. Colorado State University.Available in: http://www.nrel.colostate.edu/projects/srs/ 13 of 41

2 main reasons why do I care about Cerrado

1. Ecological Theory

• Equilibrium x Non-equilibrium

• Stability

2. Conservation Biology

Bio

dive

rsity

Hotspot

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Stable

Unstable

Climatically determined savannas

Disturbance-driven savannas

Disturbances such as fire and

herbivore, although capable to modify

tree to grass ratios, are not necessary

for coexistence

Disturbances such as fire, grazing and

browsing are required to maintaing

both trees and grasses in the system

Sankaran et al. (2005)15 of 41

About 50% of Cerrado is Deforested

Deforested

48%

Water

1%

Natural

51%

Cerrado cover type (%) IBGE (2004)

Forest

32%

Grassland

7%

Savanna

61%

Cerrado vegetation type (%) IBGE (2004)

Total Area: 2.047.146,35 Km2

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Remaining areas

Deforested area accumulated until 2008

Cerrado + Poor acid, aluminum toxicity soils + State-of-the-Art Technology + Farmers =

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Amount of soybean production (ton) in 2005 per municipality

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Aerial view Panoramic view

Phys

iog

no

mie

s Pla

nts

heig

ht

General Structure of Cerrado

OM

and

So

il Fe

rtili

ty %

Co

ver

%Cerrado vegetation characteristics

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Research question

How to use the GeoLinked data approach to

integrate datasets along with qualitative reasoning

ecological models, in order to improve the

understanding of ecological mechanisms and

facilitate access and management of environmental

information?

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Exploring hypothesis

The use of qualitative conceptual simulation

models, associated to data sources made available

by geolinked data semantic techniques, can

improve the interpretative and predictive capacity

over the data available about the dynamics of

Cerrado vegetation.

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Qualitative Model

OWL format

Data and Metadata

(RDF)

Export Recover

Recover

Ad-hoc

application

Data

repository

Qualitative

Model

Repository

GeoLinkedData

Browser

(map4RDF)

QR

Ontology

Cerrado

Ontology

Fire

Ontology

Fire and

Meteorological

Data (INPE)Vegetation

Dynamics

OBOE

Meteor.

Ontology

Data

cube

Geosparql

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Study A

Species: Ouratea hexasperma

Density: 73

Fire frequency: Fire Protected

+

geographical information

meteorological data

agriculture

Study B

Species: Ouratea hexasperma

Density: 83

Fire frequency: Low

+

geographical information

meteorological data

agriculture

Simulationowl:sameAs

owl:sameAs

owl:sameAs

GeoLinked data to retrieve appropriate models

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Methodological aspects: the Life Cycle Model

Specification

Modeling

RDF generation

Links

Generation

Publication

Exploitation

Iterative incremental life cycle 24 of 41

Specification

• Ontology Requirements Specification DocumentOntology Requirements Specification Document

1 Purpose

The purpose of the Cerrado ontology network is to represent the scientific knowledge about the ecology and dynamics of

Cerrado plants, it should express how the structure of the plant communities in Cerrado is and how they change over time.

2 Scope

Because of the complexity and extend of the domain, the scope of the ontologies will focus to cover the following subdomains:

plant community dynamics and fire.

3 Implementation Language

The Ontologies will be developed using the Web Ontology Language OWL, once it is part of the W3C recommendation for the

Semantic Web.

4 Intended End-Users

1. Researchers and scientists seeking to understand the functioning of savannah plant community.

2. Environment managers of conservation units and those responsible for making the public policies for environment and

biodiversity conservation.

3. Ecological and environmental information and data about Brazilian Cerrado users.

5 Intended Uses

1. To store data and provide information about diversity, composition and dynamics of Cerrado wood plants.

2. To propose a standard and management practice of the data available about the Cerrado vegetation.

3. To propose a service in which the user can search for species, its location and assess the changes in populations over time.

6 Ontology Requirements

a. Non-Functional Requirements

NFR1: The ontology network must give support to a multilingual scenario for Portuguese and English.

b. Functional Requirements: Groups of Competency Questions

For the functional requirements it was used the competency questions technique (Gruninger and Fox, 1994) recommended by

NeOn methodology.

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Specification

• Competency Questions

# Competency Questions for CCOn

1 What is a biome?

2 What is a savanna?

3 What characterizes a savanna?

4 What are the determining factors of savannas?

5 What is Cerrado?

6 What characterizes the Cerrado?

7 What is a population?

8 What is population growth?

9 Which processes determine the size of a population?

10 What is mortality?

11 What is natality?

12 What is an ecological community?

13 What are the types of ecological communities?

14 What is biodiversity?

15 What is the species richness of a community?

16 What factors determine the species richness of a community?

17 What is a plant community?

18 What are the types of plant communities?

19 What are wood plants?

20 What are herbaceous plants?

21What are the main measurements of biological diversity of a community or ecosystem?

# Competency Questions for Fire Ontology

65 Where does occur the wildfires in Cerrado?

66 How often Cerrado vegetation burns?

67 In what period of the year does wildfires occur in Cerrado?

68 What is wildfire?

69 Where are located the places with similar temperature range?

70Where are located the places with maximum temperature in a certain time?

71 What are the types of wildfires?

72 What is the severity of each burn event in Cerrado?

73 What is the temperature of a location in a given time?

74 What is the relative humidity of a location in a given time?

75 What causes a burn event?

76 What are the effects of a burn event?

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Modeling: ontologies reused

Reusability Usability

Extensible Observational Ontology(OBOE)

Environmental Ontology(EnvO)

FireOntology

Simple Knowledge OrganizationSystem (SKOS)

Crop-Wild Relations FAO (CWR)

EnvironmentalOntology (EnvO)

CCOn

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Reused x New Terms

Table 2. Reused Classes

Property Origen Reused in

exactMatch SKOS CCOn

mappingRelation SKOS CCOn

Table 3. Reused Properties

ResourceNumber of terms

CCOn Fire Ontology

OBOE 0 2

ENVo 3 1

CWR 24 0

Ontology N of classes N of properties N of individuals

CCOn 58 21 137

Fire Ontology 49 17 9

Total 107 38 146

Table 4. New terms

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CCOn

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CCOn

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Fire Ontology

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Fire Ontology

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LocationJatobá BiologicalReserve, Bahia,

Brazil

First inventory 1991

Last inventory 2004

Fire Protected

Mortality rate 1.93

Recruitmentrate 3.72

Study areaGerais de Balsas Colonization

Project, Maranhão, Brazil

Fragment 1 2

First inventory 1995 1995

Last inventory 2002 2002

Fire Biennial Biennial

Mean AnnualMortality rate 2.73 4.88

Mean AnnualRecruitment rate 3.25 5.86

Dataset A

Measurement

Observation

Community dynamicsRecruitment rate

has-measurement

Of-Characteristic

Cerrado sensu stricto

Wood plantTree

ofEntity

Is part of

Observation

has-measurement

Fire Characteristic

Fire frequencyOf-Characteristic

Measurement

ofEntity Fire

affects

Domain specific ontologiesOBOE

Is-a

Is characterized by

Is a

Is-a

hasCharacteristic

Dataset B

Use case example

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Ontology Evaluation

• Consistency:• Pellet reasoner

• Pitfalls (OntolOgical Pitfalls Scanner - OOPS)

• Conceptual Evaluation (experts)

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Ontology evaluation: Pitfalls

Version P02 P04 P05 P07 P08 P10 P11 P13 P22 P29 P38 Total

0.3 2 11 0 0 54 ONT 7 7 ONT 0 - 81

0.4 0 1 1 0 49 ONT 0 4 ONT 2 - 57

0.5 0 1 0 0 53 0 0 2 ONT 0 - 56

0.6 0 0 0 0 51 0 0 0 ONT 0 - 51

0.7 0 0 0 1 24 0 5 0 0 0 ONT 30

0.8 0 0 0 1 24 0 0 0 0 0 ONT 25

Table 3. Ontology Pitfalls found in Fire Ontology

Version P04 P05 P08 P11 P13 P22 P31 P35 P38 Total

0.8.1 2 0 83 8 8 ONT - - - 101

0.8.2 1 1 83 6 8 ONT - - - 99

0.9.0 0 0 88 2 0 ONT - - - 90

0.9.1 0 0 24 2 0 ONT 1 1 ONT 28

0.9.2 0 0 24 0 0 ONT 1 1 ONT 26

Table 4. Ontology Pitfalls found in Ccon Ontology

0

10

20

30

40

50

60

70

0

10

20

30

40

50

60

70

80

90

100

0.3 0.4 0.5 0.6 0.7 0.8

Critical

Important

Minor

Usability-profiling

Structural

Functional

0

20

40

60

80

100

0

20

40

60

80

100

0.8.1 0.8.2 0.9.0 0.9.1 0.9.2

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Expert Evaluation

• 2 Questionnaires were elaborated (G forms)• Quality

• Completeness

• Correctness

• Likert scale and Open Questions

CCOn

Questionnaire

Fire Ontology

Questionnaire

Evaluation

Support

material

Questionnairies

Competency

questions

Bioportal

visualization

On line

documentation

Expert Answers

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What is next

RDF generation

Links Generation

Publication

Exploitation

geometry2RDF

Google Refine

owl:sameAs

SILK

Map4RDF

Virtuoso, Pubby

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Data Sources for RDF generation

Data sources for vegetation dynamics on scientific literature:

• Souza, A. (2010). Estrutura e Dinâmica da Vegetação Lenhosa de Cerrado sensu stricto no período de 19 anos, na Reserva Ecológica do

IBGE , Distrito Federal , Brasil. 68p. Dissertação de mestrado. Departamento de Ecologia. Universidade de Brasília.

• Roitman, I.; Felfili, J.M.; Rezende, A.V. (2008). Tree dynamics of a fire-protected cerrado sensu stricto surrounded by forest plantations,

over a 13-years period (1991-2004) in Bahia, Brazil. Plant Ecology. 197: 255-267.

• Moreira, A.G. (1992). Fire protection and vegetation dynamics in the Brazilian Cerrado. Ph.D. thesis, Harvard University, Cambridge, MA,

U.S.A.

• Aquino, F. D. G., Walter, B. M. T., & Ribeiro, J. F. (2007). Woody community dynamics in two fragments of “cerrado” stricto sensu over a

seven-year period (1995-2002), MA, Brazil. Revista Brasileira de Botânica, 30(1), 113–121.

• Libano, A. M., & Felfili, J. M. (2006). Mudanças temporais na composição florística e na diversidade de um cerrado sensu stricto do Brasil

Central em um período de 18 anos (1985-2003). Acta Botanica Brasilica, 20(4), 927–936.

Meteorological

Data Source

Fire

Occurrence

and risk

Maps and

environmental

dataMMA

IBGE LAPIG

CSR

IBAMAINMET

INPE

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Outlook

• This work presents a plan for a pilot study to be a test.

• It involves linked geographical, meteorological, ecological and

environmental open data provided by Brazilian government

agencies.

• A methodology based in a Geolinked data approach is adopted

to create a case study aiming investigate the application of

linked data principles to ecology.

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Outlook

• A relevant question to be investigated in this preliminary pilot

study is how to integrate qualitative reasoning models along

with maps and other data, be able to reason with the data and

make inferences and finally to show the results.

• The topics addressed in this work have potential to boost both

applications of geolinked data technologies to new areas, and

to open new perspectives for research involving ecological data

management, integration and use.

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Thank you!

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