Presentation held by Supiah Mustaffa, Ros’aleza Zarina Ishak, Lee Chee Kiam, Michelle Lim Sien Niu, Nor Ezam Selan, Mary Sintoh at the Agricultural Ontology Service (AOS) Workshop 2012 in Kutching, Sarawak, Malaysia from September 3 - 4, 2012

1. Herbal Medicine Knowledge
Base (HMKB) System
Supiah Mustaffa
Version: 1.0 Ros’aleza Zarina Ishak
Lee Chee Kiam
Michelle Lim Sien Niu
Nor Ezam Selan
(MIMOS Berhad)
Mary Sintoh
(SEDIA)

2. Outline
• Problem Statement
• Knowledge Modeling and Engineering
• Collaborative Knowledge Management
• Value of the Proposition
• Future Works & Conclusion

3. Problem Statement
Problem:
• deterioration of herbal medicine knowledge
• scattered and unstructured information data sources
Solution:
• compile the information into a standard, reusable format
and store it into a central repository that can be referred by
different stakeholders

4. Objectives
HMKB is developed to :
1) document and preserve Malaysian herbal
medicine knowledge
2) provide collaborative platform for community of
practice
3) boost economic sector related to herbal medicine
4

5. Outline
• Problem Statement
• Knowledge Modeling and Engineering
• Collaborative Knowledge Management
• Value of the Proposition
• Future Works & Conclusion

6. High level architecture of Herbal
Medicine Knowledge Base (HMKB)
http://www.sabahinfomed.com.my/TraditionalMedicine/
Traditional
Medicine
hasHerb hasProcess
http://www.sabahinfomed.com.my/Pharmacology/
has
hasInput
Pharmacology Pharmacology Herb Process
http://www.sabahinfomed.com.my/Herb/ http://www.sabahinfomed.com.my/Process/
6

7. Knowledge Modeling and Engineering
Traditional
Medicine
Pharmacology
Herb Process
Describe the knowledge about herb include:
-scientific name, family name, origin, distribution location, suitability of
climate, rainfall requirement, soil type, propagation parts and
management information
7

8. Herb
Alkoloids <http://www.efloras.org/
florataxon.aspx?flora_id=110&ta
Nyctanthes xon_id=200017788>
sambac L. hasImageLink
Jasminum
Arabian hasFileFormat JPEG
Image
jasmine
hasChemical
{@en}
Constituent
India
hasSynonym hasImage
skos:prefLabel
Oleaceae isOriginatedFrom
China
hasFamilyName hasDistributedPlace
Jasminum sambac
propagated
Seed Soland. Ex Ait. hasNatural
By
Occurance Forest
hasAltitude
hasMeasurement hasPest Apply
Unit Herb hasPest Diazinon
hasTemperature Detail Control
Altitude JSSPest
has
Meter AnnualRainfall hasPest
hasQuantity hasDisease Thrips
Herb hasSoil Detail
hasClimate
Temperature Type JSS hasDisease
hasRequired Captan
800 Disease Control
Fertilizer Spray
hasMaximum
hasMeasurement Quantity hasDisease
Unit Nitrogen
hasMinimum Herb LeafSpot
Quantity Annual SandyLoamy
Celcius Soil Tropical
Rainfall
25 hasMaximum
40 hasMeasurement Quantity
Unit
hasMinimum 50
Quantity Instance
40 Datatype property
Centimeter Annotation property 8

9. Knowledge Modeling and Engineering
Traditional
Medicine
Pharmacology Herb Process
Consolidate important information about the prescription of certain
medicine to cure certain diseases
- required quantity of herbs, the disease cured, detailed prescription and
prescription method
9

10. Traditional Medicine
Young
Gramme Leave 150
Gallstone
hasQuantity
hasPlant
hasMeasurement Mililiter
PartUsed
10 Unit
hasMeasurement usedToTreat JSLAForGallstone hasFrequency
Unit 3 times
Prescription1
daily
hasQuantity JasminumSambac has hasMedication
JSLAFor hasDuration
HerbUsed1 Traditional Prescription
Gallstone
Medicine hasTreatmentMethod JSLAForGallstone
Duration
hasHerb hasProcess hasMeasurement hasQuantity
Drink
Unit
JSLAForGallstone
Jasminum 3
Process
sambacLAit Week
10

11. Knowledge Modeling and Engineering
Traditional
Medicine
Pharmacology Herb
Process
Explains the sequence of interdependent and linked procedures for
traditional medicine preparation
11

12. Process
Jasminum sambac hasInput JSLAForGallstone
Soland. Ex Ait. Process
expandTo
hasInitial expandTo
Process
followBy
Boil Add
Water Water
herb:hasDescription
herb:hasDescription
10 gram of young leaves, 3 cups of
water boiled to become 1 cup.
Add up to 450 ml hot water for
infusion.
12

13. Knowledge Modeling and Engineering
Traditional
Medicine
Herb
Pharmacology Process
Consist of pharmacology activity and pharmacology toxicity knowledge
13

14. Pharmacology
Microgram
per milliliter
200
hasMeasurementUnit IC50
In vitro Stree hasQuantity
hasConcentration
Unit
protectAgainst JSLA anti- extractFrom
useTestModel Stem
stress
extract hasExtract
Type Methanol
useExtract
hasPharmacology JSLA
Jasminum sambac
Soland. Ex Ait. Phamacology
hasProduced 200
hasQuantity
hasPharmacology Chemical
Activity Milligram per
JSLA anti- hasMeasurement
kilogram
stress Unit
chemical hasConcentration
hasChemical Unit
Anti-stress IC50
Extract
Benzyl acetate
14

15. Outline
• Problem Statement
• Knowledge Modeling and Engineering
• Collaborative Knowledge Management
• Value of the Proposition
• Future Works & Conclusion

16. Collaborative Knowledge Management
Customized
tree view
Navigation
Semantic
Search
Data Access
Authoring Layer
Data Validation
Collaborative
Knowledge
Management
16

17. Collaborative Knowledge Management
Customized
tree view
Navigation Semantic
Data Access
Search Layer
Authoring
Data Validation Collaborative
Knowledge
Management
17

18. Navigation, Search, Authoring
Search
Authoring
Navigation
18

19. Data Validation
19

20. Collaborative Knowledge Management
Customized class
hierarchy view
Navigation
Search Semantic Data
Access Layer
Authoring
Data Validation
Collaborative
Knowledge
Management
20

21. Collaborative Knowledge Management
• Customized tree view
Traditional medicine
Pharmacology
a b
Original tree (a) versus customized tree (b)
21

22. Collaborative Knowledge Management
Customized class
hierarchy view
Navigation
Search
Authoring Semantic Data Access
Layer
Data Validation
Collaborative
Knowledge
Management
22

23. Collaborative Knowledge Management
• Semantic Data Access Layer (DAL)
– Adopted SOA architecture
Component
Lookup
A AllegroGraph
Server 3.2
9
4
5
1 6 7
Triple Cache
Client Delegator KBInterface MySQL
11 10 8 Store
Server 5.0.84
2
KBInterface
3
Component Lucene
Authenticator
B Index
Semantic Technology Platform KBInterface
23

24. Outline
• Problem Statement
• Knowledge Modeling and Engineering
• Collaborative Knowledge Management
• Value of the Proposition
• Future Works & Conclusion

25. Value Proposition
Knowledge
enrichment
capabilities
Scalability with
SOA architecture Simple approval
workflow
Value Proposition
Support
diagnosis
decision process Drug discovery
25

26. Comparative Study
Feature TROPICOS HerbMed HMKB
Free text search √ √ √
Text completion/
suggestion √ X √
Available only for the
licensed version of the
Advance search √ database. √
Wildcard support √ √ √
Subject matter
experts are allowed
Content to contribute
contribution X X content
User Guide – User
Manual X √ √
Statistic √ X √
Navigation √ √ √
Access Free Subscription fee required Free
26

27. Outline
• Motivation/Problem statement
• Knowledge Modeling and Engineering
• Collaborative Knowledge Management
• Value of the Proposition
• Future Works & Conclusion

28. Future Works
1. Deployment stage
2. Impact study
28

29. Future Works
1. Deployment stage
• involves the internal users identified within SEDIA department
• involve 20 users
Internal Pilot • focus on system familiarization, training and data migration and transition
Test
• participation from selected government agencies and organizations
Controlled • includes engagement of selected subject matter experts
deployment
• Herbal Medicine web portal will be made available for public access to
information on pharmacology, herbs and traditional medicine
Full • the community of practice will be able to contribute their knowledge and
deployment inputs in the related fields
29

30. Future Works
2. Impact Study
Economy
• encourage the cash flow
• promote exploration and production activity
• offer job employment
Socio economy
• reduce time required in collecting and accessing
herbal medicine knowledge
• increase awareness among users
• increase usage of herbal medicine among users
• promote commercialization of herbal medicine
30

31. Conclusion
HMKB System:
• preserve the herbal medicine knowledge
• provide collaborative platform for
community of practice
• promote herbal medicine economic
demands
31

32. QUESTION AND
ANSWER
32