USERMANUALOF

PREPAREDBY:

NURULSYAFIRAHASSAN

NORAMIRAFATIHAHAZMI

NOORHIDAYAHZAKARIA

DR.ROHAYANTIHASSAN

DR.MUHAMADRAZIBOTHMAN

 

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TABLEOFCONTENTS

SECTION TITLE PAGE

1 HERBONTOLOGYOVERVIEW 3

2 DOMAINOFHERBONTOLOGY 4

3 CONTENTANDSYNTAXOFHERBONTOLOGY 8

4 STRUCTUREOFHERBONTOLOGY 10

Copyright©2011‐2013LaboratoryofBiodiversityandBioinformaticsAllRightsReserved

FacultyofComputing

UniversitiTeknologiMalaysia81310Skudai,Johor,Malaysia

 

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Section 1: Herb Ontology Overview

This project presents Herb Ontology (HO), which is a lightweight domain‐oriented

ontology, specializing in herbs. The rapid growth of interest in herbs is causing an

overwhelminggrowthinherbalinformationsources,resultingindifficultiesnavigatingthe

many information sources found online. The fundamental factors behind the difficulties

when trying to find herbal information are twofold: (i) the heterogeneity of herb data,

whichcontributestofalsedescriptionsandunrelatedanswers;and(ii)overlappingcontent

wherethesameherbsmayhavedifferentuseindifferentcountriesdependingoncultural

backgrounds.TheHOaimsinsolvingallthedifficultiesstatedabove.

TheHOformalmodelwasimplementedusingaformalontologicallanguage,OWLbyusing

Protégé4.0.Atop‐downapproachwasusedinthedevelopmentofHOclasshierarchy.

CharacteristicsofHOisasfollows:

i. Ithasup‐to‐dateherbalknowledge

ii. Itsupportcross‐referencingbetweenreusesources

iii. Itprovidesreliablestorageforherbalinformation

iv. Itisupdatedweekly

v. Itappliesmulti‐layerversioningtoprovidedistinctiveversioning

vi. Itreusespotentialexternalherbalresources

vii. Itisflexibleandcanbeextended,reusedandcontinuetoevolved.

 

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Section 2: Domain of Herb Ontology

Figure1:DomainofHO‐consistofinformationoftheherbs

There are various commonnames for Panax ginseng as it is knownwith different names in

different countries such as Japanese ginseng (Japan), renshen (China) and Korean ginseng

(Korea).IntegratingheterogeneoussourcesofherbalknowledgeinHOhelpremedyanygapin

knowledgebetweenherbalistandresearchers,andtraditionalandmodernresultsbyexplicitly

settingout the interrelationof theirvariousconcepts.Figure1showsthedomainofHOthat

consiststheinformationofthePanaxginseng.

The data sources in HO consist of a combination of ontological and non‐ontological (e.g.

classification schemes, thesauri and lexicons) data sources. The potential data sources are

analyzedbeforebeingaddedtothetermsinHO.CurrentdatasourcesusedinHOareshownin

Figure2.

Domain Specification Structure 

 

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Figure2:SourcesinHO

 

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Table1:Theresultsummaryofclass‐levelandontologylevelevaluationinProtégé.

Metrics Acronym Value

Sizeofvocabulary SOV 33

Edgenoderatio ENR 1.83

TreeImpurity TIP 1

Noofclasses NOC 286

Noofinheritance NOI 32

Noofproperties NOP 4

Noofrootclass NORC 2

Averagepopulation AP 0.11189

Classrichness CR 0.24825

Inheritancerichness IR 0.99301

Relationshiprichness RR 0.01389

Table1aboveshowstheevaluationofeverymetricsinHOthatcalculatesinProtégé.The

calculationsresultsaregetsfromthedefinitiondescribefromeachmetrics.

 

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ExamplehowHOisextended,reuseandevolve.

Table2:ExamplehowHOisextended,reuseandevolve

Extension Reuse Evolve

UseHOSchedulerto

updatenewherbsources

weekly

Useofsub‐modelas

temporaryslots

(1) Resolvemultipledefinitionsin

herbdomainbyusingsynonyms;

(2) Update/addition/changein

terminologiesandrelationswith

helpofHOScheduler

(3) HOscopeextensionandaddition

ofaxiomsbyHOcurator

Extension

Defined as the additional of new terms of particular uses based on existing vocabulary

withouthavingtoreviseexistingdefinition.Thecriteriaofextensionare:(i)extensionby

definition;and(ii)ontologicalinsertion

Reused

Occurswhensomepartsoftheontologyareextractedandusedasbuildingblockfornew

ontology.

Evolve

Refers to the changes in the ontology with the respect to the granulity, scope,

conceptualizations,andspecificationswhileontologyremainsintact.

 

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Section 3: Content and Syntax of Herb Ontology

Informal specifications were necessary to document the desirable ontology elements so

that formal specifications could be implemented. The informal specifications included

descriptions of the classes and relationships involved in HO which were delivered in a

manner understandable to the project team members. Figure 3 shows the primary

interrelationshipsbetween classes(e.g.is‐arelationship),whileFigure4showstheoverall

relationshipinHO.

Figure3:SpecificationofHO‐showthe“is‐a”relationshipbetweenclasses

HOclassification

TheinterrelationshipbetweenclassesinHOinvolvesasubsumptionrelationshipora“Is‐a

relationship”whichdescribewhilethechildtermisatypeofparentterm.

Concepts Relations Properties Axioms

Herbsprofileand

usage

Is‐a hasName,

hasUsage,

hasSynonym,

synonymOf

Null

 

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Figure4:SpecificationofHO‐showstheoverallrelationshipofHO.

Example#1,

“HerbMedicinalUsages”is‐achildof“HerbUsages”

Exampleofsynonym,

has‐synonymfor“BotanicalName”and“Synonym”or“CommonName”and“Synonym”

has‐edible‐partfor“HerbPart”and“HerbEdibleUsage”

has‐botanicalnamefor“CommonName”and“BotanicalName”

HOtermshaveattributessuchas;

term_ID,term_name,definition,synonymandroot

 

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Example#2,Theterm“Anthicholesterolemic”willhaveterm_IDHO:0011022Thedefinitionforterm“Anthicholesterolemic”is“Preventsthebuildupofthecholesterol”.Therootfortermfor“Anthicholesterolemic”is“Herb_Usages”

 

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Section 4: Structure of Herb Ontology

Figure5(a):StructuredevelopmentofHO

The structure of HO includes two class sub‐components (e.g. “HerbBotanicalInfo” and

“HerbUsages”),theprimaryinterrelationshipsbetweenclasses(e.g.is‐arelationships),the

attributesexpressed in theclasses (e.g., term_nameand term_ID), the formatused in the

ontology (e.g.OWLandRDF)and theend‐user (e.g. requester), as illustrated inFigure5

(a).

 

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Figure5(b):TheintertermrelationsinHO

HO comes from the integration of plant species collected by domain experts such as

herbalist,andturnsthemintospecificationstofinallyproducetheintegralstructureofHO.

Theprimary structureofHO includes the class sub‐components “HerbBotanicalInfo”and

“HerbUsages”, the primary interrelationships between classes (e.g. is‐a relationship), the

attributes expressed in the classes (term_name and term_ID), the format used in the

ontology (OWL and RDF) and the end‐user (e.g. requester). A brief description of the

structureofHOcanbeseeninFigure5(c).

 

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Figure5(c):ThestructureofHO

Table3showsthestructureofHOintermofnameusedandtheirdescription.Theprimary

structureofHOincludestheclasssubcomponents:

“HerbBotanicalInfo”–provideseachherbsprofile “HerbUsages”–specifiesusesofeachherbs

Theprimaryinterrelationshipsbetweenclassesknownas:

Is‐arelationship

Theattributesexpressedintheclasses:

term_name term_ID

Formatusedintheontology

OWLandRDF

 

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Table3:ThestructureofHO

 

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ThebehaviorofHO

Figure6belowshowsthatfunctionsof“improveHOrecordkeeping”and“reduceduplication

ofeffort”cannotbecarriedoutwithouttheinclusionofthe“storeherbinformation”function.

These functions are examples of the “reuse of potential external herb resources” HO

characteristicandhowexternalsourcesaremanagedinHO.

Anexampleofextensionbehaviorisshowninthebaseusecase“checkmissingdatabase”and

“checkmissingID”thatarecontinuedtotheusecase“storeherbinformation”.

IfHOistograduallymatureintoafull‐fledgedontology,itisvitalthatithavedatabase

versioningtotrackeachchangeinthedatabase.TheHODatabaseisinchargeofapplying

“Multi‐layerversioning”inHO.ExamplesofmappingtheprocessesthatoccurinHOand

UsecasesmappingarebrieflydepictedinFigure7.

Figure6:UsecaserepresentationofthefunctionalityinvolvedinHO

 

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Figure7:ExampleofmappingtheprocessesoccurredinHOwithusecases