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The Role of Networks in a Cyberinfrastructure

The Role of Networks in a Cyberinfrastructure. Zack Murrell and Derick Poindexter Appalachian State University. murrellze@appstate.edu SERNEC.ORG. Building a network. What are the issues involved? What are the benefits? What can networks do for TDWG? What can TDWG do for networks?.

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The Role of Networks in a Cyberinfrastructure

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  1. The Role of Networks in a Cyberinfrastructure Zack Murrell and Derick Poindexter Appalachian State University murrellze@appstate.edu SERNEC.ORG

  2. Building a network • What are the issues involved? • What are the benefits? • What can networks do for TDWG? • What can TDWG do for networks? murrellze@appstate.edu SERNEC.ORG

  3. Great Lakes Northern Great Plains Pacific Northwest New England California Consortium of Herbaria SERNEC CIRH Arizona & New Mexico TORCH Central Great Plains Developing Herbarium Networks Modified from: www.theodora.com/maps

  4. What information is available in a herbarium? • Keystroke label (legacy data) • Image specimen and OCR (HERBIS)

  5. State of Herbaria in the Southeast Data derived from Index Herbariorum (http://www.nybg.org/bsci/ih/ih.html) .

  6. SERNEC: SouthEast Regional Network of Expertise and Collections 215+ herbaria in the regionColleges UniversitiesState and federal parksPrivate collections SERNEC

  7. A 2020 Vision for Herbariain the Southeast A National Science Foundation Research Coordination Network RCN Award # 0542320 SERNEC: A “MODEL SYSTEM” TO BUILD A REGIONAL BIOINFORMATICS RESEARCH TOOL

  8. Cyber-infrastructure “IT TAKES A VILLAGE” teaching, research, outreach, conservation, curation Enhance biological sciences murrellze@appstate.edu SERNEC.ORG

  9. Networks and collaborations on this scale do not develop overnight The potential success of this network is rooted in the significant contributions made by biologists in the region over the past century that provide a solid foundation for this effort. The Association of Southeastern Biologists (ASB) The Southern Appalachian Botanical Society (SABS) Meeting annually for the past 60 years.

  10. WHY THE SOUTHEAST AS A MODEL? murrellze@appstate.edu SERNEC.ORG

  11. High levels of plant endemism (Estill & Cruzan 2001) New Communities discovered recently (Allison and Stevens 2001)

  12. Regional fossil pollen work allows us to compare past biogeography with present distributions to extrapolate about the future (Delcourt and Delcourt)

  13. SERNEC Partners • US Geological Survey NBII/SAIN • SunSITE – Univ. of Tennessee-Knoxville Implementation of emerging and advanced technologies and applications. • University of North Carolina and the Interdisciplinary Geospatial Research Center, Univ. Tenn-Chattanooga Dynamic mapping of Southeast collections • Robert Sandusky School of Information Science UT-K E-Research: The Contexts, Processes, and Social Order of Distributed Collective Practice • Developing collaborations with HERBIS, MORPHBANK and FILTERPUSH

  14. Goals • Network the 215 herbaria in 15 states in southeastern North America • Develop a strategy for advancing each state’s ongoing databasing effort • Publish online botanical resources that will be available to scientists, land managers, state and federal agencies, educators and the general public murrellze@appstate.edu SERNEC.ORG

  15. The challenges involved in the development of this network: • The need for community standards to increase the power of this research tool • The disparity in resources available to the various collections • The need for effective forms of communications among state, regional and taxonomic working groups murrellze@appstate.edu SERNEC.ORG

  16. Principles of the Conservation Commons • Promote Free and Open Access • Mutual Benefit (Reciprocity) • Rights and Responsibilities • Attribution • Integrity of Original Work "As access to information dramatically expands, ….. the value of the cognitive skills still unreplicable by silicon becomes greater.” L. Prusak, Where did knowledge management come from?, IBM Systems Journal Volume 40, Number 4, 2001 [ “Knowledge Management”], http://www.research.ibm.com/journal/sj/404/prusak.html

  17. Content Management for Collaborative Communities • Microsoft Research ConferenceXP • Drupal.org • Listserves With the expertise from NBII/SAIN and SunSITE murrellze@appstate.edu SERNEC.ORG

  18. SERNEC Governance Steering Committee (Robert’s Rules) Encourage buy-in Use The Society of Herbarium Curators (State Consortia and Southeast Chapter) http://glaucon.sunsite.utk.edu/shc/?q=node/2 Exist after the life of the NSF funding! Competing projects? murrellze@appstate.edu SERNEC.ORG

  19. Users: Decision-makers Users: Curators/scientists Users: Educators K-12 Users: Corporate Internet Link Analysis chain SERNEC Standards Environment Taxon mapping Ecological Modeling Phylo- analysis PLANTS Geolocate Darwin Core Herbis ITIS Application and Web Server Analysis Subsystem Importer/ exporter Specimen Herbarium & experts (with server) Database via SunSITE Herbarium & experts Derived from Swedlow et al. 2003

  20. C Users: Decision-makers Users: Curators/scientists Users: Educators K-12 Users: Corporate Internet Link Analysis chain SERNEC Standards Environment Eco- mapping Taxon mapping Phylo mapping D PLANTS Geolocate Darwin Core Herbis ITIS Application and Web Server Analysis Subsystem Importer/ exporter A Specimen Herbarium & experts (with server) Database via SunSITE Herbarium & experts B Derived from Swedlow et al. 2003

  21. GOAL 1 • Develop a business plan that will provide long-term funding for the network, and determine the best appropriate use of shared technical expertise. • Estimated cost: $10,000,000 to completely database the collections of plants, fungi, bryophytes, and algae in the Southeast. • This would include workshops on grantwriting and funding opportunities, as well as collaborative grant-seeking and resource-sharing. murrellze@appstate.edu SERNEC.ORG

  22. GOAL 2: Develop a digital library • Assess the technical needs of individual herbaria and identify barriers that currently impede progress in databasing and digitization. • Develop and promulgate best practices and community standards for databasing and digitization of collections. • Expose metadata from the network herbaria through the Global Biodiversity Information Facility (GBIF). • Facilitate the geo-referencing of specimen localities. • Make distribution maps available online for all taxa. murrellze@appstate.edu SERNEC.ORG

  23. GOAL 3: Increase scope & diversity • Recruit curators that are not yet involved in SERNEC. • Develop a regional plan to include institutions with large minority populations into the network. • Develop collaborations and educational opportunities to reach minority students and encourage their participation in botanically-based research. murrellze@appstate.edu SERNEC.ORG

  24. GOAL 4: Database expertise • Categorize the expertise by taxonomic categories and by scientific methodology (morphology, molecular, ecological, phylogenetic, etc). • Organize state, physiographic and taxonomic working groups to develop research questions. • Develop a plan for a database of “gray literature” of technical reports and other unpublished data searchable by taxon, region, or type of study. • Develop collaborations with state and federal parks, state and federal forests, state natural heritage programs, and The Nature Conservancy to assist in the curation and databasing of collections held by these groups. murrellze@appstate.edu SERNEC.ORG

  25. GOAL 5: Distribute information • Provide state-by-state meetings of curators to generate collaboration. • Publish online teaching aids for K-12. Include grade-specific inquiry-based studies that make use of the database information. • Develop a series of state-level workshops to introduce teachers, wildflower societies and garden clubs to the available resources. • Develop a series of state-level workshops to provide training in various technical aspects of systematics and taxonomy. murrellze@appstate.edu SERNEC.ORG

  26. GOAL 6: Information integration • All Taxa Biotic Inventory (ATBI) projects. • Botanical gardens. • The broader community of collections and into the broader community of taxonomic groups. • American Society of Plant Taxonomists (ASPT). • National Ecological Observatory Network (NEON). • Biodiversity Information Standards (TDWG). murrellze@appstate.edu SERNEC.ORG

  27. Taxonomic theory A taxon concept represents a unique combination of a name and a reference. . Name Concept Reference

  28. A usage represents an association of a concept with a name. Name Usage Concept • The name used in defining the concept need not be the same name used in your work. • e.g. Carya alba = Carya tomentosa sec. Gleason & Cronquist 1991. • Usage can be used to apply multiple name systems to a concept

  29. Collaboration on concept mapping

  30. Virtual Workbench (for working groups) Notify of Annotation Concept Map portal To PEET Public View (Multiple) Herbarium w/out Server Automated Automated SERNEC Federated Database SunSite = Storage SERNEC-NBII portal digitize clean Experts View Data (LOGIN) SAIN Lapham Herbarium w/ Server Automated To Shaw portal Notify of Annotation !! ALSO !! Georeference SHC portal w/ herbarium Tools Compile Toolbox Annotate Automated

  31. What can networks do for TDWG? • Provide resource of experts and students (use to reduce expenses of content development). • Develop high quality data through analysis and annotations. • Assemble species pages and interactive keys. • Provide information on phylogenetics and phyloinformatics. • Identify gray literature. • Provide expertise for concept mapping (to literature and use).

  32. What can TDWG do for networks? • Support typical workflow (layman’s guide to technical jargon). • Develop education modules for bioinformatics (for both curators and students) [Bryan Heidorn] • Provide training modules for literature mark-up. • Collaborate on development of standards within taxonomic groups.

  33. My suggestions • Use the TDWG Continental Representatives to reach out to the networks. • Encourage networks to embrace TDWG standards (within taxonomic communities). • Facilitate exchange of information and technology between networks and TDWG.

  34. SERNEC SouthEast Regional Network of Expertise and Collectionswww.sernec.org SERNEC

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