Bill’s talk is entitled “WHAT’S IN A NAME? How Kew helps drug regulators disambiguate the messy welter of medicinal plant names to shore up regulation and save lives”. It’s really eye-opening to realize how complicated and imprecise names can get, with multiple scientific, pharmaceutical and popular names for the same thing or with one name used for completely different things.
This has real-world consequences. For example, the EU mistakenly banned a useful plant we use every day when intending to ban a poisonous one because of a naming problem. How Kew is using semantic and taxonomic tools and technologies to bring order to this complexity (I almost said chaos) is really fascinating. They’re also helping to disambiguate nomenclature and provide links to authoritative information for botanical terms for use in journal articles, among other things.
Invasive Alien Plants: Valuable Elixir with Pharmacological and Ethnomedicina...ijtsrd
Use of herbal medicines is propagating day-by-day and several tribes still rely upon this green treasure against their ailments. Being unfortunate to the environment, invasive plants species hold supreme remedies that are unique. Besides ethnoremedial uses they embrace anticancerous, antidiabetic, antimicrobial, antitubercular and other pharmacological attributes in them. In the present review, authors aimed to compile the segregated ethnomedicinal information of invasive plant species. The literature study revealed a significant ethnoremedial importance of invasive alien weeds that may serve to establish a ground for future researchers to explore in pharmacognostic field with safe and natural drug resource. Shaiphali Saxena | P. B. Rao"Invasive Alien Plants: Valuable Elixir with Pharmacological and Ethnomedicinal Attributes" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-2 | Issue-3 , April 2018, URL: http://www.ijtsrd.com/papers/ijtsrd11636.pdf http://www.ijtsrd.com/pharmacy/pharmacognosy-/11636/invasive-alien-plants-valuable-elixir-with-pharmacological-and-ethnomedicinal-attributes/shaiphali-saxena
These slides represent a comprehensive view of history of using natural products caused to appearance of pharmacognosy as a science and show several aspects of pharmacognosy and natural products use and final their importance in discovering new drugs.
Ethics in international research: Scholarly integrity workshop - 2013Cassandra Quave
In 2013, Dr. Quave led a workshop entitled: "Ethics in International Research: Navigating International Policies Concerning Human Subjects and Bioprospecting" for the Emory Program for Scholarly Integrity.
FORMATION OF HERB-BASED EXPORT ORIENTED AGRO-MEDICINE INDUSTRY USING THE JUICE AND PIECES OF MEDICINAL PLANT PARTS.Like the ancient and ethnic people as well as a part of the people residing at the rural areas are still accustomed with the use of readily available herbal preparations made from the locally available plants mainly at its raw, pure, fresh and crude form for cure of the ailments of themselves as well as same or related type of ailments of their domestic animals.
Invasive Alien Plants: Valuable Elixir with Pharmacological and Ethnomedicina...ijtsrd
Use of herbal medicines is propagating day-by-day and several tribes still rely upon this green treasure against their ailments. Being unfortunate to the environment, invasive plants species hold supreme remedies that are unique. Besides ethnoremedial uses they embrace anticancerous, antidiabetic, antimicrobial, antitubercular and other pharmacological attributes in them. In the present review, authors aimed to compile the segregated ethnomedicinal information of invasive plant species. The literature study revealed a significant ethnoremedial importance of invasive alien weeds that may serve to establish a ground for future researchers to explore in pharmacognostic field with safe and natural drug resource. Shaiphali Saxena | P. B. Rao"Invasive Alien Plants: Valuable Elixir with Pharmacological and Ethnomedicinal Attributes" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-2 | Issue-3 , April 2018, URL: http://www.ijtsrd.com/papers/ijtsrd11636.pdf http://www.ijtsrd.com/pharmacy/pharmacognosy-/11636/invasive-alien-plants-valuable-elixir-with-pharmacological-and-ethnomedicinal-attributes/shaiphali-saxena
These slides represent a comprehensive view of history of using natural products caused to appearance of pharmacognosy as a science and show several aspects of pharmacognosy and natural products use and final their importance in discovering new drugs.
Ethics in international research: Scholarly integrity workshop - 2013Cassandra Quave
In 2013, Dr. Quave led a workshop entitled: "Ethics in International Research: Navigating International Policies Concerning Human Subjects and Bioprospecting" for the Emory Program for Scholarly Integrity.
FORMATION OF HERB-BASED EXPORT ORIENTED AGRO-MEDICINE INDUSTRY USING THE JUICE AND PIECES OF MEDICINAL PLANT PARTS.Like the ancient and ethnic people as well as a part of the people residing at the rural areas are still accustomed with the use of readily available herbal preparations made from the locally available plants mainly at its raw, pure, fresh and crude form for cure of the ailments of themselves as well as same or related type of ailments of their domestic animals.
Moringa is a plantfood of high nutritional value, ecologically and economically beneficial and readily available in the countries hardest hit by the food crisis. http://miracletrees.org/ http://moringatrees.org/
Medicinal plants are in use in many countries and cultures as a source of medicine. Biotechnological tools like tissue culture are important for selection, multiplication and conservation of medicinal plants genotypes. In addition, in-vitro regeneration plays a great role in the production of high-quality plant-based medicine. Plant tissue culture techniques offer an integrated approach for the production of standardized quality phytopharmaceutical through mass production of consistent plant material for physiological characterization and analysis of active ingredients. A number of medicinal plants reported to regenerate in vitro from their various parts but still, fewer are grown in soil, while their micropropagation on a mass scale has rarely been achieved. Micropropagation protocols for cloning of some medicinal plants had been developed by using different concentrations of plant growth regulators in a Murashige and Skoog media variant (Murashige and Skoog, 1962). Regeneration occurred via organogenesis and embryogenesis in response to auxins and cytokinins. The production of secondary metabolite is also becoming familiar by tissue culture for pharmaceutical use. The integrated approaches of culture systems will provide the basis for the future development of safe, effective, and high-quality products for consumers.
Abu Dhabi TCAM Conference: From the field to the pharmacy - 2013Cassandra Quave
This is a presentation given at the UAE Health Authority sponsored TCAM conference in Abu Dhabi in 2013. The title of the talk was: "From the field to the pharmacy: The important role of TCAM to the future of public health"
Abstract:
Ethnobotanical studies concerning knowledge and use of TCAM are critical for laying the groundwork for both pharmaceutical development and public health policy. In this talk, I will review some of the translational aspects of medical ethnobotany research, highlighting the importance of documenting local knowledge of TCAM practices and investigating the efficacy, safety and potential for broader public health applications (i.e. herbal supplements and pharmaceuticals). Methodology for implementation of such studies will be reviewed and potential applications of the data in UAE public health policy and practice will be discussed.
Multilingual Ontology for Plant Health Threats Media MonitoringRoberto García
Development and testing of the media monitoring tool MedISys for the early identification and reporting of existing and emerging plant health threats guided by a plant health threats ontology
Antioxidant Activity and Cytotoxicity against Cancer Cell Lines of the Extrac...Juan Hernandez
Xylaria species associated with termite nests or soil have been considered rare species in nature and the few which have been reported upon have been found to act as a rich source of bioactive metabolites. This study evaluated 10 ethyl acetate extracts of five new Xylaria species associated with termite nests or soil for their antioxidant activity, and cytotoxicity against different cancer and normal cell lines. DPPH and ABTS radical scavenging activities of the extracts demonstrated strong capacity with low IC50 values. The highest observed activities belonged to X. vinacea SWUF18-2.3 having IC50 values of 0.194 ± 0.031 mg/mL for DPPH assay and 0.020 ± 0.004 mg/mL for ABTS assay. Total phenolic content ranged from 0.826 ± 0.123 to 3.629 ± 0.381 g GAE/g crude extract which correlated with antioxidant activities. The high total phenolic content could contribute to the high antioxidant activities. Cytotoxicity was recorded against A549, HepG2, HeLa and PNT2 and resulted in broad spectrum to specific activity depending on the cell lines. The highest activities were observed with X. subintraflava SWUF16-11.1 which resulted in 11.15 ± 0.32 to 13.17 ± 2.37% cell viability at a concentration of 100 µg/mL. Moreover, LC-MS fingerprints indicated over 61 peaks from all isolates. There were 18 identified and 43 unidentified compounds compared to mass databases. The identified compounds were from various groups of diterpenoids, diterpenes, cytochalasin, flavones, flavonoids, polyphenols, steroids and derivatives, triterpenoids and tropones. These results indicate that Xylaria spp. has abundant secondary metabolites that could be further explored for their therapeutic properties
Moringa is a plantfood of high nutritional value, ecologically and economically beneficial and readily available in the countries hardest hit by the food crisis. http://miracletrees.org/ http://moringatrees.org/
Medicinal plants are in use in many countries and cultures as a source of medicine. Biotechnological tools like tissue culture are important for selection, multiplication and conservation of medicinal plants genotypes. In addition, in-vitro regeneration plays a great role in the production of high-quality plant-based medicine. Plant tissue culture techniques offer an integrated approach for the production of standardized quality phytopharmaceutical through mass production of consistent plant material for physiological characterization and analysis of active ingredients. A number of medicinal plants reported to regenerate in vitro from their various parts but still, fewer are grown in soil, while their micropropagation on a mass scale has rarely been achieved. Micropropagation protocols for cloning of some medicinal plants had been developed by using different concentrations of plant growth regulators in a Murashige and Skoog media variant (Murashige and Skoog, 1962). Regeneration occurred via organogenesis and embryogenesis in response to auxins and cytokinins. The production of secondary metabolite is also becoming familiar by tissue culture for pharmaceutical use. The integrated approaches of culture systems will provide the basis for the future development of safe, effective, and high-quality products for consumers.
Abu Dhabi TCAM Conference: From the field to the pharmacy - 2013Cassandra Quave
This is a presentation given at the UAE Health Authority sponsored TCAM conference in Abu Dhabi in 2013. The title of the talk was: "From the field to the pharmacy: The important role of TCAM to the future of public health"
Abstract:
Ethnobotanical studies concerning knowledge and use of TCAM are critical for laying the groundwork for both pharmaceutical development and public health policy. In this talk, I will review some of the translational aspects of medical ethnobotany research, highlighting the importance of documenting local knowledge of TCAM practices and investigating the efficacy, safety and potential for broader public health applications (i.e. herbal supplements and pharmaceuticals). Methodology for implementation of such studies will be reviewed and potential applications of the data in UAE public health policy and practice will be discussed.
Multilingual Ontology for Plant Health Threats Media MonitoringRoberto García
Development and testing of the media monitoring tool MedISys for the early identification and reporting of existing and emerging plant health threats guided by a plant health threats ontology
Antioxidant Activity and Cytotoxicity against Cancer Cell Lines of the Extrac...Juan Hernandez
Xylaria species associated with termite nests or soil have been considered rare species in nature and the few which have been reported upon have been found to act as a rich source of bioactive metabolites. This study evaluated 10 ethyl acetate extracts of five new Xylaria species associated with termite nests or soil for their antioxidant activity, and cytotoxicity against different cancer and normal cell lines. DPPH and ABTS radical scavenging activities of the extracts demonstrated strong capacity with low IC50 values. The highest observed activities belonged to X. vinacea SWUF18-2.3 having IC50 values of 0.194 ± 0.031 mg/mL for DPPH assay and 0.020 ± 0.004 mg/mL for ABTS assay. Total phenolic content ranged from 0.826 ± 0.123 to 3.629 ± 0.381 g GAE/g crude extract which correlated with antioxidant activities. The high total phenolic content could contribute to the high antioxidant activities. Cytotoxicity was recorded against A549, HepG2, HeLa and PNT2 and resulted in broad spectrum to specific activity depending on the cell lines. The highest activities were observed with X. subintraflava SWUF16-11.1 which resulted in 11.15 ± 0.32 to 13.17 ± 2.37% cell viability at a concentration of 100 µg/mL. Moreover, LC-MS fingerprints indicated over 61 peaks from all isolates. There were 18 identified and 43 unidentified compounds compared to mass databases. The identified compounds were from various groups of diterpenoids, diterpenes, cytochalasin, flavones, flavonoids, polyphenols, steroids and derivatives, triterpenoids and tropones. These results indicate that Xylaria spp. has abundant secondary metabolites that could be further explored for their therapeutic properties
Like the ancient and ethnic people as well as a part of the people residing at the rural areas are still accustomed with the use of readily available herbal preparations made from the locally available plants mainly at its raw, pure, fresh and crude form for cure of the ailments of themselves as well as same or related type of ailments of their domestic animals.
The growing prominence of natural / herbal/ phytogenic interventions in global animal feed supplement and even therapeutic market is worth niticing , but to separate wheat from chaff on the basis of strong standarisation protocols are very important, so that the credibility of the users is not put on stake .
Pharmacology is study of the substances which interact with living system by activating or inhibiting normal body processes. It includes physical and chemical properties, biochemical and physiological effects, mechanism of action, therapeutic uses and adverse effects of drugs.
Have you ever wondered how search works while visiting an e-commerce site, internal website, or searching through other types of online resources? Look no further than this informative session on the ways that taxonomies help end-users navigate the internet! Hear from taxonomists and other information professionals who have first-hand experience creating and working with taxonomies that aid in navigation, search, and discovery across a range of disciplines.
Making AI Behave: Using Knowledge Domains to Produce Useful, Trustworthy ResultsAccess Innovations, Inc.
In today's highly charged atmosphere of anxiety and anticipation about AI, and especially LLMs,
one of the biggest concerns is how to ensure that it returns accurate results (meaning both true
and pertinent to its audience). This is particularly important to scholarly, scientific, and other
technical organizations, whose constituents are often in very specific domains, such as
medicine, engineering, history, biology, chemistry, etc. One extremely useful tool to incorporate in an AI-based process in such cases is a comprehensive and well-structured knowledge domain which is based on a controlled vocabulary.
Smart Submit and Client Support
Michael Millar, Junior Software Developer, and Frank Coates, Client Support Manager
Get a peek at the new and improved Smart Submit and learn about new, easier ways to contact the support team at Access Innovations.
How a Good Taxonomy Can Provide Valuable Business Insights
Kristen Monahan, Public Library of Science (PLOS)
Kristen is a business analyst and she won’t be talking about the PLOS taxonomy but rather how she uses that taxonomy to drill down into the massive amount of content, metadata, and usage and process data that is PLOS for deep, detailed analysis and to drive business decisions. Much of this work involves trend analysis. For example, trend analysis of submissions can look at the time it takes from submission to decision by subject (narrow subjects like Covid, broad subjects like biotechnology), or by institution, or by country, etc. to see not just the overall big picture but where in their submission and peer review workflows the bottlenecks might be. A trend analysis of topics over time can prompt them to issue a call for papers for a topic they think needs to be better covered–and then look at both short-term and long-term trends resulting from that call to papers. Their taxonomy doesn’t just make their content smarter–it makes how they publish that content smarter too.
Editor and Peer Reviewer Assignments Using Data Harmony
Andrew Smeall, Hindawi Publishing
Andrew will show how Hindawi, an open access publisher, applies their taxonomy to make editor and reviewer assignments for incoming submissions to their journals.
Cloud Deployment of Data Harmony
Jeffrey Gordon, Lead Developer, Access Innovations, Inc.
Jeffrey will describe the cloud deployment of the Data Harmony software.
Marjorie M. K. Hlava, President, Chair of the Board, and Chief Scientist, Access Innovations, Inc.
During this annual highlight of the DHUG meetings, Margie will discuss the exciting new changes and additions to the Data Harmony software. She will be joined by some members of our software development team to talk about specific initiatives we have worked on over the past year.
Access Innovations and Atypon: Beyond Content Tagging
Hong Zhou and Gerasimos Razis, Atypon
Gerasimos and Hong will discuss the changes to the Atypon platform since DHUG 2020.
Getting to the Point: Using AI and Taxonomies to Craft Meta -Titles
Travis Hicks, American Society of Clinical Oncology (ASCO)
Looking to better leverage SEO and include key terms in the url construct for research abstracts, ASCO is working with Access Innovations to evaluate how to programmatically create short titles for abstracts. The idea is to index titles against existing taxonomies as a way of producing a short title that succinctly identified what an abstract is about for purposes of constructing a new url configuration. Travis will discuss the need, challenges, and early results of the project.
Expanding the Use of MAIstro at ASCE
Xi Van Fleet, American Society for Civil Engineers
Using MAIstro, ASCE created the subject/topic taxonomies for their publications to enhance content discovery and business insight. After achieving their primary goal, they have been expanding its use for other applications.
Lessons Learned From Building a Taxonomy and Indexing 140 Years of Content
Michael Darr, Project Manager, D33 – American Chemical Society Pubs IT
Michael will talk about the things they would do differently if they were to build a new taxonomy and index a legacy file, and the things they did right the first time.
Daniel Vasicek discuss the processes undertaken to OCR various kinds of content from the University of Florida Special Collections to make them machine readable for indexing.
Explore our comprehensive data analysis project presentation on predicting product ad campaign performance. Learn how data-driven insights can optimize your marketing strategies and enhance campaign effectiveness. Perfect for professionals and students looking to understand the power of data analysis in advertising. for more details visit: https://bostoninstituteofanalytics.org/data-science-and-artificial-intelligence/
Levelwise PageRank with Loop-Based Dead End Handling Strategy : SHORT REPORT ...Subhajit Sahu
Abstract — Levelwise PageRank is an alternative method of PageRank computation which decomposes the input graph into a directed acyclic block-graph of strongly connected components, and processes them in topological order, one level at a time. This enables calculation for ranks in a distributed fashion without per-iteration communication, unlike the standard method where all vertices are processed in each iteration. It however comes with a precondition of the absence of dead ends in the input graph. Here, the native non-distributed performance of Levelwise PageRank was compared against Monolithic PageRank on a CPU as well as a GPU. To ensure a fair comparison, Monolithic PageRank was also performed on a graph where vertices were split by components. Results indicate that Levelwise PageRank is about as fast as Monolithic PageRank on the CPU, but quite a bit slower on the GPU. Slowdown on the GPU is likely caused by a large submission of small workloads, and expected to be non-issue when the computation is performed on massive graphs.
2. BobAllkin,Manager,PlantNamesServices,Kew
Bob Allkin’s role is to manage Kew’s Medicinal Plant Names Services (MPNS)
which is a key reference for global health regulators, natural product
researchers, trade and practitioners, and provides a control vocabulary for
ISO’s standard“Identification of Medicinal Products”. Currently we seek to
expand these services to address the needs of those working with food
supplements, allergens and poisonous plants. He works in the department
of Biodiversity Informatics and Spatial Analysis at the Royal Botanic Gardens,
Kew, where they are Applying computational techniques to analyse, edit,
curate, organise, mine and disseminate data and to evaluate trends and
patterns through time and space. Bob holds a Bachelor of Science with
Honors in Biology from Queen Mary College, London University, and a PhD in
Computer-assisted plant identification fromWestminster University and the
Natural History Museum in London.
3. What's in a name?
Herbal remedies & public health
4. 1. Curation of collections as global assets for research
2. Discovering and understanding plant and fungal diversity
and its uses for humanity
3. Dissemination of knowledge about plants and fungi for
impact on science, education, conservation and livelihoods
Kew: “Unlocking why plants and fungi matter”
2
5. 3
Our 350+ scientists work collaboratively and globally, making an invaluable
contribution to solving some of the biggest challenges facing humanity
6. Kew’s collections
Herbarium
collections
• ca 7 million dried pressed
plants
• 40,000 plants preserved in
alcohol
• 20,000 dried (non-viable) seeds
and fruits
Mycology
collections
• ca 1.25 million dried fungi
• 1,100 living fungal cultures
stored in liquid nitrogen
• 500 isolates of mycorrhizal
fungi
Economic
Botany
collection
• ca 110,000 artefacts & samples
of known plant origin
• ca 40,000 wood samples
(xylarium) Basket in
Economic Botany
collection
Dried herbarium
material ready for
mounting
Iridescent fruits
preserved in
alcohol
8. Open Access to:
• Core collections data
• Higher taxonomy
• Backbone taxonomy
• Descriptive data
Species Pages:
• Description(s)
• Distribution maps
• Taxonomy
• Common names
• Bibliography
Plants of the World Online Portal (POWOP)
6
9. Herbal Medicines &
Natural Products
• Growing use
• Global Trade: US$ 30 billion 2015
- 300% growth since 2000
• TCM, Ayurveda, Kampo, Jamu
• 80% of world population rely on
herbals for their primary healthcare
(WHO)
• Plants a primary source
of pharmaceutical drugs:
122 in last 2 years
10. 8
Products with active ingredients from plant parts:
e.g. leaves, roots or flowers.
Being "natural" doesn't necessarily mean they're safe for you to take
- Like conventional medicines, herbal medicines have effects on the body.
- Herbal medicines can be potentially harmful if not used correctly.
12. One plant – many names “Synonyms”
Common names:
yarrow millefeuille
achillekraut
herba militaris
nosebleed
woundwort
old man’s pepper
10
Y Luo
蓍草
rölleka
الياروأخلية
Yaru
milfolhada
Obstacle to finding information
13. Common names:
One name – many plants “Homonyms”
“Bluebell”
11
Ambiguity: false conclusions
14. 12
ALWAYS Plant &
Part
What is a ‘herbal drug’?
MPNS captures Plants, Parts and Trade Forms
USUALLY Form
and/or Preparation
e.g. “Root of Panax ginseng C.A.Mey.”
e.g. “Whole dried root of Panax ginseng C.A.Mey”
e.g. “Tincture of Whole dried root of Panax
ginseng C.A.Mey”
+
18. “Ginseng” is cited in legislation or pharmacopoeias
to refer to drugs derived from…
Herbal Drug Names
Panax ginseng C.A.Mey.
Panax quinquefolius L.
Eleuthrococcus senticosus (Rupr.&Maxim.) Maxim.
Hebanthe erianthos(Poir.) Pedersen
Withania somnifera(L.) Dunal
…..16 different species
Each plant has a unique chemistry
i.e. Great Ambiguity / Risks
16
20. US and
European
Pharmacopoeia
(2012)
“Cimicifugae rhizoma”
Japanese Pharmacopoeia (2005)
Chinese Pharmacopoeia (2010)
1 Name | 5 Species | Differing chemistries and uses!
Actaea simplex Actaea cimicifuga Actaea heracleifolia Actaea dahurica Actaea racemosa
18
Pharmaceutical names
21. Aristolochia fangchiStephania tetrandra
2008: Belgian clinic substituted one product for the other
“Fang ji” (Chinese Pharmacopoeia)
= 105 cases of renal failure, urinary cancer and death
• Anti-inflammatory
• Protection kidney
• Prevention diabetes
• Diuretic
• Dysuria
19
22. Global Inconsistency
US Herbs of Commerce
▪ “fen fang ji”
▪ “han fang ji”
British Pharmacopoeia (2012 ed)
▪ “Stephania Tetrandra Root”
European Pharmacopoeia (2012 ed)
▪ “Stephaniae tetrandreae radix”
“Fang Ji”
20
24. What is a Scientific Plant Name ?
22
• written in Latin
• Genus + species + author
• International Code of Nomenclature - formal procedures
e.g. Author must…
• Describe how plant is different
• Cite specimen(s)
“TYPE specimens”
• Formally publish
“Hocus pocus Bob”
25. 23
Specialist identifies specimen
as being from a NEW species.
Digital id (Barcode):
Links specimen to DNA,
Chemistry, seeds, etc.
Unique ID =
Collector’s name
+
unique collection no.
Establish NEW name &
publish name with description.
Reference this collection.
Specimen recognised as
‘TYPE’
27. Why Use Scientific Names?
meaning
Fixed
25
Unique
Global
Legislation
& Regulation
28. Global - Comprehensive - Authoritative
Nomenclature:
International Plant Names Index (IPNI)
ALL 1.6 million names; Persistent identifiers;
300k edits/yr.
Electronic Submission
Taxonomy:
World Checklist
ALL 340K plants; synonymy + geography
250K edits/yr
Peer reviewed
Information:
Plants of the World Online
Multiple digital resources – incl images
Ambition: Encyclopaedic
26
30. Too many names: 1.6 million scientific names for 350K plants
c. 16 synonyms/medicinal plant
28
Obstacles to using scientific names
31. US Food and Drug Administration (FDA)
Legislation citing 2,046 scientific names
Kew validated FDA names and found:
58% correct and follow current taxonomy
20% correct but older synonyms
(24 plants listed under >1 name) => Inconsistent regulation
Synonymy: Ineffective regulation
29
}
16% ambiguous
3% misspelt => Ineffective regulation
3% not plant names!
32. Too many names: 1.6 million scientific names
c. 16 synonyms/medicinal plant
Ambiguity: One binomial - multiple authors
c. 4% of scientific names
30
Obstacles to using scientific names
33. Obstacles to using scientific names
Homonyms: binomial published by >1 author
Ambiguity:
• “Viburnum fragrans Bunge”
• “Viburnum fragrans Loisel”
4 - 5 % of scientific names
“only” 64,000 scientific names !
31
2 scientific names:
referring to 2 different plants}
34. Regulatory failures: homonyms
2002 EU Commission Decision:
OJEC L 2.2.2002 L 33/31
“The botanical variety Illicium anisatum is
scientifically recognised as highly poisonous and
banned from import into the EU…..”
32
effectively banned the import of Star Anise!
35. Homonyms
33
‘Japanese Star Anise’ (Toxic)
Illicium anisatum Linnaeus
common synonyms:
Illicium religiosum S&Z.
Bandianifera anisatum Kuntze
‘Star Anise’
Illicium verum Hook.f.
common synonyms:
Illicium anisatum Lour.
Illicium san-ki Perr.
Bandianifera officianarum Kuntze
And two further homonyms:
Illicium anisatum Bartr. ex Michx.
Illicium anisatum Gaertn.
Ambiguity
36. Too many names: 1.6 million scientific names
c. 16 synonyms/medicinal plant
Ambiguity: One binomial - multiple authors
c. 4% of scientific names
Taxonomy improves: => 10,000 name changes published/yr.
- 2,000 new species
- 4,000 plants move between Genera
- 4,000 species ‘split’/’lumped’
34
Molecular data major driver for
continuing change
Obstacles to using scientific names
37. 35
The World Flora Online
eMonocot
Who do I believe?
Obstacles to using scientific names
38. Consequence: Imprecision in literature
36
Rivera et al. 2014
J. Ethnopharmacology
& J. Phytomedicine
308 articles
9178 names
38% Names:
ambiguous,
imprecise or
misleading
Natural Products Research Nutrition/Food
Multiple journals
50 articles
502 names
93%
Nesbitt et al. 2010
Names:
ambiguous,
imprecise or
misleading
40. Public Health
Herbal Trade
Border Control
Natural Product
Research
Medicinal Plant Names Services
Kew Resources
Authoritative
Enriched
38
MPNS
Resource
Medicinal Data
• Source: Regulations, Pharmacopoeias,
Ethnobotany…
• Pharmaceutical, Drug & Common names
• Misspelt scientific names
• Plant Parts
• Trade Forms
World
Checklist
IPNI
Services
41. 39
Version 9 – January 2020 - 28,000 species
170 major health, medicinal references
> 0.4 million alternative (unique) names
+ plant parts and trade forms
Global Comprehensive Unique
The MPNS Resource
42. Finding Data Using MPNS - example
Mu Xiang: Chinese Herb: widely used
But which species is used? What should we call it?
40
➢ Flora of China: “Aucklandia costus Falc.”
➢ Pharmacopoeia: China and Korea: “Aucklandia lappa Decne”
➢ US Herbs of Commerce (FDA): “Saussurea costus (Falc.) Lipschitz”
➢ Pharmacopoeia: Japan & Ayurvedic: “Saussurea lappa Clarke”
➢ Kew’s checklist cites 5 scientific synonyms
WHAT HAS BEEN PUBLISHED ABOUT THIS PLANT?
44. 42
Search PubMed using
ALL Synonyms
‘Aucklandia costus’ OR
‘Aucklandia lappa’ OR
‘Aplotaxis lappa’ OR
‘Saussurea costus’ OR
‘Saussurea lappa’ OR
‘Theodorea costus’
768 publications in
PubMed
(compared with 367)
45. CONSULTANCY AND TRAINING
SUPPLYING DATA
MPNS Scientific Services
MANAGING YOUR NAMES DATA
4343
Validation: check and enrich your lists of plant names
Harmonisation: map plant lists onto those used by others
Vocabularies & Data: authoritative lists
Web Services: electronic refresh
Consultancy: system design, workflows, standards
Training: best practice and resources
46. MPNS in global drug regulation
44
ISO standard: Identification of Medicinal Products (IDMP):
ISO Standard 2018
‘Controlled
Vocabulary’ from
MPNS
Our Partners
Chinese Pharmacopoeia
Japanese
Health Regulator
49. 47
Type of name Example # Issues in published article
Latin binomials “Artemisia annua” 8
None complete:
all potentially ambiguous
Common names “dandelion” 4
Imprecision:
scores of plants from multiple families
Herbal formula
“Radix isatidis
granula”
4
Complex mixtures of plants of uncertain
identity
Inconsistent use of pharmaceutical
names
Ingredients “quinine”
12
“Quinine” is common name of >16 plants
– as well as that of a chemical compound
derived from ONE species
50. What’s next ?
Plant Names Services for Health:
- expand scope:
food supplements, allergens, poisonous plants
- improve digital access/ data sharing
- widen audience:
food safety,
poisons clinics,
pharmacovigilance
clinical trials
48
51. MPNS potential applications for Publishing
For managing content
1. comprehensive retrieval – all synonyms
2. disambiguation – detecting and forewarning
3. content enrichment – semantic links
49
For editorial control
1. Automated validation of m/s prior to publication
53. Kew Medical Plant Names Service
Access Innovations, Inc.
A Partnership for Data Enrichment
www.kew.org/mpns
54. The Kew MPNS Data Treasure Trove
• Medical Plant Names Service (MPNS)
• Plant Names Service for Health (PNSfH).
• 28,187 species
• Average of 14.7 synonyms (up to 16 in v9)
• Harvested from at least 170 reference files
• Over 415,180 unique names
• Full information records with references
55. Three Files of Plant Information
• 36,980 unique plant names, & IDs,
• Along with confidence level, and
• hierarchy, (family, genus, species, authors, …)
• 257,764 synonyms for
• 30,641 of the 36,980 plants
• 160,479 “common” names
• for 27,125 of the 36,980 plants
56. Merging Technology and Science
• MPNS database
• 14.7 synonyms / alt names per plant
• Access Innovations Data Harmony MAIstro software
• Term management
• AI for term disambiguation, identification, extraction
• Preferred term use solves misidentification
57. How to do that?
• First tag all the articles with the preferred name
• Use the worlds authoritative database to make that happen
• Use the Kew MPNS AutoTagging service
• Tag both the retrospective collection – back file
• All forthcoming publications as they are submitted for publication
• Add a synonymy capability to search
• Make all the alternative names searchable
• Insure the search system points to the authoritative / preferred name
• Then all tagged documents are found and presented
58. Thesaurus Master
Machine Aided Indexer
(M.A.I.™)
Enriched
Database
Repository
Search
Presentation Layer
Increases
Accuracy
Preferred form mapped
Browse by Subject
Auto-completion
Synonymy
Broader Terms
Narrower Terms
Related Terms
Client Taxonomy
Search
Software
Client Data
Full Text
HTML, PDF,
Data Feeds, etc.
MPNS
Source data
The Workflow
Tag with
correct name
update
database
with tags
Build
Search
inverted index
Provide
enhanced
search
Source
Data / articles
59. What Else Could I Do?
• Link the internal reference to the MPNS Database
• Provides a resource for your community
• Links to the prime references
• Provides vetted information on all medicinal plants
60. Expanding the Data
• 10 % or 2,540 plant ids have no synonyms.
• These quickly get a match rule
• 90% of the data file have extensive synonyms
• Programmatic rules built for all
• Synonymy and proximity
Let’s look at some more details …
66. Why Support MPNS?
• Can’t search all the names! 14.7 synonyms
• Difficult for any researcher to find all the pertinent literature
• Especially the well documented uses and variety within the
database.
• Negative consequences of misidentification
• Misidentification fosters illegal trade in bogus herbals
• That cheats both consumers and indigent farmers in developing
nations
67. Helping the Reader /Public
• Taxonomic nomenclature is not native to most authors
• They use what was handed to them as a named sample
• Others will use a different name
• How do we get everyone to the same name?
68. Helping the Searcher
• Use a main preferred term so that search can surface all relevant
articles
• Need all the articles about this plant’s medicinal use
• Do not need things about another plant known by a similar common
name
69. Value
• Semantic enrichment supports metadata and search
• Time savings
• More accurate and in-depth research.
• It allows the formation of a platform for better science
• Better communication between researchers world wide
• Being able to reference a widely available authoritative source is crucial to all
world health
• Enhance scholarly and learned publishing and the research communities it
represents worldwide
70. The Service Offered
Test publisher content using the Medical Plants database
• To
• learn if the science outlined in the paper is valid,
• provide supplemental information, and
• leverage the knowledge and terminology authentication of the MPNS
• How
• API – Full text or a selection of articles
• To the Hosted MPNS
• Using Data Harmony rulebase
71. What Do I Get?
• Using your article content
• Provides the preferred plant name
• Provides full official name
• Links to the full data record
• Supplies the full right name
• Provides a valid trusted reference source
• Enhances the offering to authors
• Enables information sharing by ensuring it is the same plant that
everyone is writing about
72. Similar Files for Adding Metadata and Filtering
• Suspect or Defective Cell lines projects (two projects)
• Suspect Science
• SciGen Detection
• TaxoGene – The Human Genome – 19 synonyms average
• Remove pseudo science /poor science
• Etc.
•Make your data as good as it can be!
74. 51
Further information
Medicinal Plant Names Services: www.kew.org/mpns
MPNS Newsletter: mailchi.mp/732a7ac370d8/mpns-sign-up
Recent WHO Podcast:
“Drug Safety Matters”
http://www.drugsafetymatterspod.org/618871/4302125-3-
navigating-the-plant-names-jungle-bob-allkin
“State of the World’s Plants” report https://stateoftheworldsplants.com/2017/useful-plants.html
Plants of the World Online www.plantsoftheworldonline.org
ISO Identification of Medicinal Products https://www.fda.gov/industry/fda-resources-data-
standards/identification-medicinal-products-idmp