Names are not sufficient: the challenge of documenting organism identity

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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
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Biodiversity data structure
Community Type
Community type database
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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!

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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
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Multiple concepts of Rhynchospora plumosa s.l.
Gray 1834
Kral 2003
Peet 2006?
Chapman 1860
Elliot 1816
R. plumosa
R. plumosa v. plumosa
R. plumosa
R. sp. 1
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R. plumosa v. plumosa
R. plumosa
R plumosa v. intermedia
R. intermedia
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R. plumosa v. interrupta
R. pineticola
R. plumosa v. pineticola
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Multiple concepts of Andropogon virginicus L. sl

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The Taxonomic database challengeStandardizing
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.
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• 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.

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Taxonomic theory A taxon concept represents a
unique combination of a name and a reference.
Report -- name sec reference.
.
Name
Reference
Concept
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A usage represents an association of a concept
with a name.
Name
Concept
Usage

• 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

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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.

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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

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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

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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. --
• lt Potentilla sec. Cronquist 1991
• Potentilla simplex sec Cronquist 1991
• Potentilla canadensis sec Cronquist 1991

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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)

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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.

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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)

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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.

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Relationships among concepts

• Exactly equal (identification)
• Congruent, equal ()
• Includes (gt)
• Included in (lt)
• Overlaps (gtlt)
• Disjunct ()

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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.

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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.

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The way ahead

• Step 3 Development and provision of tools to
  facilitate mark-up of data and manuscripts with
  taxonomic concepts

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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

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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

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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