cyberinfrastructure and earthscope science goals: a geon perspective what is cyberinfrastructure?...

Cyberinfrastructure and EarthScope Science goals: A GEON perspective

What is Cyberinfrastructure?What is GEON?How will GEON research facilitate discovery and integration of earth science data?What are the benefits of such a research initiative for EarthScope?How can earth scientists participate in Cyberinfrastructure research opportunities?

CYBERINFRASTRUCTURE FOR THE GEOSCIENCES A.K.Sinha, Virginia Tech, 2005

Cyberinfrastructure

National Science Foundation’s Cyberinfrastructure

• Cyberinfrastructure is the organized aggregate of technologies enabling access and coordination of information technology resources to facilitate science, engineering, and societal goals.

– Data access from distributed systems

– Data inter-operability– Computation: grid based and workflows– Visualization– Tools

– Integration: highlighted today

NSF Blue Ribbon Panel (Atkins) Report provided a compelling and comprehensive vision of an integrated Cyberinfrastructure

Modified from Berman, SDSC, 2005


A KEY OBSERVATION IN SUPPORT OF CYBERINFRASTRUCTURE RESEARCH IN GEOSCIENCES

“Large team** efforts are required to build a federation of data and tools; but smaller groups or individuals working independently and given access to these data and tools can (and likely will) make fundamental discoveries”

MODIFIED FROM BLUE RIBBON ADVISORY PANEL ON CYBERINFRUSTRUCTURE REPORT, NSF

** such as GEON and other projects


Towards an Integrated

Earth Science data and

knowledge base to achieve

EarthScope Science and education

goals

Science InvestigatorsEducators and the Public

USArray PBO SAFOD

InSAR

EarthScope Instrumentation and Data

Cyberinfrastructure Resources

Plus semantic integration of other earth science data


Adapted from D.Seber,SDSC


Three dimensional view of the lithosphere-asthenosphere boundary and surface topography of the northern Appalachians. Base of lithosphere interpolated from migrated Ps waveform images at 6 labeled stations. (From Rychert et al. 2005)

New knowledge about evolution of continents requires complex integration of geophysical data with those associated with sub-crustal lithosphere ages, its composition and physical properties (seismic, thermal etc), surface geology and associated events chronology



What is the geologic and geophysical

record of Super-Continent

assembly and dispersal?

EarthScope Science Targets: Examples from eastern North America

• What is the geologic and geophysical record of Super-Continent assembly and dispersal?

• What are the architectures of terrane boundaries at depth? • How do composition, temperature and strain fabrics vary within the

lithosphere and asthenosphere? Are lithospheric and asthenospheric strain coupled?

• How sharp is the lithosphere-asthenosphere boundary? What defines it?

DATA NEEDED TO ADDRESS THESE QUESTIONS ARE DISTRIBUTED ACROSS THE COUNTRY, IN DIFFERENT FORMATS AND CANNOT BE INTEGRATED IN A WEB ENVIRONMENT WITH

EXISTING TECHNOLOGIES

—overcoming heterogeneity is a priority cyberinfrastructure challenge


Outline

• Data integration problem and solutions• GEON data integration solution: ontology

enabled semantic mediation• What is ontology• Registering data to ontologies• Discovering data and using workflows in a web

environment to go from queries to questions


• Platform heterogeneity: different OS platforms• DBMS heterogeneity: different database systems, e.g.

SQLServer, mySQL, DB2• Data type heterogeneity• Schema heterogeneity• Heterogeneity in units, accuracy, resolution• Semantic heterogeneity

( modified from Baru, SDSC, 2005)


GEON Architecture addresses problems of :1. Variety of data sources and types2. Discovery and relevance3. Addressing needs of different communities

What is GEON ? How can GEON help integrate heterogeneous and distributed

data?


GEON: The Geosciences Networkwww.geongrid.org

GEON is a NSF funded collaborative research between IT and Earth Science researchers with the goal of developing cyberinfrastructure to enable new integrative modes of geosciences research GEON is developing a pioneering system to use knowledge-based techniques to discover, query, and integrate data in the Geosciences Project participants include 14 PI institutions, as well as partners from other projects, agencies, and industry. GEON has deployed a Web services-based, distributed computing infrastructure, called the GEONgrid, across the PI and partner sites. GEONgrid provides access to distributed data collections, tools, and applications

Research and Education Products and Results: Technologies for “Smart Search”, On-the-fly Data Integration, GIS Map Integration, Distributed Portals, and 4D Visualization Earth Science Research within GEON on

3D Lithospheric Structure Integrated Geoscience Modeling Geologic Evolution of North America Ontologic Framework for the Geo-sphere

Cyberinfrastructure Summer Institute for Geoscientists and Graduate Courses in Geoinformatics


GEON and Cyberinfrastructure

• Develop cyberinfrastructure that enables interlinking and sharing multidisciplinary Earth Science data resources, software and tools

• Create a scientist-friendly portal to access data, software for analysis , modeling, and visualization

• Create the GEONgrid to enable seamless data integration and analysis environment


Physical model

Model results

HPCC

Data

Modeling Environment

GEON: GEOsciences Network

Core Grid ServicesGT3, OGSA-DAI, GSI, CAS, gridFTP, SRB, PostGIS, mySQL, DB2

Portal (login, myGEON)

Physical GridRedHat Linux, ROCKS, Internet, I2, OptIPuter (planned)

Registration Services

Data Integration Services

Indexing Services

Workflow Services

Visualization& Mapping Services

Registration GEONsearch GEONworkbench


Discovering, sharing and using data in a web environment: GEON style

• Discovery of data resources (e.g., gravity, geologic maps, etc) requires registration through use of high level index terms

• GEON has deployed extension of AGI Index terms-will be cross indexed to others such as GCMD, AGU

• Discovering Item level content of databases requires registration through data level ontologies (e.g. column in geochemical database that represents SiO2 measurement) and is a requirement for semantic integration

• Item detail level registration through ontologies reduces schema based data heterogeneities

• Computation and modeling tools can be registered for use by community

• Visualization capabilities• Easy access to data through

GEON Portal• Individual workbench built into

GEON Portal• Scientific Workflow Systems

provide computational and query capabilities in a web environment


Index terms from AGI used for identifying type of data

AGI Index Terms

GEON Index Ontology


Integration: a buzz word but with complex solutions

• What is Integration? – Relationships in information contained in

heterogeneous and multi-disciplinary databases

What are our choices?– Layering of data (commonly used)– View based techniques (create a virtual schema)– Schema based integration (merging of schema, but

user must be knowledgeable about the organization, e.g. semantics of schema)

– Ontology based semantic integration utilizing workflows….favored by GEON

Data Registration is Important for integration!


What is Ontology? Why use Ontology?What is Ontology? Why use Ontology?

• Ontology : An explicit formal specifications of the terms in the domain (e.g. Geology) and relations among them (Gruber 1993)

• Why use ontology To share and reuse of domain knowledge To make explicit domain assumptions To separate domain knowledge from the operational knowledge To analyze domain knowledge

• Ontology Languages: RDF and RDFS OIL DAMP+OIL OWL: Ontology Web Language fromW3C


Motivations for Using Ontologies in GEON

• A better way to discover and understand datasets Use the knowledge in ontologies to find datasets

• A better way to query datasets Query through ontologies without knowing the details of the schemas

• A better way to integrate multiple datasets Integrate multiple datasets on-the-fly if they are registered to ontologies

• A Better way to segment large data basesTransfer only parts of data bases required for integration

Modified From Kai Lin, SDSC, 2005


An emerging research frontier- Geo-Ontology

Class Diagrams - The Basic Building Block for Semantic Integration

Earth Scientists create disciplinary ontologies!!!

Earth Science research : stages in developing ontologies


GEON Planetary Structure conceptsNapkin Stage

Concept Map StageHigh Level Ontology: integrated GEON,

SWEET and NADM stage

GEON formal ontology

High Level Ontology Packages : representing relationships

Planetary Material

Phy sicalProperty Planetary Structure

Imports Phy sical Property Ontology

Imports Units Ontology

Imports Time Ontology

Imports Numerics Ontology

ImportsSpace Ontology

Location


Planetary Material

ElementalConcentration

element : Elementconcentration : ValueWithUniterrorOfConcentration : ValueWithUnit

Gas

Rock = Petrology

Fluid

Need to add ...

Solid

NaturalMineral

name : Stringsize : ValueWithUnithas_cleavage : Booleanis_fractured : Booleanis_oriented : Booleanis_twinned : Booleanis_altered : Booleanis_primary : Booleanis_secondary : Booleanis_accessory : Booleanis_heavy_mineral : Booleanis_reworked : Booleanis_zoned : Booleancolor : Stringdensity : ValueWithUnitage : Stringcrystalline : Booleanamorphous : Booleanstriations : Booleanhardness : DoubleindexOfFraction : Doublefusibility : ValueWithUnitthermalConductivity : ValueWithUnitexpansion : ValueWithUnitspecificHeat : ValueWithUnitelectricalConductivity : ValueWithUnittaste : Stringodor : Stringluster : String

(from Mine...

Rock

color_index : Stringis_monomineralic : Booleanis_polymetamorphic : Booleanis_polydeformed : Boolean

(from R...

0..n

1

0..n

1

For registration of Physical Property data: The user needs to first select a Mineral or Rock Sample then select the attribute from the physical property list under StateOfMatter

Liquid

Water

pHeH

Additional properties to be added

ChemicalCompound

StateOfMatter

density : ValueWithUnitresistivity : ValueWithUnitanisotropy : ValueWithUnitseismic_velocity : ValueWithUnitcompressive_strength : ValueWithUnitmagnetic_susceptibility : ValueWithUnitthermal_conductivity : ValueWithUnitother_physical_property : ValueWithUnitTemperature : ValueWithUnitPressure : ValueWithUnitthermalCoefficientofExpansion : ValueWithUnit

Micronex Classific...

NormativeMineral

name : Stringsymbol : Stringfomula : StringgramEquivilentWeight : Double

Need a Kepler workflow to work in the background: Normative Vs. Modal

PlanetaryMaterial

Element

name : StringatomicWeight : ValueWithUnitsymbol : StringatomicNumber : Integercolor : StringatomicRadius : ValueWithUnitmeltingPoint : ValueWithUnitboilingPoint : ValueWithUnitdensity : ValueWithUnitspecificHeat : ValueWithUnitionizationPotential : ValueWithUnitelectronAffinity : ValueWithUnitheatOfFusion : ValueWithUnitheatOfVaporization : ValueWithUnitbondingRadius : ValueWithUnitelectronNegativity : Double

(from Elem...

1..n

1

1..n

1

AnalyticalOxide

1..n

1

1..n

1

RockSample

ssID : StringfieldID : Stringage : StringdateOfCollection : StringimageanalyticMethod : String

(from R...

IsotopeAbundance

isotope : Isotopeabundance : ValueWithUniterrorOfAbundance : ValueWithUnit

1..n

1

1..n

1

IsotopeRatio

value : Doubleis_radiogenic : Booleanis_common : Booleanis_stable : Booleanerror : ValueWithUnit

(from Elem...1..n

1

1..n

1

1..n

1

1..n

1

AnalyticalOxideConcentration

analyticalOxide : AnalyticalOxideconcentration : ValueWithUniterrorOfConcentration : ValueWithUnit

1..n

1

1..n

1

1..n

1

1..n

1

NormativeMineralAbundance

normativeMineral : NormativeMineralabundance : ValueWithUnit

1..n

1

1..n

1

MineralSample

minID : Stringimage

(from Mine...

1..n

1

1..n

1

1..n

1

1..n

1

1..n

1

1..n

1

1..n

1

1..n

1 1..n

1

1..n

1

Minerals

Instance of Normative Minerals : Basic Analyti...

Minerals

Rocks

State of Matter

Element

Data Types


GEON Cyberinfrastructure …

More than just about the data, GEON is about going from simple Queries to complex Questions


A Home Buyer’s Information Integration Problem

What houses for sale under $500k have at least 2 bathrooms, 2 bedrooms, a nearby school ranking in the upper third, in a neighborhood

with below-average crime rate and diverse population?

??Information Information IntegrationIntegration

RealtorRealtor DemographicsDemographicsSchool RankingsSchool RankingsCrime StatsCrime Stats

““Multiple-Worlds”Multiple-Worlds”MediationMediation

Bertram Ludäscher, SDSCBertram Ludäscher, SDSC


http://www.epa.gov/opptintr/kids/hometour/images/house.jpg

http://www.ftb.ca.gov/education/images/schools.jpg

A query example: Use SQL to ask a database to show you all white wines from California of 2003 vintage….

A question: "Tell me what wines I should buy to serve with each course of the following menu. And, by the way, I don't like Sauternes." … from W3C

This requires two databases (e.g. food and wine) and prescribed relationships between them that are defined for computers as Ontologies

Bertram Ludäscher, SDSCBertram Ludäscher, SDSC


The Problem: Scientific Data Integration

or: … from Queries to Questions


Data Registration: key to integrationClick on Submissionto register a dataset Input a data set name

Select a zippedshapefile

Choose an ontology class


SiO2 is an instance of class AnalyticalOxideConcentration and has all

information about the element Si

Planetary Material Ontology

Registration at the item detail level using data ontology: working with data


GEONsearch:building on data registration

Choose subject (from a “base” ontology)

Choose location (from a gazetteer Webservice)

Choose a time (numeric range or from a time ontology Webservice)

Choose concepts from ontologies Kai Lin, SDSC, 2005


Ontology Enabled Map Integration :A Case Study

• Geologic Data sets Arizona, Idaho, Montana, Utah, Nevada, Colorado, Wyoming, New Mexico

• Ontologies Geologic Time Scale Multihierarchial Rock Classification from Canada Geologic Survey British Rock Classification Scheme

Snapshot after querying “Paleozoic”CYBERINFRASTRUCTURE FOR THE GEOSCIENCES A.K.Sinha, Virginia Tech, 2005

Scientific Workflow Systems in GEON

• Adding computational capability in a web environment

– Promote “scientific discovery” by providing tools and methods to generate scientific workflows

– Support computational infrastructure for modeling,classification,computation

– Design frameworks which define efficient ways to connect to the existing data and integrate heterogeneous data from multiple resources


PointInPolygoPointInPolygonn

algorithmalgorithm

Find data on the basis of ontologic

registration

Workflow layout for rock

classification, but can be used for any query that

requires a classifier


Integration Scenario: A-type pluton query• Classifying A-types from an Igneous rock database• Integrating between Relational and Spatial (shapefiles) databases to query and interactively display GIS results


I & S type

A type

Ontology SystemOntology System• Location States Virginia•Classification System Rock Classifiers Igneous Pluton

A-type•Mineral Zircon•Geologic Time Dating Methods U-Pb Zircon Methods

Integration Scenario: Stages for access to data and tools in a workflow environment

The integration scenario: What is the distribution and U/Pb Zircon ages of A-Type Plutons in Virginia?

104 Ga/Al

Zr

1

23

3

4

5

6

6

5 6


Distribution and ages of A-Type plutons and their ages based on integration of

multiple databases

How do earth scientists participate in Cyberinfrastructure research?

• Know your data……its content and definitions

• Think more broadly…..integration is between databases that are different from yours

• Learn more about how to use IT through summer workshop at SDSC, as well as others sponsored by Societies

• Register your data using Index Terms through GEON Portal to facilitate discovery of databases; use data ontology for discovery of data

• Build and Share tools and services for use in a web environment

• Construct concept maps in your discipline….leads to formal ontologies required for semantic integration……remember Geo-Ontology

• EarthScope requires integrative capabilities


Some processes and objects typically involved in crustal melting.

“fe rtile ”c rusta l so urc e

a m phibo lite

pa rtly-m olte nc rust

m e ta -gra ywa c ke

re sid ua lso lids

m ixe dso urc e

m e lt

m e ta pe lite

c um ula tepha se s

c rusta lm e lting

und erp la ting

de hydra tio nm e lting

ra dioa c tivehe a ting

intra p la ting

wet m elting

de c om p re ssio nm e lting

melting

heating

From Cal Barnes,Texas Tech, 2005


From Objects to Processes---- just the beginning of a

new integrative world

now where?

transition

parts of

componentsproc ess

ob je c t

Two important events at GSA

DIVISION OF GEOINFORMATICS

Data to Knowledge

FIRST Business Meeting will take place during the upcoming National GSA meeting ,Salt Lake City

Tuesday,18 October, Ballroom D, 5.45-7.45pm

GEON and EarthScope Reception

Monday, 17 October,Hilton Salt Lake City Center

Alpine West Ballroom5.00-7.00pm

cyberinfrastructure and earthscope science goals: a geon perspective what is cyberinfrastructure?...

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