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 PanelThe SEEK development team

• 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.

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.

Carya ovata(Miller) K. Koch

Carya carolinae-septentrionalis(Ashe) Engler & Graebner

Carya ovata(Miller) K. Koch

sec. FNA 1997 sec. USDA 2005

Three concepts of shagbark hickory

Splitting one species into two illustrates the ambiguity often associated with scientific names.

High-elevation fir trees of western North America

AZ NM CO WY MT AB eBC wBC WA OR

Abies lasiocarpa

var. arizonica

Abies lasiocarpa var. lasiocarpa

Distribution

USDA - ITIS

Flora North America

Abies bifolia Abies lasiocarpa

R. plumosa

R. plumosa

R plumosav. intermedia

R. plumosav. plumosa

R. intermedia

R. plumosav. interrupta

R. pineticola

R. plumosa

R. sp. 1

R. plumosav. plumosa

R. plumosav. pineticola

Multiple concepts of Rhynchospora plumosa s.l.

Elliot 1816

Gray 1834

Kral 2003

Peet 2004?

1

2

3

Chapman1860

Aus aus L.1758 Aus aus L.1758

(v) Aus L.1758

Xus Pargiter 2003

Xus beus (Archer) Pargiter 2003.

in Pargiter 2003

(ii) Aus L.1758

Aus bea Archer 1965

in Archer 1965

(i) Aus L.1758

Aus aus L.1758

in Linneaus 1758

Aus bea Archer 1965

Aus cea BFry 1989

(iii) Aus L.1758

in Fry 1989

Aus ceus BFry 1989

Aus aus L. 1758

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

Tucker publishes his revison without noting Pyle’s corrigendum of the name of Aus cea

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.

Aus aus L.1758

in Tucker 1991

(iv) Aus L.1758

Aus cea BFry 1989

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

Name ReferenceConcept

Taxonomic theory

A taxon concept represents a unique combination of a name and a reference.

Report -- name sec reference.

.

Name ConceptUsage

A usage represents an association of a concept with

a name.

• 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

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

Relationships among concepts

• Exactly equal (identification)• Congruent, equal (=)• Includes (>)• Included in (<)• Overlaps (><)• Disjunct (|)

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.

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.

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.

Best Practices

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

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

Best Practices

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

Best Practices

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

Best Practices

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

Distributed information systems - and 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.

The way ahead

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.

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.

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

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.

The way ahead

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)

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

Data SetData Set

Data Set

Ecological Data Set

Ecological data set providers

Concept Provider 1e.g. Fishbase

Concept Provider 3e.g. Prometheus

Concept Provider 2e.g. ITIS

Taxonomic concept providers

Taxonomy transfer schema- TML

Concept matching/expansion/…Weighted concepts

Semantic Mediation SystemReturn list of Data Sets

User’s Taxonomic concept + quality measure

Name/Concept Repository

Ecological metadata language- EML (Containing Collector’s

Taxonomic concept(s))

EML repository

Taxon coverage

SEEK High-Level Approach