collaborative package-based ontology building and usage
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Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Collaborative Package-based Ontology Building and Usage
Jie Bao and Vasant HonavarArtificial Intelligence Research Laboratory
Computer Science Department
Iowa State University
Ames IA USA 50010
{baojie,honavar}@cs.iastate.edu
2005 Nov 27 Houston. IEEE Workshop on Knowledge Acquisition from Distributed, Autonomous, Semantically Heterogeneous Data and Knowledge Sources, in ICDM2005.
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
What is it about?Package-based Ontology (PO), a modular
approach for cooperative and scalable building and reuse of large-scale ontologies
The motivations of PO The basic definitions of PO Example language: Package-based
Hierarchy
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Outline
Why package-based ontologyWhat is package-based ontologyExample of package-based ontology
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Why – Local vs Global Semantics Ontologies represent local views of its producer
s Biologist: dog species only eats animal Pet owner: my dog eats food from the supermarket
Global semantics could lead to semantic conflicts Dog is Carnivore and Carnivore only eats Animal PetDog is Dog and some PetDog eats DogFood; Dog
Food is CannedFood and not Animal some dog food is both animal and not animal
Terms and semantics should have its ‘scope’ Don’t make everything global
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Why – Partial vs All Or None Reuse
General Pet
Poultry Livestock
Animal Ontology(Centralized)
MyPet
General
Pet
Poultry
Livestock
MyPet
Animal Ontology(Package-extended)
Semantic importing
Semantics incorporated in MyPet ontology
Semantics not presented in MyPet ontologyLegend:
Lack of modularity: all or none Eg: how to import part
of WordNet?
Modular ontologies : more flexible and efficient reuse Less communication Less memory Less parsing time. Less junk!
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Why – Organizational vs Semantic Structure
Animal
is a part of
Organizational structure: how to arrange terms for better usage and understanding Eg: Computer Science Dictionary and
Biology Dictionary
Semantic structure: how meanings of terms are related Eg: ‘Mouse’ is a kind of ‘Animal’ or ‘M
ouse’ is part of ‘PC’
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Why – Hiding vs Sharing Ontology reflects shared
knowledge However, the provider may be
willing to expose not the entire ontology but only part of it. Copyright, Privacy, Security
Hiding definition details of an ontology module helps safer ontology organization Reduce unexpected coupling Separate “implementation” and
“interface”
Locally visible:Has personal date
Globally visible:Has activity
schedule
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology Languages Today DL, RDF(S) and OWL, OBO (for
hierarchies) However, the state of art in ontology
languages is reminiscent of the early programming languages Uncontrolled use of global terms Unwanted and uncontrolled interactions
between fragments Difficult to reuse: all or none
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology Languages Needed Modularity
Enables collaborative and scaleable tools Has localized terminology and semantics Allows partial ontology reuse Utilizes both organization and semantic structure
Knowledge Hiding Copyright, Privacy, Security concerns Controls term access in collaborative ontology b
uilding Semantic encapsulation: hide details of module
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Outline
Why package-based ontologyWhat is package-based ontologyExample of package-based ontology
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
PO: Overview
P1
P2
public
private
P1
P2
public
private
P3
protected
1. Whole ontology consists of a set of packages
2. Packages are organized in hierarchies
3. Terms (sometimes also axioms) are defined in packages with scope limitation
4. Ontology modules can be partially reused and connected with views and interfaces
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Package
A package is an ontology module with clearly defined access interface;
Each package is defined with certain ontology language and Import: a set of terms that
is imported from other ontologies
Interface: a set of terms that is visible to other ontologies
P1
P2
P1
P2
1. Whole ontology consists of a set of packages
General Pet
Poultry Livestock
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Nested Package
A nested package is part of another package
Could be used to represent organizational structure
Transitive nesting: packages are organized in a tree
P1
P2
P3
P1
P2
P3
2. Packages are organized in hierarchies
Animal
Pet
Animal Ontology(Package-extended)
Dog
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Scope Limitation Modifier SLM of an ontology term t
is a boolean function V(t,r), where r is a package Package r could access t if and only if V(t,r) = Tru
e. Predefined SLMs
Public (t,r): t is accessible from anywhere Private (t,r): t is only available in the home packa
ge Protected(t,r): t is accessible from the home pack
age and its descendants in the package hierarchy.
Term Scope is the set of packages from which t is visible
3. Terms has scope limitation
P1
P2
P3
P1
P2
P3
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
SLM: exampleThe schedule ontology(In description logics)
Hidden: details of the activity
Visible: there is an activity
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
View and Interface View and interface serve as a ‘digest’ of the ont
ology View is a selected subset of terms in one or more o
ntology packages. Interface is view defined on a single package
Usage fine-grained organization for efficiency or convenien
ce. eg: GO Slim Customization of the ontology: same ontology, differ
ent interfaces. Reusable integration of modules
P1
P2
P3
P1
P2
P3
4. Ontology modules can be partially reused and connected with views and interfaces
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
View and Interface - example Packages:
PAnimal: Dog, Cat, Carnivore,… Pplant: Tree, Grass, Flower…
Partially reuse package by interface Iamerican over: Panimal
terms: Bison; Turkey;Coyote; PrairieHog... Iasian over: Panimal
terms: AsianBuffalo; Panda; Tiger; ChineseAlligator.
Integrate package by view VYellowStoneWildLife over: Panimal; Pplant
terms: Bison;Elk; GrizzlyBear; LodgeP olePine; Sagebrush
A Package with multiple interfaces
P1
P2
P3
A View can be built upon multiple packages and can be referred to by
multiple modules
P1
P3 P4
P2
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Summary of PO
∆P is the domain of all package, ∆ S is the set of terms
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Outline
Why package-based ontologyWhat is package-based ontologyExample of package-based ontology
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Package-based Partial-order Ontology
Based on partial-order ontology Partial-order ≤ over a set S is a relati
on over S×S such that ≤ is transitive, self-reflexive, anti-symmetric.
Eg. is-a, part-ofE
C
O1(DAG) O2(tree)
A
B
DF
G
E
C
A
B
DF
G
An ontology language for modular hierarchies Trees and DAGs Hierarchy example: Yahoo directory, Gene Ontology
(GO)
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
PPO Branch Packages: A big hierarchy
may be divided into smaller branches each is a package. Example 1: in a library ontology, Q is for
science, QA76 is the branch for computer science
Example 2: metabolism is a branch of biological process in GO
Aspect Packages: An ontology may use multiple hierarchies to describe different aspects of data Example 1, the library ontology contains
both topic hierarchy and media type hierarchy
Example 2: GO has 3 ‘domains’ branches
Aspects
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Collaborative Building of PPOThe modularity of PPO facilitates collaborative
ontology building Each package can be autonomously developed Different curators can concurrently edit the
ontology on different packages Ontology can be only partially loaded to save
memory Unwanted coupling is minimized by limiting term
visibility Module access privileges is controlled by the
package hierarchy
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
The PPO Editor
The PPO Editor
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Features of the Editor Collaborative Scaleable database storage Multiple hierarchies e.g. both is-a and part-of User profile management e.g. as ontology admin
or package admin I/O from/to OWL and OBO format Communication among people Handy GUI
Download: http://boole.cs.iastate.edu/indus/ppo
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Other Package-based Ontologies
P-DL: package-extended
description logics
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ongoing work Formal description for package-based
description logics Distributed reasoning for package-based
ontologies Inconsistency detecting and reconciliation in
PO Reasoning with knowledge hiding Improve existing tools
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
AcknowledgementsGrants National Science Foundation (0219699) National Institutes of Health (GM 066387) Grant USDA
Discussions Zhiliang Hu and Jame Reecy of ISU, the Animal
Science Department Members of ISU AI Lab
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
The Story about the Semantic Web
Berners-Lee, T., Hendler, J., and Lassila, O. (2001).The semantic web. Scientific American, 284(5):34-43.
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
More Stories about the Semantic Web• Distributed• Possibly Inconsistent• Partially Hidden
Lucy
Lucy's agent asks the hospital agent for available doctors
Lucy's agent asks the hospital agent for available doctors
Lucy‘s agent
1Hospitalagent
Dr. Smith‘sagent
Dr. Black‘sagent
Hospital agent has a local but incomplete calendar list for all doctors therefore asks doctors' agents for updates.
2
Dr. Smith's agent decides not to expose the details about the 3pm-5pm date, but gives a less informative answer.
4
Hospital agent finds the inconsistency between its local calendar and the recent answers and decides to use the newer information.
3
Dr. Black's agent sends back new calendar
Hospital agent tells Lucy's agent only Dr. Smith is available 11am-3pm today.
5
3
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Example from programming language (Java)
Organizational structure Semantic structure
Why – Organizational vs Semantic Structure
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
PPO Embedded in OBO[Term]id: GO:0000009name: alpha-1,6-mannosyltransferase activity![attribute]author: baojie![attribute]modified: ![attribute]package: molecular_function![attribute]slm: publicdef: Catalysis of the transfer of …def_xref: PMID:2644248, SGD:mccxref_analog: EC:2.4.1.-
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