Developing taxonomic names services to enhance findability
David Remsen
ECAT Programme Officer
October 22, 2007
WWW.GBIF.ORG

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Overview of GBIF and data portal
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Informatics challenges relating to taxon data
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What we are doing about it
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Wider implications of our efforts

…to make the world’s biodiversity data freely and universally available via the Internet
What is biodiversity?
GBIF follows the broadly outlined CBD recognition of levels of biological diversity:
• Molecules / genes
• Species
• Ecosystems / ecology

 http://data.gbif.org
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Core data types on
GBIF network
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Taxon names
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Taxon occurrence information
 specimen records from natural history collections
 observational records
Fields used in indexing records
Mandatory
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Scientific name
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Institutional code
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Collection code
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Catalogue number
Highly desirable
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Geospatial location
Collection date
Higher taxon info
Date last modified

Users
List species recorded in Costa Rica
Find all occurrences of Papilio machaon
Find type specimen for Coffea odorata
Find occurrences of Primates from
Madagascar
Find occurrences from
Antananarivo Province
Portal
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Registry
DiGIR
DiGIR
DiGIR
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TAPIR
DiGIR
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Mirror
Databases

 http://data.gbif.org
/
Species: Achillea millefolium Kingdom: Animalia
Country: Madagascar Dataset: Continuous Plankton
Recorder Database

 http://data.gbif.org
/

taxon data http://data.gbif.org/ws/rest/taxon occurrence record data http://data.gbif.org/ws/rest/occurrence occurrence density data http://data.gbif.org/ws/rest/density
GBIF
Data Portal
Web Services http://data.gbif.org/ws/rest/resource dataset metadata http://data.gbif.org/ws/rest/provider data provider metadata http://data.gbif.org/ws/rest/network data network metadata

http://data.gbif.org/ws/rest/occurrence/list/?taxonConceptKey=14724348&format=darwin

 iSpecies

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Hundreds of Institutional providers
Thousands of Resources
Millions of Records
Collective & Integrated Access
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Wide Taxonomic, Temporal and Geographic Scope
Free and Open Access to all
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Go forth and integrate!
Parallel: GenBank

Everything I Just Said
Meets
The names problem in biology
All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge.
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Grimaldi & Engel, 2005, Evolution of the Insects

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Access to data is via limited points of entry
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Biology has a “names problem.”
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This names problem impacts these data access entry points.
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Exacerbated by:
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Wide taxonomic, temporal scope
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Federated origins of data

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Synonymy
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A single concept may reference multiple names
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Equivalent
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Inclusive
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Homography (Homonymy)
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A single name may refer to multiple concepts
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Definition
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A single name may refer to multiple KINDS of concepts

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A lexical “concept”
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A set of character strings
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A nomenclatural concept
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A Code-regulated fact
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A taxonomic concept
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A Hypothesis or opinion
Synonyms
Homonyms
All of these are important to distinguish

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Lexical/Orthographic
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Informed by: Nomenclators, Taxonomies, Algorithm
Nomenclatural
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Informed by: Nomenclators, Monographs (with interpretation)
Taxonomic
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Informed by: Monographs, Floras, Faunas, derived checklists
Different classes of equivalence are addressed by different resources

Lexical synonym: A single concept may reference multiple names
ILPIN
IPNI
MOBOT
Gerardia paupercula (Gray) Britt. var borealis (Pennell) Deam
Gerardia paupercula var borealis (Pennell) Deam
Gerardia paupercula Britt. var borealis Deam
Informed by: Nomenclators, Taxonomies, Algorithm
Identifies the preferred lexigraphy of the name
Automates the grouping of lexical variation

Orthographic synonym: A single concept may reference multiple names
Loligo pealeii Loligo pealii
Loligo pealei Loligo plei
Informed by: Nomenclators, Taxonomies, Algorithm

Vernacular synonym: A single concept may reference multiple names

Nomenclatural synonym: A single concept may reference multiple names

Nomenclatural synonym: A single concept may reference multiple names
ILPIN Gerardia paupercula (Gray) Britt. var borealis (Pennell) Deam
IPNI
MOBOT
Gerardia paupercula var borealis (Pennell) Deam
Gerardia paupercula Britt. var borealis Deam
MOBOT
IPNI
Agalinis paupercula (Gray) Britton var.
borealis Pennell (Zenkert 1934)
OHIO DNR Agalinis paupercula (Gray) Britt. var.
borealis Pennell
Agalinis paupercula Britton var. borealis Pennell
ITIS Agalinis paupercula var.
borealis Pennell
Informed by: Nomenclators and generally NOT by taxonomy

Taxonomic synonym: A single concept may reference multiple names (or it may not)
Informed by: Taxonomic Sources

Synthesized synonymy: A bit of everything
Informed by: Algorithm, Nomenclators,Taxonomic Sources

Another example
Aedes calopus | Stegomyia Aegypti | Culex aegypti

Synonymy: Inclusive
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Classifications
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Catalogue of Life Integrated Classification
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Annotated Checklist of the Neuroptera - Mansell 2006
NCBI Taxonomy
Cladograms, Phylograms
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Phylogenetic representations
Regional lists
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Cetacea of the Hebrides
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Flora of China
Thematic Lists
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2006 IUCN RedList of Threatened and Endangered Species
WoRMS/OBIS Marine Taxa
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100 of the World’s Worst Invasive Alien Species (in GISIN)

Implications for data retrieval
Frost 2005 AMNH
• Notopthalmus viridescens
• Triturus viridescens
• Notopthalmus viridescens
• Notophthalmus viridescens
• Notophthalma viridescens
• Diemyctylus viridescens
• Triton viridescens
• Molge viridescens
• Diemyctylus minatus viridescens
• Triturus viridescens dorsalis
• Diemyctylus viridescens dorsalis
• Notophthalmus viridescens dorsalis
• … 24 others
Dolbe 2004
• Notopthalmus viridescens viridescens
• Triturus viridescens
• Notopthalmus viridescens
• Notophthalmus viridescens
• Notophthalma viridescens
• Diemyctylus viridescens
• Triton viridescens
• Molge viridescens
• Notophthalmus viridescens dorsalis
• Triturus viridescens dorsalis
• Diemyctylus viridescens dorsalis
• Notophthalmus viridescens louisianensis

Homography (Homonymy)
A single name may refer to multiple concepts

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Homographs
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Virginia (the state) & Virginia Baird & Girard 1853 (the genus)
Tumor (cancer) & Tumor Huang in Huang Dawei 1990
Informed by: Algorithms/Lexicons (word sense disambiguation)
Homonym
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Agathis montana (the conifer) & Agathis montana (the wasp)
Wagneria Meladze 1967 & Wagneria Heilprin 1887 & 12 other Wagneria
Informed by: Nomenclators and Taxonomists
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Nomenclators establish the factual basis of homonyms and partial disambiguation method
Taxonomy provides a disambiguation method
Taxon Concept (Polysemes)
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Gorilla gorilla Wilson and Reeder 1992 vs Gorilla gorilla Groves 2003
Informed by: Taxonomic opinion via monographs, floras, faunas, derived lists

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The names problem is inherent to all taxon data
We need a Global Taxonomic Resource
Needs to treat all names
Support multiple taxonomic opinion
Depends on many different source data
The Informatics sum is more than the content parts
Can only work in a federated enviroments
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Requires communal exchange data standards communications protocols

Current GBIF Taxonomic Infrastructure
(ECAT)
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Catalogue of Life
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International Plant Names Index (IPNI)
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Index Fungorum
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Is not enough

EXPAND to Global Taxonomic Infrastructure
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Mobilize wide array of “checklist resources”
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Promote the use of nomenclatoral GUIDS in all taxonomic checklists
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Enable synthesis of resources
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Enable informatics web services

Address Synonymy
Wider access to, and explicit classing of synonyms
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Access to multiple lexical grouping algorithms
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Access to, and support of, development of nomenclators
Promote the use of nomenclatoral GUIDS in all taxonomic checklists
More Taxonomic, Regional, Thematic checklists
Comprehensive Vernacular Names catalogue

Address Homography, Polysemy
Rapid cataloguing of homography
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Access to multiple lexical grouping algorithms
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Catalogue and classify all genera
Development of multiple disambiguation methods
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Standardized representation of taxon concepts
Development of taxon concept comparators
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Explicit assertions of concept relations

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As a consumer of taxonomic data resources
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As a consumer of name services
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As a provider of taxonomic metadata
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Increased interoperability

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Data portal: www.gbif.net
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