The Role of Networks in a Cyberinfrastructure Zack Murrell and Derick Poindexter Appalachian State University

Building a network What are the issues involved? What are the issues involved? What are the benefits? What are the benefits? What can networks do for TDWG? What can networks do for TDWG? What can TDWG do for networks? What can TDWG do for networks?

Modified from: New England SERNEC Great Lakes Northern Great Plains Pacific Northwest California Consortium of Herbaria Arizona & New Mexico CIRH Central Great Plains TORCH Developing Herbarium Networks

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

State of Herbaria in the Southeast Data derived from Index Herbariorum (

SERNEC: SouthEast Regional Network of Expertise and Collections 215+ herbaria in the region Colleges Universities State and federal parks Private collections SERNEC

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

Cyber-infrastructure “IT TAKES A VILLAGE” teaching, research, outreach, conservation, curation Enhance biological sciences

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.

WHY THE SOUTHEAST AS A MODEL?

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

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

SERNEC Partners US Geological Survey NBII/SAIN US Geological Survey NBII/SAIN SunSITE – Univ. of Tennessee-Knoxville 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 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 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 Developing collaborations with HERBIS, MORPHBANK and FILTERPUSH

Goals 1. Network the 215 herbaria in 15 states in southeastern North America 2. Develop a strategy for advancing each state’s ongoing databasing effort 3. Publish online botanical resources that will be available to scientists, land managers, state and federal agencies, educators and the general public

The challenges involved in the development of this network: 1. The need for community standards to increase the power of this research tool 2. The disparity in resources available to the various collections 3. The need for effective forms of communications among state, regional and taxonomic working groups

Principles of the Conservation Commons 1. Promote Free and Open Access 2. Mutual Benefit (Reciprocity) 3. Rights and Responsibilities Attribution Attribution Integrity of Original Work 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”],

Content Management for Collaborative Communities Microsoft Research ConferenceXP Microsoft Research ConferenceXP Drupal.org Drupal.org Listserves Listserves With the expertise from NBII/SAIN and SunSITE

SERNEC Governance Steering Committee (Robert’s Rules) Steering Committee (Robert’s Rules) Encourage buy-in Encourage buy-in Use The Society of Herbarium Curators Use The Society of Herbarium Curators (State Consortia and Southeast Chapter) Exist after the life of the NSF funding! Competing projects? Competing projects?

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

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

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. 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. 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. This would include workshops on grantwriting and funding opportunities, as well as collaborative grant-seeking and resource- sharing.

GOAL 2: Develop a digital library Assess the technical needs of individual herbaria and identify barriers that currently impede progress in databasing and digitization. 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. 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). Expose metadata from the network herbaria through the Global Biodiversity Information Facility (GBIF). Facilitate the geo-referencing of specimen localities. Facilitate the geo-referencing of specimen localities. Make distribution maps available online for all taxa. Make distribution maps available online for all taxa.

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

GOAL 4: Database expertise Categorize the expertise by taxonomic categories and by scientific methodology (morphology, molecular, ecological, phylogenetic, etc). 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. 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 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. 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.

GOAL 5: Distribute information Provide state-by-state meetings of curators to generate collaboration. 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. 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 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. Develop a series of state-level workshops to provide training in various technical aspects of systematics and taxonomy.

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

NameReferenceConcept Taxonomic theory A taxon concept represents a unique combination of a name and a reference..

NameConceptUsage A usage represents an association of a concept with a name. 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 Usage can be used to apply multiple name systems to a concept

Collaboration on concept mapping

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

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

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

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

SERNEC SouthEast Regional Network of Expertise and Collections SERNEC