Plant names: Obstacles and Solutions to access information about plants

Plant names:

obstacles and solutions

Bob Allkin, Royal Botanic Gardens Kew, UK

to accessing information about plants

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?

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?

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!

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

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

Saussurea costus (Falc.) Lips. has a root widely used in medicine – imported to EU

So what does it look like?.... Google it!

51 PubMed Records

215

GenBank Records

Searching with Accepted name

Searching witha synonym

03 PubMed Records

14

GenBank Records

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

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.

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

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:

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)

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

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

Thanks for your attention!

Questions?

Ideas to pursue?

PS Biodiversity Information StandardsTaxonomic Databases Working Group TDWGhttp://www.tdgw.org/

Ontologies / Vocabularies / Schemas / LSIDs