Names are not sufficient: the challenge of documenting organism identity

1. Names are not sufficient: the challenge of documenting organism identity • R.K. Peet, J.B.Kennedy, and N.M. Franz • and • The Ecological Society of America Vegetation Panel • The SEEK development team

2. Accurate identification and labelling of organisms is a critical part of collecting, recording and reporting biological data. • Increasingly research in biodiversity and ecology is based on the integration (and re-use) of multiple datasets. • What was a minor annoyance for a few tens of records becomes intractable when looking at a million records.

3. The 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.

4. Three concepts of shagbark hickory Splitting one species into two illustrates the ambiguity often associated with scientific names. Carya carolinae-septentrionalis (Ashe) Engler & Graebner Carya ovata (Miller) K. Koch Carya ovata (Miller) K. Koch sec. FNA 1997 sec. USDA 2005

5. High-elevation fir trees of western North America AZ NM CO WY MT AB eBC wBC WA OR Distribution Abies lasiocarpa var. arizonica Abies lasiocarpa var. lasiocarpa USDA - ITIS Abies bifolia Abies lasiocarpa Flora North America

6. Multiple concepts ofRhynchospora plumosas.l. Gray 1834 Chapman 1860 Kral 2003 Peet 2004? Elliot 1816 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

7. (ii) Aus L.1758 (i) Aus L.1758 Aus bea Archer 1965 Aus aus L.1758 (iv) Aus L.1758 in Archer 1965 in Linneaus 1758 Aus aus L.1758 Aus cea BFry 1989 in Tucker 1991 Tucker publishes his revison without noting Pyle’s corrigendum of the name of Aus cea A diligent nomenclaturist, Pyle (1990), notes that the species epthithets of Aus bea and Aus cea are of the wrong gender and publishes the corrected names Aus beus corrig. Archer 1965 and Aus ceus corrig. BFry 1989 Pargiter publishes his revison using Pyle’s corrigendum of the epithet bea to beus and Aus cea to Aus ceus. Timeline showing taxonomic history (revisions and nomenclatural changes) pertaining to species comprising the imaginary genus Aus. (v) Aus L.1758 (iii) Aus L.1758 Aus aus L.1758 Aus aus L. 1758 Aus aus L.1758 Aus bea Archer 1965 Aus ceus BFry 1989 Aus cea BFry 1989 Xus Pargiter 2003 Xus beus (Archer) Pargiter 2003. in Fry 1989 in Pargiter 2003

8. Standardized taxon lists failto allow dataset integration • The reasons include: • Taxonomic concepts are not defined (just lists), • Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled, • The user cannot reconstruct the database as viewed at an arbitrary time in the past. • This is the single largest impediment to large-scale synthesis in ecology

9. Taxonomic theory A taxon concept represents a unique combination of a name and a reference. Report -- name sec reference. . Name Concept Reference

10. 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

11. Data models and data exchange standards • Numerous data models incorporate concepts. The IOPI, VegBank, and Taxonomer models are optimized for different uses. • SEEK, GBIF, and TDWG, are seeking a consensus model to be voted on August 2005 by TDWG

12. Relationships among concepts • Exactly equal (identification) • Congruent, equal (=) • Includes (>) • Included in (<) • Overlaps (><) • Disjunct (|)

13. Best Practices 1. When reporting identity of organisms in publications or data, provide not only the full scientific name of each kind of organism recognized, but also the reference that formed the basis of the taxonomic concept. e.g., Abies lasiocarpa sec. Flora North America 1997.

14. Best Practices 2. Reference high quality sources for taxon concepts such as a major compendium that provides its own defined concepts or a source that references the concepts of others.

15. Best Practices 3. Avoid comprehensive, synonymized checklists (e.g. ITIS) as they typically lack true taxonomic descriptions or circumscriptions; then can be considered if they contain taxonomic concepts sufficient for documenting organism identity.

16. Best Practices 4. Identifications for organisms should be by reference to credible, authoritatively published taxonomic concepts, rather than merely references to other identifications.

17. Best Practices 5. Identifications should include linkage to at least one concept, but need not be limited to a single concept. Eg. -- < Potentilla sec. Cronquist 1991 + ~ Potentilla simplex sec Cronquist 1991 + ~ Potentilla canadensis sec Cronquist 1991

18. Best Practices 6. Where appropriate, recorded identifications should be modified by supplemental information. Metadata is good, but is hard to use.

19. Best Practices 7. Use Internet-based taxonomic resources that document concepts only if they archive old versions and enable tracking of concepts time.

20. Distributed information systems - and the way ahead Step 1:Adoption of minimum standards and best practices by high-quality journals, funding agencies, and professional organizations.

21. The way ahead Step 2: Creation, availability, and maintenance of databases that document core sets of taxonomic concepts and the relationships of these concepts to each other.

22. Registration system and standard identifiers for names, references, and concepts • Essential for data exchange • SEEK is in the early design stages for a identifier system and central database.

23. True concept-based checklists • Equivalent of ITIS but with concept documentation and including how other concepts map onto the concepts accepted by the party. • Several are operative or in development including EuroMed, IOPI-GPC, Biotics, VegBank. Concept documentation planned for ITIS/USDA.

24. The way ahead Step 3:Development and provision of tools to facilitate mark-up of data and manuscripts with taxonomic concepts

25. The way ahead Step 4:Development and availability of a full information infrastructure to exploit the potential of concept-enriched data and publications for information discover and analysis.

26. Publishers, curators and data managers need to tag taxon interpretations with concepts • Precedence exists with tagging literature citations and GenBank accessions • Presses are linking scientific names in many ejournals to ITIS (e.g. Evolution, Ecology)

27. Tools to develop and map concepts • Taxonomists need mapping and visualization tools for relating concepts of various authors. SEEK will build prototypes for review and possible adoption. • Aggregators need tools for mapping relationships among concepts. • Users need tools for entering legacy concepts. Several are in development

28. User’s Taxonomic concept + quality measure Semantic Mediation System Concept matching/expansion/… Weighted concepts Return list of Data Sets Name/Concept Repository Taxon coverage EML repository Ecological metadata language - EML (Containing Collector’s Taxonomic concept(s)) Taxonomy transfer schema - TML Concept Provider 3 e.g. Prometheus Concept Provider 2 e.g. ITIS Concept Provider 1 e.g. Fishbase Ecological Data Set Data Set Data Set Ecological data set providers Taxonomic concept providers Data Set SEEK High-Level Approach