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names are not sufficient: the challenge of documenting organism identity

Biodiversity data structure. Community Type. Community type database. . . . . . . . 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! Particularly acute problem in a diverse community like SERNEC.

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names are not sufficient: the challenge of documenting organism identity

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    3. 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! Particularly acute problem in a diverse community like SERNEC

    7. High-elevation fir trees of western North America

    13. More successful queries Maps derived from multiple data layers Relevant specimens more easily discovered Large dataset integration

    14. 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. FNA 1997.

    15. 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

    16. Standards for concept data Several data models incorporate taxon concepts. The IOPI, VegBank, and Taxonomer data models are optimized for different uses. TCS was adopted by TDWG in August 2005 and is being implemented by SEEK and SEEK

    17. 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

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

    19. Step 1: Adoption of minimum standards and best practices by professional organizations, journals, and funding agencies.

    20. Publishers, curators, and data managers need to tag taxon identifications 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) Largely missing from collection databases

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

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

    24. 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.

    25. 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. IPNI started serving GUIDs in December

    26. Step 3: Development and adoption of tools to facilitate mark-up of data and manuscripts with taxonomic concepts

    27. Tools to develop and map concepts Taxonomists need mapping and visualization tools for relating concepts of various authors. Aggregators need tools for mapping relationships among concepts. Users need tools for entering legacy concepts.

    28. Concept mapper

    29. Multiple groups are building IT tools but lack data to populate the tools We have a critical mass of taxon concepts and concept relationships SERNEC funding & organization provides a community approach Potential for SERNEC to establish best practices and set standards

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