Taxon Services

Introduction to Taxon Services
Data Cleaning/Publishing workshop
Empowering Biodiversity Research

Transcript

1. TAXON SERVICES TAXON SERVICES Data cleaning/publishing Workshop 9th November 2015 André Heughebaert Belgian Biodiversity Platform
2. SUMMARY SUMMARY 1. 2. 3. 4. 5. 6. 7. Scientific names Nomenclature(s) Taxonomy Web pages Web services Demo Hands-on
3. SCIENTIFIC NAMES SCIENTIFIC NAMES Binomial names in latin : genus species author, year Homo sapiens Linnaeus, 1758
4. SCIENTIFIC NAMES SCIENTIFIC NAMES Scientists believe that Earth is home to about 8.7 million different forms of life, and of those only about 1.8 million have been identified.
5. SCIENTIFIC NAMES SCIENTIFIC NAMES Acaridae Ewing & Nesbitt, 1942 Acarus nidicolus Griffiths, 1970 Accipiter cirrocephalus subsp. cirrocephalus Accipiter madagascariensis J. Verreaux, 1833 Acmaea pustulata Helbling, 1779 Acmaeodera (Acmaeodera) revelierei Mulsant & Rey, 1859 Acmaeoderella (Carininota) flavofasciata (Piller & Mitterpache Acmaeoderella (Carininota) flavofasciata placida (Baudi, 1870) Well formated names? Existing names? Accepted names?
6. NOMENCLATURE(S) NOMENCLATURE(S)
7. ALL SORT OF NAMES ALL SORT OF NAMES valid (Animalia, Protozoa, Bacteria, and Archaea) or accepted (Plantae, Chromista, and Fungi) invalid (Animalia, Protozoa, Bacteria, and Archaea): homonym & junior synonymjunior homonym, junior synonym, misapplied, nomen dubium, nomen oblitum, original name/combination... or not accepted (Plantae, Chromista, and Fungi): database artifact, homonym (illegitimate), horticultural, invalidly published, nomen nudum, invalidly published, other, misapplied, orthographic variant (misspelling)...
8. TAXONOMY TAXONOMY Catalog of Life consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.6 million species. It integrates data from more than 150 species databases. COL COL
9. TAXONOMY TAXONOMY GBIF Backbone holds 2.5 million Species and 4.4 million Taxa. GBIF GBIF
10. TAXONOMY TAXONOMY PESI Pan-European Species directories Infrastructure (aka EU-NOMEN) holds 300.000+ Species and 450.000+ Taxa and 190.800 vernaculars names in 117 languages. ...and much more taxonomical databases related to projects, regions, countries, habitats, taxonomical groups... PESI PESI
11. WEBPAGES FOR HUMANS WEBPAGES FOR HUMANS Human readable responses(HTML) to human (click) requests.
12. WEBPAGES FOR HUMANS WEBPAGES FOR HUMANS
13. WEBSERVICES FOR MACHINES WEBSERVICES FOR MACHINES Machine readable responses(JSON/XML) to machine requests.
14. WEBSERVICES FOR MACHINES WEBSERVICES FOR MACHINES HTTP Request: HTTP Response: http://api.gbif.org/v1/species/match?name=milvus%20milvus {"usageKey":5229168,"scientificName":"Milvus milvus (Linnaeus, "canonicalName":"Milvus milvus", "rank":"SPECIES","status":"AC "confidence":100,"matchType":"EXACT","kingdom":"Animalia","phy "order":"Accipitriformes","family":"Accipitridae","genus":"Mil "kingdomKey":1,"phylumKey":44,"classKey":212,"orderKey":719114 "synonym":false,"class":"Aves"}
15. INVOKING WEBSERVICES INVOKING WEBSERVICES require 'rubygems' require 'net/http' require 'CSV' require 'JSON' require 'pp' def check_data(inpath, outpath) tags= ["scientificName", "type","genusOrAbove", "specificEpi CSV.open(outpath, "wb", :headers => true, :col_sep =>";") do # :headers option indicates the file has a header row out << tags CSV.foreach(inpath, :headers => true, :col_sep => ";") do name=row['scientificname'] name=name.gsub(/[ïí]/, 'i') name=name.gsub(/[éèë]/, 'e')
16. DEMO DEMO 1. Name Parsing GBIF 2. Name Search GBIF Catalogue of Life PESI Using both browser(webpage) and API(webservices).
17. HANDS-ON HANDS-ON TOOLS YOU NEED TOOLS YOU NEED any web browser any text editor your programing language: Python, Ruby, R, Java... (or REST client)
18. REFERENCES REFERENCES ECAT Name parser GBIF Species search CoL PESI Taxamatch
19. QUESTIONS? QUESTIONS? Made with - HTML Presentations made easy Belgian Biodiversity Platform a.heughebaert@biodiversity.be reveal.js