The challenge of biodiversity: Plot, organism and taxonomic databases Robert K. Peet

1. The challenge of biodiversity: • Plot, organism and taxonomic databases • Robert K. Peet • University of North Carolina • The National Plots Database Committee • John Harris • NCEAS

2. A case study: The US National Plots Database Project organized and directed by: Robert K. Peet, University of North Carolina Marilyn Walker, USDA Forest Service & U. Alaska Dennis Grossman, The Nature Conservancy / ABI Michael Jennings, USGS-BRD & UCSB Project supported by: National Center for Ecological Analysis & Synthesis U.S. National Science Foundation USGS-BRD Gap Analysis Program ABI / The Nature Conservancy

3. Biodiversity data structure Locality Observation/Collection Event Plot databases Object or specimen Specimen databases Taxon Taxonomic databases

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

5. Current standards • Biological organisms are names following international rules of nomenclature. • Database standards are being developed by TDWG, GBIF, IOPI, etc. • Metadata standards have been developed. For example, the Darwin Core is a profile describing the minimum set of standards for search and retrieval of natural history collections and observation databases. (http://tsadev.speciesanalyst.net/DarwinCore/)

6. There exist numerous compilations of organism names. For example: • Species 2000 http://www.sp2000.org/default.html(Composed of 18 participant databases) • All Species http://www.all-species.org • ITIS http://www.itis.usda.gov/(The US government standard list) • Index to organism nameshttp://www.biosis.org.uk/triton/indexfm.htm

7. Taxon-specific standard lists are available. Representative examples for higher plants include:North America USDA Plants http://plants.usda.gov/ ITIS http://www.itis.usda.gov/ ABI http://www.natureserve.org World IPNI International Plant Names Checklist http://www.ipni.org/ IOPI Global Plant Checklisthttp://iopi.csu.edu.au/iopi/iopigpc1.html

8. Most standardized plant lists fail to allow effective integration of datasets. • The reasons include: • The user cannot reconstruct the database as viewed at an arbitrary time in the past, • Taxonomic concepts are often not defined, • Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled.

9. Three concepts of shagbark hickory Splitting one species into two illustrates the ambiguity often associated with scientific names. If you encounter the name “Carya ovata (Miller) K. Koch” in a database, you cannot be sure which of two meanings applies. Carya carolinae-sept. (Ashe) Engler & Graebner Carya ovata (Miller)K. Koch Carya ovata (Miller)K. Koch sec. Gleason 1952 sec. Radford et al. 1968

10. Multiple concepts of Rhynchospora plumosa s.l. Elliot 1816 Gray 1834 Chapman 1860 Kral 1998 Peet 2002 R. plumosa R. plumosa v. plumosa R. plumosa R. sp. 1 1 R. plumosa v. plumosa R. plumosa R plumosa v. intermedia R. intermedia 2 R. plumosa v. interrupta R. pineticola R. plumosa v. pineticola 3

11. An assertion represents a unique combination of a name and a reference Assertion is equivalent to Potential taxon & taxonomic concept Name Assertion Reference

12. Five shagbark hickory assertions Possible taxonomic synonyms are listed together Assertions (One shagbark)C. ovata sec Gleason ‘52 (Southern shagbark)C. carolinae-s. sec Radford ‘68C. ovata australis sec FNA ‘97 (Northern shagbark) C. ovata sec Radford ‘68 C. ovata sec FNA ‘97 Names Carya ovata Carya carolinae-septentrionalis Carya ovata var. australis References Gleason 1952 Britton & Brown Radford et al. 1968 Flora Carolinas Stone 1997 Flora North America

13. A usage represents a unique combination of a taxon and a name. Usages can be used to track nomenclatural synonyms Name Usage Taxon

14. Usage Speciesconcepts Publishednames 1. Carya ovata 2. C. carolinae-septentrionalis 3. C. ovata var. australis 1-A 1-C 2-B 3-B A. One shagbark B. Southern shagbark C. Northern shagbark An example of a nomenclatural synonym is the linkage of the assertion “Carya ovata var. australis sec. FNA 1997” with the name “Carya carolinae-septentrionalis” by both ITIS and ABI.

15. A usage (name assignment) and assertion (taxon concept) can be combined in a single model Name Usage Assertion Reference

16. Party Perspective • The Party Perspective on an Assertion includes: • Status – standard, nonstandard, undetermined • Correlation with other assertions – Equal, Greater, Lesser, Overlap, Undetermined. • Lineage – Predecessor and Successor assertions. • Start & Stop dates.

17. Party Assertion ITIS FNA CommitteeABI Carya ovatasec Gleason 1952 Carya ovata sec Radford 1968 Carya carolinae sec Radford 1968 Carya ovata sec FNA 1997 Carya ovata australis sec FNA 1997 Status Party Assertion Status Start Name ITIS ovata – G52 S 1996 ITIS ovata – R68 A 1996 ovata ITIS carolinae – R68 A 1996 carolinae ITIS carolinae – R68 S 2000 ITIS ovata aust – FNA A 2000 carolinae

18. Concept-based taxonomy is coming soon • All organisms in databases should be identified by linkage to an assertion = name and reference! • Various standards are being developed by FGDC, TDWG, IOPI, GBIF, etc. • Most major databases are working toward inclusion of assertions (e.g. ITIS, IOPI, ABI). • Until standard assertion lists are available, databases that track organisms should include couplets containing both a scientific name and a reference.

19. National Taxonomic Database? • Concept-based • Party-neutral • Synonymy and lineage tracking • Perfectly archived An upgrade for ITIS & Species 2000?

20. Specimen/object databases • Information on specimens/objects should be tracked by reference to • Place (place or collection) • Unique identifier (accession number) • Time • A museum is a place

21. Database systems for tracking specimens • The following are a few of the many available • BioLink http://www.ento.csiro.au/biolink/index.html • Specify http://usobi.org/specify/default.htm • Biota http://viceroy.eeb.uconn.edu/Biota • Taxis http://taxis.virtualave.net/ • TDWG maintains links to multiple software systems • http://www.bgbm.fu-berlin.de/TDWG/acc/Software.htm

22. Core elements of the National Plots Database Project Plot Plot Observation Taxon Observation Taxon Interpretation Plot Interpretation

23. Support multiple interpretations of which concept applies to an organism or community. • Various observers will associate different taxonomic concepts with records in a database • Provision must be made for inclusion of these taxonomic interpretations. • Minimal attributes include • Concept applied • Date applied • Who made the interpretation • Links to supporting information

24. Interface tools • Desktop version for data preparation and local use. • Loaders for legacy data. • Data export. • Tools for linking taxonomic concepts. • Standard query, flexible query, SQL query. • Flexible export. • Local data refresh • Easy web access with consistent interface

25. Conclusions for database designers • Records of organisms should always contain (or point to) couplets consisting of a scientific name and a reference where the name was used. • Design for future annotation of organism concepts. • Track specimens/objects by location, unique identifier & time. • Design for reobservation! Separate permanent from transient attributes. • Archival databases should provide time-specific views.