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