Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2
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Global Digital Infrastructure for biological nomenclature and taxonomy Ellinor Michel 1,2 Richard Pyle 2,3 Robert Guralnick 4 Jon Todd 1,2 1 The Natural History Museum, London UK 2 Int’l Committee on Bionomenclature 3 Bishop Museum, HI, USA 4 Univ of Colorado, Boulder, USA
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Global Digital Infrastructure for Biological Nomenclature and Taxonomy Ellinor Michel, Dep’t of Life Sciences, The Natural History Museum, London, UK, ([email protected]) Richard L. Pyle, Natural Sciences Dep’t, Bishop Museum, Honolulu, HI, USA Robert P. Guralnick, Dep’t of Ecology & Evolutionary Biology, Univ Colorado, Boulder, CO, USA Jon Todd, Dep’t of Earth Sciences, The Natural History Museum, London, UK, The future for interoperable scientific information is digital, yet scientific names, the handles for all biodiversity information, remain without an integrated system tied to published descriptions and museum type specimens. Descriptions and type specimens provide standards for the otherwise fluid concepts of biological taxa. We are working to unify the infrastructures for biological nomenclature across nomenclatural codes (including zoological (ICZN - http://iczn.org/), botanical (ICNafp - http://www.iapt-taxon.org/nomen/main.php) and bacterial (ICNB) codes) through the Global Names Architecture (GNA). Our initial focus is on animal names, as these comprise the largest component of metazoan biodiversity and ZooBank (zoobank.org) is the first code-related online nomenclatural registration system. Users are applied scientists in agriculture, medicine, veterinary science and climate change research; biodiversity researchers such as ecologists, physiologists; archives such as museums; the scientific publishing community – in short, all users of scientific names of organisms based on the work of taxonomists.
Transcript of Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2
Global Digital Infrastructure for
biological nomenclature and
taxonomy
Ellinor Michel1,2 Richard Pyle2,3
Robert Guralnick4
Jon Todd1,2
1The Natural History Museum, London UK 2Int’l Committee on Bionomenclature
3Bishop Museum, HI, USA4Univ of Colorado, Boulder, USA
THE LINNAEAN ENTERPRISE
(E.O. Wilson) ________
the task of identifying all of
Earth’s biodiversity
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.
- Grimaldi & Engel, 2005
Names and the information revolution
Note: they don’t say THE scientific name (i.e., singular)
Names, meanings and how to manage them
Image: Biodiversity Heritage LibraryImage: Wikimedia Commons
Carolus Linnaeus1707-1778
Images: Biodiversity Heritage Library
4,398 Species
Estimated 2-6 names for every valid (=currently considered definable and ‘real’) species
Equivalent of 359 volumes of Systema Naturae
Nomenclature Taxonomy
Type specimen
Is the objective physical standard for a name that anchors the name.
Type Principle Stabilizing biological names with a physical standard
… the type specimen
From Linnaeus’ Fish Collection held at the Linnean Society of London
From living animals to ….
Pomatomus saltator (Linnaeus 1766)
Nomenclatural Codes:
• Zoology• Botany• Bacteria
• Viruses• Cultivated
Plants
Type Specimen = NameStabilizing biological names with a physical standard
Gasterosteus saltatrix Linnaeus, 1766Pomatomus saltator (Linnaeus 1766)
Whole Organism✔Types for the Future
Organism Part✔Tissue Sample✔
PCR Product?DNA Sequence✗
DNA Extraction?
Whole Organism✔Types for the Future
Organism Part✔Tissue Sample✔
PCR Product - reproduced?DNA Sequence
- derived & interpreted
✗
DNA Extraction?
Sequence data is a (usually high fidelity, fine granularity) representation of
molecules
DNA, RNA or proteins are single kinds of organismal data
Sequencing Type SpecimensData enrichment of existing types
✔
Types for the Future
Sequencing ‘Epitypes’(‘botanical’ term, new specimens from type locality, etc.)
Risk of losing stability
?
‘Type Sequence’✗
A name = ‘computer’ readable code
that links information
FFF7160A-372D-40E9-9611-23AF5D9EAC4C
Hard for a human;Easy for a computer
Easy for a human;Hard for a computer
“Pomatomus saltator Linn.”
A name = ‘computer’ readable code
GenBank
HymenopteraNameServer
BDWB
CalPhotos
Namesconnecting information
ToL Where AreBiodiversity Data?
GenBank
HymenopteraNameServer
BDWB
CalPhotos
“Pomatomus saltator”
ToL “Pomatomus saltatrix”
“Pom. salt.”
“P. saltator”
“Pomatomus saltator (Linnaeus 1766)”
“Pomatomus saltatrix (L.)”
“Gasterosteus saltatrix Linn., 1766”
“Gasterosteus saltator Linnaeus”
“G. saltator L.”
“Gaſteroſteus Sallatrix”
“P. saltator”“G. saltatrix”
“Pomatomus mediterraneus (Rafinesque, 1810)”
“Pomatomus pallasii (Eichwald, 1831)”
“Pomatomus conidens (Castelnau, 1861)”
“P. nalnal (Rochebrune, 1880)”
“Pomatomus tubulus (Saville-Kent, 1893)”
“Pomatomus heptacanthus (Lacépède, 1801)”“P. skib Lacépède, 1802”
“P. lophar (Suckow)”
A Global Names Architecture
• Taxon Names are the fundamental link among virtually all biodiversity information
• Biodiversity Information relates to species concepts, but data resources are usually tied to text-string names
• Text-string names are difficult to cross-link due to spelling variations, different genus-species combinations, homonyms, synonyms, etc.
• Linking text-string names to concepts requires source-based (literature-based) approach
• The key challenge is to cross-link thousands of biodiversity datasets through taxon concepts, using only text-string names
A Global Names ArchitectureRationale
Funding & Support (2007- to date)
National Science Foundation BiSciCol (DBI-0956415) GNA (DBI-1062441)Encyclopedia of LifeGBIFPBIN / NBIIVarious others (e.g., NOAA, other NSF projects)More NSF & EU Proposals in Process
Partners & Governance
CoL (Species2000 / ITIS), EOL, BHL, GBIF, IPNI, Index Fungorum, ICZN / ZooBank, Landcare Research, MOBOT / Tropicos, Bishop Museum, WHOI, IRMNG, PESI, ALA (and numerous others)
Global Names Architecture Advisory Panel (GNAAP)
A Global Names Architecture
What GNA is NOT
Yet another database
A Global Names Architecture
What GNA IS (…intended to be…)
Easy for a human;Hard for a computer
“Pomatomus saltator Linn.”
Name or Text-string name
What GNA is NOT
A Global Names Architecture
Yet another database
What GNA IS (…intended to be…)
FFF7160A-372D-40E9-9611-23AF5D9EAC4C
Hard for a human;Easy for a computer
Easy for a human;Hard for a computer
“Pomatomus saltator Linn.”
Name or Text-string name UUID or GUID (Universally or Globally Unique Identifier)
Data Components
A Global Names Architecture
Global Names Index (GNI)• Database and services
optimized for taxon names represented as raw text strings. (“Dirty Bucket”)
• ~17+ million text strings
• Parsing Services
• Lexical Grouping
• Links back to sources
• Developed at Woods Hole
Data Components
Global Names Usage Bank(GNUB)• Database and services
optimized for taxon names represented as “curated” Taxon Name Usages.(“Clean Bucket”)
• >70K Agents
• >73K References
• >523K Taxon Name Usages(>186K Protonyms)
• Developed at Bishop Museum
A Global Names Architecture
Global Names Index (GNI)• Database and services
optimized for taxon names represented as raw text strings. (“Dirty Bucket”)
• ~17+ million text strings
• Parsing Services
• Lexical Grouping
• Links back to sources
• Developed at Woods Hole
Taxon Name Usage (TNU)A usage of a taxon name within the context of a Reference.
Protonym (≈Basionym)A usage of a taxon name representing the Code-Compliant “creation” of a new name.
ReferenceAny static document source (Publication; Specimen Determination Label; Field Notes, Correspondence, etc.).
tnuID Reference NameString Rank
123 Fowler & Bean, 1930:181 Belonoperca Genus
ProtonymID
123
ValidUsageID
123
234 Fowler & Bean, 1930:182 chabanaudi Species 234 234
ParentUsageID
123
tnuID Reference NameString Rank
123 Fowler & Bean, 1930:181 Belonoperca Genus
ProtonymID
123
ValidUsageID
123
234 Fowler & Bean, 1930:182 chabanaudi Species 234 234
ParentUsageID
123
567 Baldwin & Smith, 1998:325 Diploprionini Tribe 876
678 Baldwin & Smith, 1998:325 Epinephelinae Subfamily 765
789 Baldwin & Smith, 1998:325 Serranidae Family 654
987 Baldwin & Smith, 1998:325 Teleostei Order
... ... ... ...
567
678
789
678
789
987
345 Baldwin & Smith, 1998 pylei Species 345 345 456
456 Baldwin & Smith, 1998:325 Belonoperca Genus 123 456 567
That’s cool…
(But how does it help?)
“Pomatomus saltator Linn.”
A Global Names Architecture
“Pomatomus saltator Linn.”
Global Names Architecture
Pomatomus | saltator | Linn.
FFF7160A-372D-40E9-9611-23AF5D9EAC4C
4D4EC609-D241-411E-BA54-DD4E0530E494Pomatomus Lacépède, 1802
3437CC89-8D7F-4D2C-9813-F64EFA22FDD3Pomatomus Risso, 1810
A Global Names Architecture
“Pomatomus saltator Linn.”
Global Names Architecture
Pomatomus | saltator | Linn.
FFF7160A-372D-40E9-9611-23AF5D9EAC4C
Gasterosteus saltatrix Linnaeus, 1766
A Global Names Architecture
GNIE FFF7160A-372D-40E9-9611-23AF5D9EAC4C
Lopharis mediterraneus Rafinesque, 1810 A3BE1320-806C-4585-B5FE-5CAB2FB5DDF9 8C7E3E5A-3B36-4D23-AA0A-035F726DFBCD 1
Pomatomus mediterraneus (Rafinesque, 1810) 4D4EC609-D241-411E-BA54-DD4E0530E494 8C7E3E5A-3B36-4D23-AA0A-035F726DFBCD 1
Pomatomus pallasii (Eichwald, 1831) 4D4EC609-D241-411E-BA54-DD4E0530E494 969F0B46-2FD1-42BC-A5C9-22D2410076B3 1
Sypterus pallasii Eichwald, 1831 288B17D4-3133-4893-8998-74FD115DBB31 969F0B46-2FD1-42BC-A5C9-22D2410076B3 1
Pomatomus conidens (Castelnau, 1861) 4D4EC609-D241-411E-BA54-DD4E0530E494 64873DE7-934E-4603-8815-2EA90B66482B 1
Temnodon conidens Castelnau, 1861 67D18558-763F-48B2-8F5A-44DBCF827931 64873DE7-934E-4603-8815-2EA90B66482B 1
Gonenion serra Rafinesque, 1810 95CA3EFA-4A11-4C71-9325-5926652E6E84 DC567BAA-2C8B-4065-9A9F-4E91441ACC9A 1
Pomatomus serra (Rafinesque, 1810) 4D4EC609-D241-411E-BA54-DD4E0530E494 DC567BAA-2C8B-4065-9A9F-4E91441ACC9A 1
Pomatomus tubulus (Saville-Kent, 1893) 4D4EC609-D241-411E-BA54-DD4E0530E494 25DE7CC4-E19F-4ADB-A590-582951E60AB1 1
Temnodon tubulus Saville-Kent, 1893 67D18558-763F-48B2-8F5A-44DBCF827931 25DE7CC4-E19F-4ADB-A590-582951E60AB1 1
Pomatomus nalnal (Rochebrune, 1880) 4D4EC609-D241-411E-BA54-DD4E0530E494 C33CA532-4060-4710-9533-7756F66B86C7 1
Sparactodon nalnal Rochebrune, 1880 921EE8B0-5C5C-45EB-BCDB-CD2AA724229D C33CA532-4060-4710-9533-7756F66B86C7 1
Pomatomus pedica Whitley, 1931 4D4EC609-D241-411E-BA54-DD4E0530E494 86ADEBD2-8F52-492E-9792-946B1CCFBFA8 2
Perca lophar Forsskål, 1775 85AA15EB-BF9B-44D6-9DF2-4BE36017768C 00AB9C96-5FCA-4358-98E4-A186D8DE5490 1
Pomatomus lophar (Forsskål, 1775) 4D4EC609-D241-411E-BA54-DD4E0530E494 00AB9C96-5FCA-4358-98E4-A186D8DE5490 1
Cheilodipterus heptacanthus Lacépède, 1801 FBDC898C-F1EA-4768-85B0-521417959096 F848129B-E72A-4C84-918B-B98BEA1FF7AC 1
Pomatomus heptacanthus (Lacépède, 1801) 4D4EC609-D241-411E-BA54-DD4E0530E494 F848129B-E72A-4C84-918B-B98BEA1FF7AC 1
Pomatomus skib Lacépède, 1802 4D4EC609-D241-411E-BA54-DD4E0530E494 EC88117C-C83F-4088-8347-BF9C0491D874 2
Pomatomus sypterus (Pallas, 1814) 4D4EC609-D241-411E-BA54-DD4E0530E494 7CFC2F1F-1B81-4F03-9B31-E4CC81E20185 1
Scomber sypterus Pallas, 1814 86791AEA-32C5-4492-96B8-8273AB440742 7CFC2F1F-1B81-4F03-9B31-E4CC81E20185 1
Chromis epicurorum Gronow in Gray, 1854 EBF02DF4-0D67-4865-AFA1-A71FCB56BBBA 4A4BFEAE-ACC5-4E12-98E1-F89B37896193 1
Pomatomus epicurorum (Gronow in Gray, 1854) 4D4EC609-D241-411E-BA54-DD4E0530E494 4A4BFEAE-ACC5-4E12-98E1-F89B37896193 1
Anthias lophar Suckow, 1799 4E43AEB3-D6EB-478A-9039-46F8370C4F93 E28B3C39-6412-4F30-BED1-FFA67225EDC8 1
Pomatomus lophar (Suckow, 1799) 4D4EC609-D241-411E-BA54-DD4E0530E494 E28B3C39-6412-4F30-BED1-FFA67225EDC8 1
Gasterosteus saltatrix Linnaeus, 1766 97CE20CD-4D6E-4A59-8266-CD161B5521FB FFF7160A-372D-40E9-9611-23AF5D9EAC4C 1
Gaſteroſteus Sallatrix Linnaeus, 1766 97CE20CD-4D6E-4A59-8266-CD161B5521FB FFF7160A-372D-40E9-9611-23AF5D9EAC4C 1
Pomatomus saltator (Linnaeus, 1766) 4D4EC609-D241-411E-BA54-DD4E0530E494 FFF7160A-372D-40E9-9611-23AF5D9EAC4C 16
Pomatomus saltatrix (Linnaeus, 1766) 4D4EC609-D241-411E-BA54-DD4E0530E494 FFF7160A-372D-40E9-9611-23AF5D9EAC4C 35
79 Taxon Name Usages
Homotypic Synonyms
Heterotypic Synonyms
Genus Protonym UUID Species Protonym UUID Refs.
California Academy
of Sciences
AnimalBase
DEncyclopedia of Life
Marine Species Identification
Portal
DCatalog of Life
D
FishBase
D
WoRMS
D
ITIS
D
IRMNG
D
GBIF
California Academy
of Sciences
BHL
DAnimalBase
Amphibian Species of the World
DHymenoptera
Online
D
FishBase
D
IPNI
GenBank
HymenopteraNameServer
BDWB
CalPhotos ToL
FFF7160A-372D-40E9-9611-23AF5D9EAC4C
A Global Names Architecture
ToL
GenBank
HymenopteraNameServer
BDWB
CalPhotos
FFF7160A-372D-40E9-9611-23AF5D9EAC4C
A Global Names Architecture
Current Numbers- 1,236 Contributors- 70,404 Agents (Authors)- 73,779 References
- 8,547 Journals- 4,302 Books- 2,205 Book Sections- 51,205 Articles- 7,520 Other
- 523,700 Taxon Name Usages- 185,772 Protonyms
Scaling Content
~2M Species~5-10M Protonyms~50M Name-Strings?~100M’s TNUs???
Bulk Import- Sherborn’s Index Animalium (7,700+ References, 430K TNUs)- Hymenoptera Name Server- Systema Dipterorum (35K References, 130K TNUs)- Dozen+ other nomenclator databases- BHL (3,400 Journals, 55K Books, 100’sK Articles)
Publication Workflow (Pensoft, Zootaxa, Others)
Global
Names
Usage
Bank
BHL scanned text is processed to discover taxon names in Global Names Index.
Taxon names in GNI are anchored to Protonyms in GNUB.
BHL References cross-linked to Protonyms to
generate Taxon Name Usages.
Nomenclature Taxonomy
Type specimen
But we all know that some names aren’t simple
• Sometimes name strings have multiple meanings
• In these cases a name string cannot act as a taxon-identifier without knowing how it has been interpreted
Taxonomy
In birds there are many allopatric subspecies and different authorities interpret inclusiveness of taxa in different ways (= different taxon concepts)
Different taxon concepts identified with unique IDs (UUIDs)
• Taxon Names are the fundamental link among virtually all biodiversity information
• Biodiversity Information relates to species concepts, but data resources are usually tied to text-string names
• Text-string names are difficult to cross-link due to spelling variations, different genus-species combinations, homonyms, synonyms, etc.
• Linking text-string names to concepts requires source-based (literature-based) approach
• The key challenge is to cross-link thousands of biodiversity datasets through taxon concepts, using only text-string names
A Global Names ArchitectureConclusions
Thanks!
Nomenclature Taxonomy
Questions?
