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Names are not sufficient: the challenge of documenting organism identity

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. Locality. Observation/ Collection Event. Co-occurrence database. Specimen or Object.

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Names are not sufficient: the challenge of documenting organism identity

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

  3. 1. Biodiversity informatics depends on accurate and precise taxonomy • 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. • New tools are producing flawed results!

  4. 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

  5. Multiple concepts ofRhynchospora plumosas.l. Gray 1834 Chapman 1860 Kral 2003 Peet 2006? 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

  6. Multiple concepts ofAndropogon virginicus L. sl

  7. 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.

  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 biodiversity & 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. 2. Always report a taxon by reference to a concept When reporting the identity of organisms in publications, data, or on specimens, 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.

  12. Choice of concepts • 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. • Avoid checklists (e.g. ITIS) as they typically lack true taxonomic descriptions or circumscriptions

  13. SEEK & GBIF are working to provide standards for concept data • Several data models incorporate taxon concepts. The IOPI, VegBank, and Taxonomer models are optimized for different uses. • SEEK, GBIF, and TDWG developed TCS, which was adopted by TDWG in August 2005 and is being implemented by GBIF and SEEK

  14. 3. Concepts and identifications are distinct. • A name in a publication could be either a concept or an identification. • 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

  15. 4. Biodiversity informatics depends on standards and connectivity Darwin Core and EML are widely used and under continued development, but effectively obsolete. • Names (Linnean Core) • Publications (Alexandrian core, etc) • Observations (proposed TDWG standard) • Identifications (proposed EML extension) • Taxonomic concepts (TCS) • GUIDS (under development by GBIF)

  16. 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.

  17. 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)

  18. 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.

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

  20. 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.

  21. Registration system and standard identifiers for names, references, and concepts • Essential for data exchange • GBIF is hosting a set of international workshops to design the GUID infrastructure.

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

  23. 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

  24. The Opportunity Build on the infrastructure provided by • The VegBank data model • The NVC peer review system • GBIF & TDWG standards • The Weakley concept dataset for the Southeast

  25. (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

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