plant names: obstacles and solutions to access information about plants
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Post on 21-May-2015
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Plant names:
obstacles and solutions
Bob Allkin, Royal Botanic Gardens Kew, UK
to accessing information about plants
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Talk structure
1. What is a scientific plant name?
2. Names as obstacles to accessing data
3. Examples of impact
4. Resources / standards available
5. New integrating initiatives
6. Moving forward – what are your needs?
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a) Genus name (in Latin)
b) Species name (in Latin)
c) Author e.g. “Hocus pocus Bob”
d) 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
What is a scientific name?
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Q1: How many plants are there?• New plants being discovered
(4 to 6K scientific names published / yr)
• No authoritative central referencec. 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!
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Structural Obstacles1. Most plants have many names (synonyms)
2. The same binomial may be published by different authors (“Hocus pocus Bob” & “Hocus pocus John”) who refer to different plants (homonyms)
3. 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
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Avoidable Obstacles:
1. Plant name authors are abbreviated in different ways – there IS a standard
2. “Noise” increases as names are copieda. New errors introducedb. Existing errors replicated
3. Information published about a plant cannot be verified unless specimen(s) are cited
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Saussurea costus (Falc.) Lips. has a root widely used in medicine – imported to EU
So what does it look like?.... Google it!
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51 PubMed Records
215
GenBank Records
Searching with Accepted name
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Searching witha synonym
03 PubMed Records
14
GenBank Records
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Conclusions1. Do not expect to find all information that
is published using just one name across the internet or within a single information source
2. You will have to work hard to find all synonyms of a given plant
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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.
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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
Available resources / standards:1) Nomenclators
> Kew + Harvard + Australian Botanical Inst> 1.5 million published plant names (>96%)> 37,000 authors > 15,000 publications
Target audience – systematists, db compilers
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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?
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
Available resources / standards2) Checklists
Kew’s World Checklist of Selected Plant Families – covers 150 plant familieshttp://www.kew.org.uk/wcsp/ 45-50% complete
Example:
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4% 2%
94%
Names in both systems
Names in NCBI alone
Names in Kew alone
Comparison of names in NCBI and Kew systems (106 families)
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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 )
2) Catalogue of Life (Sp2000 + ITIS) (www.sp2000.org)
Serves existing checklists for all organisms (plants, animals, insects etc)
Much of Kew’s checklist data served. Offers alternative / conflicting views
3) Global Biodiversity Information Framework (www.gbif.org )
Serves specimen records from collections worldwide
Name catalogue served from “Catalogue of Life”
4) 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
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Moving forward:improving Kew’s plant name services
1) Tailored consultancies – for target groupse.g. Medicinal Plants - WHO, EMEA, ICHreporting on existing lists of plant namesvalidating, cleaning & completing name listsbuilding and maintaining subsets for focus groups
2) Designing & developing web servicesautomated responses to queries from other system / APImaintenance of name lists avoiding costs for userssubscription services
3) Seeking to develop partnerships with user groupsinform design of services / user needsdevelop resource to meet specific demands
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Thanks for your attention!
Questions?
Ideas to pursue?
PS Biodiversity Information StandardsTaxonomic Databases Working Group TDWGhttp://www.tdgw.org/
Ontologies / Vocabularies / Schemas / LSIDs