Why do we need a taxonomic concept transfer standard and for whom?

1. Why do we need a taxonomic concept transfer standard and for whom? Jessie Kennedy

2. 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?

3. 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…

4. Schema Development Plan… • Consult with several of the major taxonomic database developers and users spanning the range of taxonomic interests • 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

5. Acknowledgements • Teams visited or consulted in preparation of the schema • 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

6. TDB - perspectives • Revisionary Taxonomist • 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 • 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 • Taxonomer; Nomencurator • Taxonomic assertions from publications • Revisions, new species, identifications, sightings, descriptions • Recording any useful statement regarding a taxon in any publication • might give the taxonomist additional information regarding a taxon although not part of the original definition of the concept

7. TDB – perspectives contd. • Species focussed taxonomy • Species 2000; ITIS; Biodiversity World • Assumption that there is a definitive list of species • 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. • Name based taxonomy • IPNI; APNI • published names + validity according to rules of nomenclature • Recording the first publication of any name by an authority • Noting the validity of the name according to the rules of nomenclature

8. TDB – perspectives contd. • Database taxonomy • GBIF; SEEK; VegBank • Taxonomic assertions as recorded in existing databases • Whatever information is stored in existing taxonomic systems • All notions of taxonomic concept • Cross referencing between concepts • Views according to particular authorities/parties as of a particular date • As this data becomes available

9. 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

10. 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

11. 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

12. 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?

13. 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

14. 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?

15. 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?

16. 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

17. 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.