Why do we need a taxonomic
concept transfer standard and for
whom?
Jessie Kennedy
Many Taxonomic Databases….
• Majority of taxonomic databases are name based…
– Single entry for each scientific name
– List of synonyms associated with these names
• No rationale recorded for synonymy
– Difficult to relate to names not considered on the synonymy list
– They are the major source of on-line taxonomic information…
• Some databases model taxonomic concepts….
– Different perspectives on what a taxonomic concept is.
– Not much data available in these databases
• Do we need to store taxonomic concepts?
Taxonomic Concepts…
• Do we need them?
– YES - for any serious scientific work communicating about taxa….
– Matching data from disparate sources on names causes erroneous
results
• What is a taxonomic concept?
– Depends on your perspective….What you want to do with them…
• Should we have a common shared definition of a taxonomic
concept?
– YES – will allow us to share/exchange/integrate data more easily
– speed up and improve the process of taxonomy and its dissemination
• Can we agree on some common definition of a taxonomic
concept?
– “Using Taxonomic Concepts:integrating taxonomic concept models”,
• TDWG (Lisbon)
– TDWG(GBIF/SEEK) we need to develop a concept transfer schema…
Schema Development Plan…
• Consult with several of the major taxonomic database developers and users
spanning the range of taxonomic interests
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understand their notion of taxonomic concept
what information they consider important
what they currently do and would do with taxonomic concepts
where they are going in their development
what are the important issues for them
• Determine the differences and similarities in understanding of taxonomic
concept in the different taxonomic user groups
– All of the systems were designed for a specific purpose
• all have particular strong points
• Amend and extend the abstract model (Lisbon) into transfer schema
– Straw man + Glossary of terms for Edinburgh, May
– Follow-on consultation
– Final version + exchange protocol for TDWG in October
Acknowledgements
• Teams visited or consulted in preparation of the
schema
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Berlin Model: Walter Berendsohn, Marc Geoffrey, Karl Glück
GBIF: Donald Hobern, Per de Place Bjrn
(IPNI: Sally Hinchcliffe) (APNI: Greg Whitbread)
ITIS: Paula Huddleston, David Nicolson
Nomencurator: James Ytow, Dave Roberts, Dave Morse
Prometheus: Martin Pullan
SEEK: Jim Beach, Matt Jones, Bob Peet
Species 2000, Biodiversity World, IOPI: Frank Bisby,
Andrew Jones, Richard White
– Taxonomer: Richard Pyle
– VegBank: Bob Peet, Michael Lee
TDB - perspectives
1.
Revisionary Taxonomist
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Berlin Model; Prometheus
Full classification hierarchy for the revised group
Explicit opinion on concept synonymy to other concepts listed
Recording information on specimens used during the revision
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2.
Type/non-type specimens
Automatic naming of taxa based on type specimens
– Requires names(classifications) for all the type-specimens
– Implicit synonymy based on specimens
Taxonomy as recorded in publications
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Taxonomer; Nomencurator
Taxonomic assertions from publications
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Revisions, new species, identifications, sightings, descriptions
Recording any useful statement regarding a taxon in any publication
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might give the taxonomist additional information regarding a taxon
although not part of the original definition of the concept
TDB – perspectives contd.
3. Species focussed taxonomy
– Species 2000; ITIS; Biodiversity World
– Assumption that there is a definitive list of species
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Assumes an authority group of experts can agree on what species
concepts exist and what their valid names are.
Not clear what the concept for each name is or who defined it.
– NB. Even if this list could be decided today, any changes to a
concept on the list would require versions to allow data to be
meaningful in the long term.
4. Name based taxonomy
– IPNI; APNI
– published names + validity according to rules of nomenclature
– Recording the first publication of any name by an authority
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Noting the validity of the name according to the rules of nomenclature
TDB – perspectives contd.
5. Database taxonomy
– GBIF; SEEK; VegBank
– Taxonomic assertions as recorded in existing databases
– Whatever information is stored in existing taxonomic systems
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All notions of taxonomic concept
Cross referencing between concepts
Views according to particular authorities/parties as of a particular date
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As this data becomes available
Taxonomy
• Three distinct but related areas:
– Classification
• Ordering of groups of specimens/taxa into hierarchical groups (taxa)
• Selecting type specimens to “represent” new taxa
– Nomenclature
• Application of names to taxa based on existing type specimens and rules
– Identification/determination
• Designating a name to an organism according to the concepts in an
existing classification framework
• Problem is we don’t keep these distinct
– Names and taxa get confused
– Defining new taxa gets confused with data on identification or
description of species already defined
Names versus Concepts
• Taxon Name :- label/word/string
– Used for communicating ideas about organisms
– Meaningless without a definition
• First time the name is used the definition is that in the mind (hopefully
recorded in a publication) of the taxonomist who introduced the name.
– Full Scientific name
• Scientific name + author abbreviation [+ date]
• Carya floridana Sarg. (1913) or Carya floridana Sarg.
• Full scientific name implies an original concept
• Original Concept
– Full Scientific name “according to” Author + Publication + Date (+
Definition)
• Carya floridana Sarg. (1913) Charles Sprague Sargent, Trees & Shrubs
2:193 plate 177 (1913) (+Definition)
• Revisionary taxonomy combined with the rules of
nomenclature mean names have more than one meaning
Names versus Concepts contd..
• Revised Concept
– Original concept except according to author and date are different from
author and date in full scientific name
– Carya floridana Sarg. (1913) Stone FNA 3:424 (1997) (+Definition)
• Reference Concept
– Reference from a revision concept to some other concept that might not
be well referenced and will not be defined
• Full Scientific name
• Full Scientific name “according to” Author + Publication + Date
– Over time we would expect all reference concepts to be replaced by
either original or revision concepts.
• Vernacular Concepts
– Label
• Scrub Hickory
– Used to allow access to possible original or revision concepts
How do we define a concept?
• Character circumscription?
– During a revision data recorded by taxonomists is
• context dependent; differentiates taxa rather than fully describes them;
• uses natural language with all its ambiguities
• Taxon circumscription
– i.e. in terms of its lower level taxa
• Specimen circumscription
– Type specimen
– Complete specimen set used in the revision
• Relationships to other taxa
– Synonymy
• Instance of the publication in which the concept was defined?
Aims of workshop
• Present Taxonomic Concept Transfer Schema
– Clarify the semantics of the schema
– Highlight the main features
• Globally Unique Identifiers: what, why, when, which and what
now?
– Present and discuss the possible roles for GUIDs
• Experience from Mapping Existing Models to the Transfer
Schema
– To discuss how we have mapped date from 2 different sources and
perspectives to the transfer schema to show the feasibility
• Preliminary description/outline of proposed exchange
protocols
– How the transfer schema might be used.
• Capture the results of the discussion to form a report on the
workshop
Questions…..
• Can we talk about names independent of concepts?
– When, what does it mean?
• Are Common names important?
– In what sense?
– Not important in scientific work
• Therefore not so important to deal with concepts related to common names
• Is it possible to change the definition of an existing concept?
– Can we add more information to the description of a concept
– E.g. extend the Geographic range?
– Add additional characters
• We know the definition of a name evolves and changes but
when are we really talking about a new concept
– when a new revision has been done?
– Every time someone says something new about a concept?
Questions….
• There is a difference between identification (and description)
according to an already described taxon and definition (and
description) of a (possibly) new taxon
– Attributing new knowledge to a taxon should not be considered part of
the definition of a taxon.
• Who owns concepts?
– Who gets the rights to them?
Taxonomic Concept Issues….
• We don’t even have a comprehensive online list of taxonomic
names …
• Lack of high quality legacy data regarding taxa
– Sometimes all we have is a name and if we’re lucky a publication..
• Too much inconsistency and errors in data
– Cost of resolving errors…
– How do you know that this has been done well…
• The problem needs to be tackled sooner rather than later
Outcome of the workshop
• Are there any major problems with the schema for anyone?
– If so what are they?
• Are these common to everyone?
– If not are you convinced about its usability
• How can you be convinced?
• What are the areas we haven’t addressed enough yet?
• We have adopted the general element list with type attribute
rather than specifying every type specifically
– Others have taken the explicit approach – does this matter?
• Do we want to try and move towards GUIDs to represent
concepts, publications etc.