Building a TAPIR-Lite Toolkit for the Global Invasive Species Information Network (GISIN)

Jim Graham and Catherine Jarnevich

GISIN Applications

• GISIN is going to help:– Resource managers find information on new

or potential invaders to manage them and prevent invasions more effectively

– Data modelers provide improved predictive capability to decision makers to prioritize funding to areas where it will be the most effective

– The public understand invasive species and what they can do to minimize damage

Highlights of Survey & Interview Results

• At least 3 languages/frameworks important (php, asp, jsp)

• Data providers willing to commit from one hour to “as long as it takes”

• Minimal web service expertise

• Various installation scenarios

• DiGIR did not meet all needs– Complex queries not needed– Database performance problems

Results Since Last Year

• Initial Web Portal

• Finalized 3 data models

• PHP Toolkit Available

• ASP Toolkit in the works

• Two meetings held for data providers and standards development

GISIN Web Portal

www.niiss.org/gisin

Protocol Approach

• TAPIR-Lite– Eliminated complex queries (Key Value Pair

Only)– “Flat” data models (no complex hierarchies)

• Data Models defined for Invasive Species Research and Management

GISIN Protocol Transaction

Location

Obser. Obser.

Org2Org1Org1

SQL QuerySELECT *FROM AreasJOIN Surveys…JOIN Organisms…WHERE Genus=‘Tamarix’

Latitude Longitude Date Scientific

Name

-105 40 10/2/2007 Tamarix ramossima

-110 35 2/10/1999 Tamarix chinensis

Requesthttp://provider.org/GISIN.php?Op=Inventory&Model=Occurrences&Count=true&Genus=Tamarix&Concept=Latitude&Concept=Longitude&Concept=Date&Concept=ScientificName

Response<response> <inventory> <records> <record> <Latitude>-105</Lattiude> <Longitude>40 <Date>10/12/2000</Date> <ScientificName> Tamarix ramosissma </ScientificName> </record> … </records> </inventory></response>

Data Model Needs

• Single standardized data models

• Controlled Vocabularies

• Flat as possible

• Includes accuracy, precision, and process information

• Able to eliminate duplicate records

• Able to trace data to original source

• Citations

Controlled Vocabularies

• Example of ambiguous data:– United States, USA, United States of America,

US, Estados Unidoes, etc.

• GISIN has chosen to use Country Codes:– CA = Canada, NZ = New Zealand, etc.

• Vocabulary mapping/cross-walking allows fast, reliable searching

Data Models

• Protocol: http://www.niiss.org/cwis438/websites/GISINDirectory/tech/Protocol_Home.php

• Implemented:– SpeciesStatus: Indigenous, Harmful, etc.– Occurrences: X, Y coordinates (DarwinCore)– ResourceURLs: results return URL lists and Language.

• Defined, but to be reviewed:– ImpactStatus: harm type (enviroment, economy, health)

harm impact (strong, weak, unknown) – ManagementStatus: prevention, interception, control, etc.– DispersalStatus: cause of introduction, date, vector, etc.

GISIN Toolkit Needs to be...

• Easy to install

• As small as possible

• Available in multiple programming languages

• Customizable

• Testable with built in turn-on tests– Other tests will be available in the portal

GISIN Toolkit Characteristics

• 100% open source

• Offers standard URL web service access

• Databases supported: MySQL, PostGRES, SQL Server, MS-Access, etc.

• Easy to support and customize– 8 files– ~3,000 lines of annotated code

Easy to Install

• PHP Version Now Available for Beta Testing!– One folder installation– PHP 5 required, but no additional extensions– Web-based user interface, to map database fields to

the GISIN Data Models

• Installation requirements:– Ability to copy a folder to a directory on a web server

that is accessible from the Internet– Ability to use a web page to configure the service– Understanding of the provider’s database structure

• Toolkit is preconfigured with a sample database for quick startup and testing

Admin UI

Toolkit Design: Data Flow

Provider

Web Service

DatabaseConnection

ProviderDatabase

Metadata.xml

Capabilities.xml

GISIN

Internet

Web

Date

Utilities

Typically the only files to modify

Admin Web Site

SQLBuilder

Service

Provider.xml

Current Providers

What We Have Learned

• Harvesting is required to resolve performance problems

• Funding is being sought to manage a centralized database cache and so improve system performance

• This will allow the toolkit and protocol to be further simplified

Next Steps

• ASP Version of the Toolkit• Testing:

– More databases connected– Improved error tracking

• Portal– Initial harvest model in place– Incremental improvements

• More standards group meetings• More provider meetings

Current Web Sites

• GISIN Organization Site: www.GISINetwork.org– Meeting documents– List of online invasive species databases– Network news

• GISIN Directory: www.niiss.org/GISIN– Browse Directory– Search for data from providers: BioStatus,

Occurrences, ProfileURLs– Technical Information:

• Edit Registry• Get Toolkit• Sample Provider (based on the toolkit)• Manual exercising of TAPIR-GISIN web services• Automated tests are coming!

Acknowledgements

• Funded by NSF, NBII (USGS), GBIF, TDWG, GEO

• Thanks to: Jerry Cooper, Renato De Giovanni, Roger Hyam, Donald Hobern, Markus During, Hannu Saarenmaa, Kevin Richards, Peter Fox, Debra McGuiness, Michael Browne, Brian Steves, Pam Fuller, John Pickering, Shawn Dalton, Greg Ruiz, and other GISIN members

• Contacts: jim@nrel.colostate.edu, catherine_jarnevich@usgs.gov