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TRANSCRIPT
Visualization and Indexing of Ecological & Biological Data
ICSTI Workshop, MS ResearchFebruary 8, 2011
Topics for Discussion
• Organizational Background
• Biological informatics Challenges
• Example Efforts
Biological Informatics Program
• Headquartered in Reston, VA• Responsible for biological informatics activities within USGS• Major Programs include:
– National Biological Information Infrastructure (NBII)– GAP Analysis– USGS/National Park Service Vegetation Mapping
• Supported Programs– Fire Research Management & Exchange System (FRAMES )– Integrated Taxonomic Information System (ITIS)– Inter-American Biodiversity Information Network (IABIN)– Global Biodiversity Information Facility (GBIF)– National Science Foundation (NSF) DataONE
• ~60 staff in multiple locations throughout the US
What is Informatics?• Informatics is this science of information, the practice of
information processing, and the engineering of information systems.- Source: Wikipedia
•Tools•Protocols•Standards
Collecting
Biological Informatics
•Cross-referencing
•Relationship of data
Linking
•DBMS•Central & Distributed•Security•Backups•Archival •Standards
Storage
•Structure•Governance•Standards •Policies
Organization
•Multi-levels•Difficult•Mashups•Standards
Integration
•Tools•Standards•Usability•Training•Non-biased
Analysis Synthesis
•Tools•Governance•Infrastructure•User analysis
Delivery
•Tools•Protocols•Standards
Applications
for
•Fusion•Blending•Related Integration•Analysis •Models
•Research•Decision Making•Policies•Education•Outreach
Sustainable Reliable Outreach Training
NBII: What is it?
A broad, collaborative program to provide access to data and information on our Nation’s biological resources
Contributors and Users from Diverse Sources
• Federal, State and local Government Agencies• Academic Institutions• Private sector organizations (non-profit, commercial)• Other interested groups
GOVERNMENTS
UNIVERSITIESMUSEUMSPRIVATE
Example NBII Projects
• NBII Integrated Search Tool • FDGC Biological Data Profile • NBII Species Mashups • USFWS Focal Species support• State Wildlife Action Plan project(s)• Butterflies and Moths of North America• Protected Areas Database for U.S. • GAP Serve data delivery system • Community Resource Mapper • Taxonomic services via ITIS• NBII LTER Cooperative Agreement• NBII Metadata Program • Observation Network for Earth (DataONE)
• Fire Research & Management Exchange System (FRAMES)
text
Describe and Discover
www.NBII.gov
PORTAL
My.NBII.gov
Content Management Integrated/Federated SearchCollaboration Services
Database and Web Services Model ServicesGeospatial Services
ITIS DIGR CatalogThesaurus Mapping Geoparsing CatalogGeo -referencing Discovery CatalogOperations
Dublin Core (plus)
UDDI / WSDL ??OGC/ISO FGDC/ISO
Distributed Applications , Databases , Websites , Tools and Models
Consume
Integrated View
DistributedServices
Resource and Service Catalogs
DistributedResources
Resource Catalog
Geospatial Services Catalog
Geospatial Dataset
Resource Clearinghouse
Database and Web Services
Catalog
Model ServicesCatalog
NBII Services Overview
Current Challenges
• Metadata, Metadata, Metadata• Available & usable tools• Data management culture issues• Standards adoption & applications • Sustainable & reliable infrastructure • Lack of integration• Lack of machine-parsable data• Lack of common services • Taxonomy, location• Lack of unique identifiers for data• Data silos• Large number small datasets
Some Examples
Images
Literature
NBII Species Mashups
- Images of the Environment- USGS GAP- Protected Areas- Numerous local datasets (i.e. HI)
OBIS USA Data Dashboardhttp://obisusa.nbii.gov
Mid-Atlantic Ekey
Central Southwest/Gulf Coast
Biological Metadata Clearinghouse
~ 100,000 records Based on FGDC BDP Training Program QA/QC Program Standards Cross-walks EML Dublin Core MARC
Biological Metadata Clearinghouse:Linking of results
Unique Facets of NBII Search
Dynamic biological clusters
Refine Results
Biological images
Map Display
Additional Unique Facets
Thesaurus integration
Publisher refinement
Diverse Sources
DBMSWebsites
FederationDocuments
Weighting of sources
NBII Search screen with GBIF records…
Mapping Portlets
Data Visualization Service
• Needed to support:– Viewing– Contributions– Annotations– Reuse – Integration – Review– Improvements
General Comments• Visualizations need to be user driven• Visualizations need to be available throughout life cycle• Traditional Search result lists will go away• Environmental domain – What is it and Where is it are vital.
Spatio-Temporal Exploratory Models predict the probability of occurrence of bird species across the United States at a 35 km x 35 km grid.
Patterns in Bird Species Occurrence
Land Cover
Potential Uses-• Examine patterns of migration • Infer impacts ofclimate
change• Measure patterns of habitat
useage• Measure population trends
Model resultseBird
Meteorology
MODIS – Remote sensing data
Occurrence of Indigo Bunting (2008)
Jan Sep DecJunApr
Wood Thrush
Swainson’s Hawk