developing a cyberinfrastructure: experiences from a regional network of plant taxonomists zack...
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Developing a cyberinfrastructure: Experiences from a regional network of plant taxonomists
Zack Murrell, Derick Poindexter, and Zack Murrell, Derick Poindexter, and Michael DenslowMichael Denslow
Appalachian State UniversityAppalachian State University
[email protected] SERNEC.ORG
SERNEC: SouthEast Regional SERNEC: SouthEast Regional Network of Expertise and Network of Expertise and
CollectionsCollections
A National Science Foundation A National Science Foundation
Research Coordination NetworkResearch Coordination NetworkRCN Award # 0542320
FIVE YEAR PROJECT TO BUILD A REGIONAL FIVE YEAR PROJECT TO BUILD A REGIONAL
BIOINFORMATICS RESEARCH TOOLBIOINFORMATICS RESEARCH TOOL
SERNEC: SouthEast Regional Network of SERNEC: SouthEast Regional Network of Expertise and CollectionsExpertise and Collections
215+ herbaria in 215+ herbaria in the regionthe region
Colleges Colleges
UniversitiesUniversities
State and State and federal parksfederal parks
Private Private collectionscollections
SERNEC
GoalsGoals
1.1. Network the 215 herbaria in 15 states in Network the 215 herbaria in 15 states in southeastern North Americasoutheastern North America
2.2. Develop a strategy for advancing each state’s Develop a strategy for advancing each state’s ongoing databasing effortongoing databasing effort
3.3. Publish online botanical resources that will be Publish online botanical resources that will be available to scientists, land managers, state and available to scientists, land managers, state and federal agencies, educators and the general federal agencies, educators and the general publicpublic
[email protected] SERNEC.ORG
State of Herbaria in the Southeast USA
Data derived from Index Herbariorum (http://www.nybg.org/bsci/ih/ih.html) .
• Collections vary in size from 3,000 to 750,000 specimens.
• Curators are taxonomists, ecologists, paleobotanists, population biologists.
• Some institutions with significant budgets, IT support and curatorial staff.
• Some institutions are single person operations without budgets or IT support.
• ESTIMATED 15 MILLION SPECIMENS FROM THE SOUTHEAST. “Highest fruit on the tree”
or
“Least Common Denominator”
MOBILIZATION AND COMMUNICATIONMOBILIZATION AND COMMUNICATION
WORKING GROUPS:WORKING GROUPS:1.1. IT and infrastructure - FacebookIT and infrastructure - Facebook2.2. Libraries and literature - LinkedINLibraries and literature - LinkedIN3.3. Images (specimen and live) - DrupalImages (specimen and live) - Drupal4.4. Education and outreach -DrupalEducation and outreach -Drupal5.5. Taxonomic concept mapping - DrupalTaxonomic concept mapping - Drupal6.6. State working groups - NING and listservState working groups - NING and listserv
““IT TAKES A VILLAGE”IT TAKES A VILLAGE”
[email protected] SERNEC.ORG
SERNEC Partners
• US Geological Survey NBII/SAINUS Geological Survey NBII/SAIN
• SunSITE – Univ. of Tennessee-KnoxvilleSunSITE – Univ. of Tennessee-KnoxvilleImplementation of emerging and advanced Implementation of emerging and advanced technologies and applications.technologies and applications.
• University of North Carolina and the Interdisciplinary University of North Carolina and the Interdisciplinary Geospatial Research Geospatial Research Center, Univ. Tenn-Chattanooga Center, Univ. Tenn-Chattanooga Dynamic mapping of Southeast collectionsDynamic mapping of Southeast collections
• Robert Sandusky - University of Chicago Robert Sandusky - University of Chicago E-Research: The Contexts, Processes, and Social Order of Distributed Collective PracticeE-Research: The Contexts, Processes, and Social Order of Distributed Collective Practice
• Developing collaborations with HERBIS, MORPHBANK and Developing collaborations with HERBIS, MORPHBANK and FILTERPUSHFILTERPUSH
digitize clean
Portal- individual herbarium
Portal- individual herbarium
SERNEC
Federated Database
Concept mapping
MORPHBANK
SERNEC-NBII
portal
Herbarium
w/out Server
Herbarium
w/ Server
Automated
Automated-data provided
Automated-Data provided
Experts
View Data
(LOGIN and annotate)
Public
Educators K-12
Corporate users
Decision-makers
Curators
scientistsSunSITE
Data storage/curation
SERNECCommunity
CuratorsScientistsEducators
Artists
Mirrored data storage/curation
Data transfer
Annotation
Data transfer
Annotation
Notify of Annotation
Annotation
Notify of Annotation
Annotation
GIS mapping
Virtual workbenchSHC portal w/
herbarium Tools
Using the Society of Herbarium Curators Using the Society of Herbarium Curators for for governance structuregovernance structure
State consortia
Regional Chapter
Decision-makingConsensus buildingConflict resolution
Utilize existing organization’sconstitution structure
http://www.societyofherbariumcurators.org/
Networks and collaborations on Networks and collaborations on this scale do not develop this scale do not develop
overnightovernightThe potential success of this network is rooted in the The potential success of this network is rooted in the
significant contributions made by biologists in the region significant contributions made by biologists in the region over the past century that provide a solid foundation for over the past century that provide a solid foundation for this effort. Meeting annually for the past 60 years.this effort. Meeting annually for the past 60 years.
The Association of Southeastern Biologists (ASB) The Association of Southeastern Biologists (ASB) The Southern Appalachian Botanical Society (SABS) The Southern Appalachian Botanical Society (SABS)
How can we identify “natural” groups?How can we identify “natural” groups?Associations and journals, annual gatherings, taxon based Associations and journals, annual gatherings, taxon based
societies.societies.
http://www.asb.appstate.edu/http://www.asb.appstate.edu/
Initiative to develop an Initiative to develop an all-taxa database of all-taxa database of collections in the collections in the Southeastern USASoutheastern USA
Symposium April 4, 2009Symposium April 4, 2009
Birmingham, AlabamaBirmingham, Alabama
Sponsored by:Sponsored by:
CollectionsWeb (NSF CollectionsWeb (NSF RCN)RCN)
SERNEC (NSF RCN)SERNEC (NSF RCN)
Biodiversity Informatics: Progress and Potential in the Southeastern USA
Expand domain network to all-taxa regional network
Modified from: www.theodora.com/maps
New England
SERNEC
Great LakesNorthern Great Plains
Pacific Northwest
California Consortium of Herbaria
Arizona & New Mexico
CIRH
Central Great Plains TORCH
Developing Herbarium Networks
United States Virtual Herbarium United States Virtual Herbarium (USVH)(USVH)
Will use regional networks for Will use regional networks for organizational structureorganizational structure
Support from National Biological Support from National Biological Information Infrastructure (NBII)Information Infrastructure (NBII)
What can networks do?What can networks do?
Drive change in behavior by accepting best practices Drive change in behavior by accepting best practices (mark-up new descriptions at time of publication).(mark-up new descriptions at time of publication).
Develop high quality data through analysis and Develop high quality data through analysis and annotations.annotations.
Assemble species pages and interactive keys.Assemble species pages and interactive keys. Provide information on phylogenetics and Provide information on phylogenetics and
phyloinformatics.phyloinformatics. Identify gray literature/scan literature.Identify gray literature/scan literature. Provide expertise for concept mapping (to literature and Provide expertise for concept mapping (to literature and
use).use).
How can we mobilize social networks?How can we mobilize social networks?
Support typical workflow (layman’s guide to Support typical workflow (layman’s guide to technical jargon).technical jargon).
Develop education modules for bioinformatics Develop education modules for bioinformatics (for both curators and students). (for both curators and students).
Provide training modules for literature mark-Provide training modules for literature mark-up.up.
Collaborate on development of standards Collaborate on development of standards within taxonomic groups.within taxonomic groups.
DS/CS/Inf
DS/CS/InfDS/CS/Inf
DS/CS/Inf DS/CS/Inf DS/CS/Inf
Herb Network
Museum Network
Regional Network
Herb Network Herb Network
Domain Network
“US”TDWGDS/CS/Inf
Domain ScientistsComputer ScientistsInformaticists
{Evangelical model