GBIF ChecklistBank and Backbone building
•
0 likes•178 views
The document discusses GBIF's Checklist Bank, which indexes taxonomic checklists to provide a single, consistent taxonomy or "backbone" for metrics, search, and mapping on GBIF. It summarizes the goals of indexing checklists from various sources using uniform terms, providing a source for GBIF's taxonomic backbone by linking names across checklists, and offering a name matching service. It also provides statistics on the number of indexed checklists and names in the backbone.
Recommended
More Related Content
Similar to GBIF ChecklistBank and Backbone building
Similar to GBIF ChecklistBank and Backbone building (20)
Recently uploaded
Recently uploaded (20)
GBIF ChecklistBank and Backbone building
- 1. GBIF Checklist Bank Checklist index, name matching & backbone building Markus Döring, GBIF Uppsala, October 2016
- 2. Organizing Occurrences • GBIF needs a single, consistent taxonomy • for metrics, search, maps • considerable variation in higher taxa • synonymies can be very large • Catalogue of Life largest single source • ~90% of GBIF occurrence records (thanks to birds) • ~60% of GBIF occurrence names (35% in 2010) • GBIF needs to assemble a taxonomy • originally merged (noisy) names found in occurrences. Resulted in lots of duplicates • improved by stitching together checklist datasets • include fossil names Cronquist classification Mimosaceae: 3,200 species Caesalpiniaceae: 2,000 species Fabaceae: 14,000 species “Modern” classification Fabaceae: 19,200 species Mimosoideae: 3,200 species Cæsalpinioideae: 2,000 species Faboideae: 14,000 species
- 3. Checklist Bank Goals • Index to “checklists”, i.e. full taxonomies & simple name lists • uniform API • standard use of DwC terms • Source for GBIF Backbone names • better quality than using GBIF occurrence names • stores & serves also the GBIF Backbone in the same way • Name matching service for GBIF Backbone • for dirty occurrence names • for cleaner checklist names • Link same names across checklists
- 4. Indexed Checklists Oct 2016 16.519 datasets registered 22.1 million name records Plazi (14.861), Scratchpads (998), Pensoft (217), CoL GSDs (160)
- 5. Backbone Sources • Catalogue of Life • GBIF Algae Classification • ION Taxonomic Hierarchy • World Register of Marine Species • Catalogue of Afrotropical Bees • EDIT Cichorieae • World Typhlocybinae database • Spinnengids • Afromoths • True Fruit Flies of the Afrotropical Region • Fauna Europaea • Euro+Med Plantbase • Beetles (Coleoptera) of Canada and Alaska • The Clements Checklist • IOC World Bird Names • Nomenclators • IPNI • Index Fungorum • Prokaryotic Nomenclature Up- to-date • ICTV Master Species List • Publisher • Species Files • Diversity Taxon Names • Plazi articles • Mammal Species of the World • Dyntaxa - Svensk taxonomisk databas • Artsnavnebasen • GRIN Taxonomy • Flora of Brazil • Database of Vascular Plants of Canada • Plant List • ITIS • TAXREF • The National Checklist of Taiwan • Endemic species in Taiwan • IRMNG • Index Fungorum • Paleobiology Database https://github.com/gbif/checklistbank/blob/master/checklistbank-nub/nub-sources.tsv
- 6. Backbone Building • Overlay prioritised sources • start with Catalog of Life • primary source defines status • create new name if kingdom, canonical name & authorship do not exist in current nub • Ignore source name if … • not a major Linnean rank (infraspecifc ranks are included) • higher ranks above family (configurable per source, CoL for higher taxa) • status conflicts with previously encountered status • hybrid formula, cultivar, candidatus or placeholder names !!! • Rebuild backbone every 4 month Catalogue of Life Fauna Europaea GRIN Mammal Species World Specimens 8000 Species Lists 10s of taxonomic resources Me
- 7. Backbone Metrics accepted by kingdom Animalia Archaea Bacteria Chromista Fungi Plantae Protozoa Viruses Other 100 10.000 1.000.000 names by status total accepted doubtful synonym homotypic synonym heterotypic synonym proparte synonym 100 10.000 1.000.000 accepted by rank kingdom phylum class order family genus species subspecies variety form unranked 100 10.000 1.000.000 2.693.192 1.937.869 439.243 2.525.274 401.693 22.165 1.695.892 554.581 202.943 92.247 name by various catalogue of life IRMNG IPNI basionym basionym placeholder basionym derived ex-author synonym proparte 100 10.000 1.000.000 3.175.925 733.720 114.127 458.189 638.146 5.307.978
- 8. Backbone Name Matching • Fuzzy mode for occurrence names • fuzzy name match • fuzzy classification match • allow higher rank matches, e.g. to genus or class only http://api.gbif.org/v1/species/match?kingdom=Plantae&name=Oenante • Strict mode for checklist names • kingdom match required • rank match required • canonical name match required • allow double letters and few common misspellings (ll->l, y->i, rh->r) • gender neutral epithet matching • lose authorship comparison http://api.gbif.org/v1/species/match?strict=true&kingdom=Plantae&name=Oenanthe L.
- 9. Name Matching Issues • Homonyms • legal cross code homonyms • synonyms with different authors • monomials at different rank difficult but solved !!! • Name not in backbone • regular gaps (especially fossils, molluscs & insects) • non Linnean rank (e.g. subclass Vertebrata) • No Taxon concept matching • concepts hard to define • type specimen information rare & not well structured • synonyms & included children good candidate for comparison • tough for occurrences. No taxonomies & hardly any taxonomic references used
- 10. Storing Name Matches • Avoid exponential link growth • thousands of datasets possible • store links to backbone only • allows all crosswalks in 2 steps if backbone is complete Abies alba Mill. Abies alba Miller Abies alba Abies alba Mill. Abies alba Mill. Abies alba Mill. Abies alba Mill. Abies alba Mill. Abies alba Miller Abies alba Abies alba Mill. Abies alba Mill. Abies alba Mill.
- 11. Backbone Identifier • Name identifier, not accepted taxa • Status, synonyms, classification, included taxa, description or types are ignored • Unchanged for lexical group of name strings • Macrozamia platyrhachis F. M. Bailey • Macrozamia platyrhachis • Macrozamia platyrachis Bailey • Uses strict matching service to group name strings • Stable over different backbone versions • Deleted names still resolve
- 12. Backbone Assembling Animalia Archaea Bacteria Chromista Fungi Plantae Protozoa Viruses incertae sedis • Nub build starts with 8 kingdoms
- 13. Backbone Assembling Plantae Magnoliophyta Magnoliopsida Asterales Asteraceae Helianthus L. Helianthus anuus L. • Catalog of Life is added • Defines higher classification Plantae Magnoliophyta Magnoliopsida Asterales Asteraceae Helianthus L. Helianthus anuus L.
- 14. Backbone Assembling Plantae Magnoliophyta Magnoliopsida Asterales Asteraceae Helianthus L. Helianthus anuus L. Cichorium Cichorium intybus L. • Missing genera are created • Tribe is ignored Asteraceae Cichorieae Lam & DC. [tribe] Cichorium intybus L.
- 15. Backbone Assembling Plantae Magnoliophyta Magnoliopsida Asterales Asteraceae Helianthus L. Helianthus anuus L. Cichorium Linneaus Cichorium intybus L. = C. balearicum Porta = C. byzantinum Clementi • Synonyms respect authors • Author match very loose • Existing genus author updated Plantae Asteraceae Cichorium Linneaus Cichorium intybus Linneaus = Cichorium balearicum Porta = Cichorium byzantinum Clem. = Cichorium byzantinum Clementi
- 16. Backbone Assembling Plantae Magnoliophyta Magnoliopsida Asterales Asteraceae Helianthus L. Helianthus anuus L. Cichorium L. Cichorium intybus L. = C. balearicum Porta = C. byzantinum Clem. • Prefer authors from nomenclators Asteraceae Cichorium L. Cichorium byzantinum Clem.
- 17. Backbone Assembling Asteraceae Helianthus L. Helianthus anuus L. Agoseris Agoseris apargioides (Less.) Greene = A. maritima Eastw. A. a. var. eastwoodiae (Fedde) Munz A. a. var. maritima (E. Sheld.) Baird Cichorium L. Cichorium intybus L. = C. balearicum Porta = C. byzantinum Clem. • Infraspecific names included Asteraceae Agoseris apargioides (Less.) Greene = A. maritima Eastw. A. a. var. eastwoodiae (Fedde) Munz A. a. var. maritima (E. Sheld.) Baird
- 18. Backbone Assembling Asteraceae Helianthus L. Helianthus anuus L. Agoseris Agoseris apargioides (Less.) Greene = A. maritima Eastw. A. a. var. eastwoodiae (Fedde) Munz A. a. var. maritima (E. Sheld.) Baird Agoseris eastwoodiae Fedde Agoseris maritima E. Sheld. Cichorium L. Cichorium intybus L. = C. balearicum Porta = C. byzantinum Clem. • Other source treats them as species • Same canonical maritima allowed twice - author different Asteraceae Agoseris eastwoodiae Fedde Agoseris maritima E. Sheld.
- 19. Final Cleanup - Basionyms Asteraceae Helianthus L. Helianthus anuus L. Agoseris Agoseris apargioides (Less.) Greene = A. maritima Eastw. A. a. var. eastwoodiae (Fedde) Munz = Agoseris eastwoodiae Fedde A. a. var. maritima (E. Sheld.) Baird = Agoseris maritima E. Sheld. Cichorium L. Cichorium intybus L. = C. balearicum Porta = C. byzantinum Clem. • Finally basionyms are detected • by terminal epithet & author within a family • skip epithets that are used in multiple original names • Only 1 accepted per group • the name from the most trusted source stays
- 20. Final Cleanup - Autonyms Asteraceae Helianthus L. Helianthus anuus L. Agoseris Agoseris apargioides (Less.) Greene = A. maritima Eastw. A. a. var. apargioides A. a. var. eastwoodiae (Fedde) Munz = Agoseris eastwoodiae Fedde A. a. var. maritima (E. Sheld.) Baird = Agoseris maritima E. Sheld. Cichorium L. Cichorium intybus L. = C. balearicum Porta = C. byzantinum Clem. • Create missing autonyms