VegBank and the ESA Cyber-infrastructure for Vegetation Science

1. VegBank and the ESA Cyber-infrastructure for Vegetation Science • Robert K. Peet • & • The Ecological Society of America Vegetation Panel

2. Background The ESA Vegetation Classification Panel was established in 1993 with a mandate to support the emerging U.S. Vegetation Classification.

3. ESA Guidelines forvegetationclassification The ESA Vegetation Panel has developed guidelines for vegetation classification covering requirements for: • Vegetation field plots. • Documentation & description of floristic types. • Submission & peer review of proposed types. • Management, citation, & archiving of vegetation data.

4. North American Vegetation Classification • Ecological Society of America – Standards, peer review & publication. • US Federal Geographic Data Committee –US government standards. • NatureServe – Maintenance and distribution of the Classification. • USDA & ITIS – Taxonomic standards for organisms

5. The new community ecology Intersection of 3 data types • Site data: climate, soils, topography, etc. • Taxon attribute data: identification, phylogeny, distribution, life-history, functional attributes ... • Co-occurrence data: attributes of individuals (e.g., size, age, growth rate) and taxa (e.g., cover, biomass) that co-occur at a site.

6. The Vegetation Plot • The primary unit of vegetation observation. • Universal attributes: date, location, area, species list, species importance • Optional attributes: environment, soil, disturbance • Protocols and formats: many & flexible • Available data: > 106 plot records containing > 5x107 species occurrence records.

7. VegBank • VegBank – a public archive for vegetation plot observations (http://vegbank.org). • VegBank functions in a manner analogous to GenBank. • Plot data can be deposited, discovered, viewed, cited, annotated, & downloaded. • Plot data can be used for documentation validation and reanalysis.

8. VegBank strategies • Standard exchange format – established through IAVS • Supports multiple protocols. • Flexible and expandable • Tools for data discovery, integration, and summarization. • Generalizable to most types of species co-occurrence data. • Incentives to participate.

9. NatureServe Explorer US-NVC--- Proposed data flow Extraction NatureServe Biotics Classification Mgt. NVC Proceedings US-NVC Panel Peer Review Proposal submission Legend External Action Analysis & Synthesis Internal Action VegBank & other plot archives Software Entity

10. Biodiversity data structure Locality Observation/ Collection Event Observation database Specimen or Object Occurrence database Bio-Taxon Taxonomic database Observation or Community Type Observation type database

11. Core elements of VegBank Project Plot Plot Observation Taxon / Individual Observation Taxon Interpretation Plot Interpretation

12. Taxonomic database challenge:Standardizing organisms and communities The problem: Integration of data potentially representing different times, places, investigators and taxonomic standards. The traditional solution: A standard list of organisms / communities.

13. One concept ofAbieslasiocarpa USDA Plants & ITIS Abies lasiocarpa var. lasiocarpa var. arizonica

14. A narrow concept of Abies lasiocarpa Flora North America Abies lasiocarpa Abies bifolia Partnership with USDA plants to provide plant concepts for data integration

15. High-elevation fir trees of western US AZ NM CO WY MT AB eBC wBC WA OR Distribution Abies lasiocarpa var. arizonica var. lasiocarpa USDA & ITIS Abies bifolia Abies lasiocarpa Flora North America A. lasiocarpasec USDA > A. lasiocarpasecFNA A. lasiocarpasecUSDA > A. bifoliasecFNA A. lasiocarpa v. lasiocarpasecUSDA > A. lasiocarpasecFNA A. lasiocarpa v. lasiocarpasecUSDA >< A. bifoliasecFNA A. lasiocarpa v. arizonicasecUSDA < A. bifoliasecFNA

16. www.vegbank.org

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26. VegBank Lessionsfor community participation • Usability (testing, training) • Incentives • Uploads (mandates, rewards, security) • Downloads (opportunity) • Citation (culture) • Tools and integration • Connectivity

27. VegBank Lessionsfor data sharing • Embrace established standards (e.g., TDWG, EML) • Work to establish new standards • Content, process, exchange • Design for idiosyncratic data • Anticipate distributed systems and connectivity • Leverage agency mandates • Repositories for archiving; databases for access • Respect intellectual property • Embargos, licenses, confidentiality

28. Roles & ResponsibilitiesProfessional Societies • Set standards • Data content and exchange format • Data archiving and access (discrete, well-circumscribed elements) • Assure quality control (peer review) • One of the 4 functions of publication: Certification, Validation, Awareness, Archiving

29. Roles & ResponsibilitiesDigital repositories and libraries • Archive and provide access to publications and data • Institutional responsibilities to granting agencies. Driven by lawyers and paid for by overhead • Potential security for databases

30. Roles & Responsibilities Granting Agencies • Set requirements for data archiving and sharing, but perhaps delegate implementation to societies • Pay for archiving and publication, directly or through overhead

31. Roles & Responsibilities Data Centers • Maintain a portfolio of critical, discipline-specific database systems • Maintain key infrastructure content • Digital identifiers • Common objects (e.g. taxa, publications) • Data registries

32. Roles & ResponsibilitiesPublishers • Require that specific types of data be archived (e.g., GenBank, VegBank) • Imbed deep links as a form of citation for standard elements such as taxon concepts and data elements • Provide archives for and links to supporting documentation

33. Roles & ResponsibilitiesGovernment Agencies • Formulate federal standards and policies (in context of disciplinary standards). • Mandate and implement federal standards (e.g., FGDC standards) • Assure critical infrastructure exists

34. Conclusions • VegBank is an example of a discipline-specific but public data archive (functions for deposit, discovery, withdrawal, citation, annotation) • Standards for data content, data exchange, and archiving • Standards for reference to standard elements such as taxonomic data • Work with a broader community to avoid institutional fragility.