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Plant names: obstacles and solutions

Plant names: obstacles and solutions. to accessing information about plants. Bob Allkin, Royal Botanic Gardens Kew, UK. Talk structure. What is a scientific plant name? Names as obstacles to accessing data Examples of impact Resources / standards available New integrating initiatives

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Plant names: obstacles and solutions

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  1. Plant names:obstacles and solutions to accessing information about plants Bob Allkin, Royal Botanic Gardens Kew, UK

  2. Talk structure • What is a scientific plant name? • Names as obstacles to accessing data • Examples of impact • Resources / standards available • New integrating initiatives • Moving forward – what are your needs?

  3. What is a scientific name? • Genus name (in Latin) • Species name (in Latin) • Author e.g. “Hocus pocus Bob” • Publication must follow:International Code of Botanical Nomenclature (ICBN) • include a diagnostic description of plant (in latin) • cites “type” specimen(s) - fixes identity of name for eternity • respect priority of existing names Beware: the Code evolves! • established 1753; revised every 6 yrs: Tokyo 1996; St Louis 2000; Vienna 2006

  4. Q1: How many plants are there? • New plants being discovered (4 to 6K scientific names published / yr) • No authoritative central reference c. 0.35 million flowering plants (one botanists educated guess) Q2: How many names are there? • > 1.5 million scientific plant names published • > 4 million “names” incl. common misspellings i.e. lots more names than plants!

  5. Structural Obstacles • Most plants have many names (synonyms) • The same binomial may be published by different authors (“Hocus pocus Bob” & “Hocus pocus John”) who refer to different plants (homonyms) • Names used in literature often refer to wrong plant (misapplied names) i.e. One plant may have many names & One name may refer to many plants

  6. Avoidable Obstacles: • Plant name authors are abbreviated in different ways – there IS a standard • “Noise” increases as names are copied • New errors introduced • Existing errors replicated • Information published about a plant cannot be verified unless specimen(s) are cited

  7. Saussurea costus (Falc.) Lips. has a rootwidely used in medicine – imported to EU So what does it look like?.... Google it!

  8. Searching with Accepted name 51 PubMed Records 215 GenBank Records

  9. Searching witha synonym 03 PubMed Records 14 GenBank Records

  10. Conclusions • Do not expect to find all information that is published using just one name • across the internet or • within a single information source • You will have to work hard to find all synonyms of a given plant

  11. Examples of impact • EU Health authority publish legislation (re herbal & poisonous plants) Several either meaningless (non existent names) or ambiguous (homonyms) • US & Japanese health authority lists: 20% plants names do not exist. 5%: plants recorded more than once – under different names. • World Bank funds multimillion $ forestry programme in NE Brazil local tree (“Ziziphus joazeiro Mart.”) has exciting potential 3 different species grown in the plots! • World Conservation Monitoring Centre (IUCN) maintain database70% of maintenance costs relate to entering, checking and reviewing plant names and distributions.

  12. Available resources / standards:1) Nomenclators Q1: Does name “Hocus pocus” exist? Q2: How should it be written? Q3: Where can I find the original publication? Q4: Do any homonyms exist? Q5: Who is/are the authors? International Plant Name Index http://www.ipni.org > Kew + Harvard + Australian Botanical Inst > 1.5 million published plant names (>96%) > 37,000 authors > 15,000 publications Target audience – systematists, db compilers

  13. Available resources / standards2) Checklists • coherent authoritative global list of plants (e.g. in a family) • consensus • index to ALL relevant names • resolves synonymy • provides further information e.g. geographical distribution, uses, etc Q1: What is the “accepted name” of this plant ? Q2: Are names ‘x’ and ‘y’ synonymous? Q3: How many plants are in this genus? Q4: How many plants are in this country? Q5: List all synonyms for this plant? Example: Kew’s World Checklist of Selected Plant Families – covers 150 plant families http://www.kew.org.uk/wcsp/ 45-50% complete

  14. Comparison of names in NCBI and Kew systems (106 families)

  15. Integrated Resources • 1) Global Strategy for Plant Conservation (CBD) • TARGET 1: A list of all plants by 2010 – facilitated by Kew. 60% complete Kew and Missouri work toward draft checklist + other data (www.iplants.org ) • Catalogue of Life (Sp2000 + ITIS) (www.sp2000.org) Servesexistingchecklists for all organisms (plants, animals, insects etc) Much of Kew’s checklist data served. Offers alternative / conflicting views • Global Biodiversity Information Framework (www.gbif.org )Servesspecimenrecords from collections worldwide Name catalogue served from “Catalogue of Life” • Encyclopedia of Life (www.eol.org) Species pages – coordinating existing knowledge (video/ text/ images etc) No additional name data. Use “Catalogue of Life” as backbone

  16. Moving forward:improving Kew’s plant name services • Tailored consultancies – for target groups • e.g. Medicinal Plants - WHO, EMEA, ICH • reporting on existing lists of plant names • validating, cleaning & completing name lists • building and maintaining subsets for focus groups • Designing & developing web services • automated responses to queries from other system / API • maintenance of name lists avoiding costs for users • subscription services • Seeking to develop partnerships with user groups • inform design of services / user needs • develop resource to meet specific demands

  17. Thanks for your attention! Questions? Ideas to pursue? PS Biodiversity Information StandardsTaxonomic Databases Working Group TDWGhttp://www.tdgw.org/ Ontologies / Vocabularies / Schemas / LSIDs

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