Transcript Graham 18 02 GISINtoolkit

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
Request
Response
http://provider.org/GISIN.php
?Op=Inventory
&Model=Occurrences
&Count=true
&Genus=Tamarix
&Concept=Latitude
&Concept=Longitude
&Concept=Date
&Concept=ScientificName
<response>
<inventory>
<records>
<record>
<Latitude>-105</Lattiude>
<Longitude>40
<Date>10/12/2000</Date>
<ScientificName>
Tamarix ramosissma
</ScientificName>
</record>
…
</records>
</inventory>
</response>
SQL Query
SELECT *
FROM Areas
JOIN Surveys…
JOIN Organisms…
WHERE Genus=‘Tamarix’
Location
Obser.
Org1
Obser.
Org1
Org2
Latitude
Longitude
Date
Scientific
Name
-105
40
10/2/2007
Tamarix
ramossima
-110
35
2/10/1999
Tamarix
chinensis
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
Internet
Provider.xml
Web Service
Provider
Metadata.xml
Typically the only files to modify
Capabilities.xml
Service
SQLBuilder
GISIN
Database
Connection
Utilities
Web
Provider
Database
Date
Admin Web Site
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: [email protected],
[email protected]