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Anchoring Biodiversity Information: From Sherborne to the 21st century and beyond
Biodiversity Informatics – GBIFs role in linking information through scientific names.
David RemsenSenior Programme OfficerGlobal Biodiversity Information Facility (GBIF)
28 October 2011
BIODIVERSITY INFORMATICS
“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.”
PRIMARY BIODIVERSITY DATA
PRIMARY BIODIVERSITY DATA
Primary Biodiversity Databases
GBIF ISA FEDERATED NETWORK
A “network of networks”
COMMON COMMUNICATIONSREGISTRY
GLOBAL DATA INDEX
310,132,149 data records9,290 datasets
6,112,683 “names”
DATA PORTAL
DISCOVERY
ACCESS
Use of Primary Biodiversity Data
Build Provisional Species Lists
Validate range maps
Predict species distributon
Change in suitability for cultivating common bean across the world, from present to 2020, showing a global loss in suitability, especially in Africa.
Predict distribution changes
CBD Access & Benefit Sharing (Nagoya) Protocol
Challenges to presentingTaxon-oriented data
Tealia crassicornis (Müller)
Urticina crassicornis (Müller)
Urticina felina (Linnaeus 1767)
Tealia felina, Tealia felina, Urticina crassicornis, Urticina columbiana, Tealia crassicornis, Urticina felina, Urticina coriacea, Stomphia churchiae, Rhodactinia crassicornis, Tealia lofotensis, Leiotealia spetsbergensis, Madoniactis lofotensis, Tealia tuberculata, Bolocera eques, Tealia greenii, Cereus coriaceus, Actinia felina, Bunodes crassicornis, Actinea tuberculata, Actinea coriacea, Actinia gemmacea, Actinia crassicornis, Actinia dævisii, Actinia coriacea, Actinia holsatica,
Gap in Synonymies
UNTRUSTWORTHY SCIENCE
Trochilidae
UNTRUSTWORTHY TAXONOMY
TRUSTED TAXONOMY
BETTER SCIENCE
Plantae Magnoliophyta Magnoliopsida Apiales Umbelliferae Oenanthe
Plantae Oenanthe Oenanthe
Plantae Magnoliophyta Magnoliopsida Apiales Apiaceae Oenanthe
? Orchidaceae Oenanthe
Animalia Chordata Aves Passeriformes Muscicapidae Oenanthe
Animalia Chordata Aves Passeriformes Turdidae Oenanthe
Unraveling Homonyms
Oenanthe
Difficult for user to interpret
Accurate search results
Yesterday
Today
Unraveling Homonyms
A need for nomenclators
Actinobacillus actimomycetemcomitansActinobacillus actimycetemcomitansActinobacillus actinmycetemcomitansActinobacillus actinomicetemcomitansActinobacillus actinomyActinobacillus actinomyceActinobacillus actinomycemcomitansActinobacillus actinomyceremcomitansActinobacillus actinomycetamActinobacillus actinomycetamcomitansActinobacillus actinomycetecomitansActinobacillus actinomycetemcmitansActinobacillus actinomycetemcomintansActinobacillus actinomycetemcomitance
Actinobacillus actinomycetemcomitansActinobacillus actinomycetemcomitantsActinobacillus actinomycetemcommitansActinobacillus actinomycetemocimitansActinobacillus actinomycetencomitansActinobacillus actinomycetumActinobacillus actinomyctemcomitansActinobacillus actinomyectomcomitansActinobacillus actinomyetemcomitansActinobacillus actinonmycetemcomitansActinobacillus actionomycetemcomitansActinobacillus actynomicetemcomitansActinobacillus antinomycetemcomitans
…and TaxaMatch
Agalinus paupercula borealisAgalinus pauperculum borealisAgalinis paupercula var. BorealisAgalinus pauperculum var. borealisAgalinus paupercula var. borealisAgalinus paupercula var. borealis PennellAgalinus paupercula Britton var. borealis PennellAgalinus paupercula (Gray) Britt. var. borealis PennellAgalinis paupercula (A.Gray) Britton var. borealis PennellAgalinus paupercula (Gray) Britton var. borealis (Pennell) Zenkert 1934
Issues of Orthography
Reconciling different forms of the same name
Parsing
Dictionaries
Rapidly mines names from literature
Effective Biodiversity Informatics requires
Taxonomic and nomenclatural authority files & services
• Classification to organise• Status to perpetuate proper
use• Synonymy (Objective and
Subjective) to group• Homonymy to disambiguate• Orthography for consistency
A GLOBAL NAMES ARCHITECTURE
Another federated network
• Global Resource Discovery• Uniform Access• Integration
• Consolidated nomenclatural index• Use
• Biodiversity Information Services