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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

NBII Distributed Network

* Thematic

* Infrastructure

* Regional

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

NBII Species Mashups

Species

Taxonomy

Global Museum occurrences

Species of concern by State

NBII Species Mashups

Ecology of Species

Datasets of reference

NBII Species Mashups

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

Metadata Provider Dashboard:

QA/QC Portal

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

Questions & Comments

Jeff Falgoutjfalgout@usgs.gov303.202.4261

Mike Framemike_frame@usgs.gov865.576.3605