collaborative package-based ontology building and usage

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.


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


Outline

Why package-based ontologyWhat is package-based ontologyExample of package-based ontology


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


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!


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’


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


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


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


Outline



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


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


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


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


SLM: exampleThe schedule ontology(In description logics)

Hidden: details of the activity

Visible: there is an activity


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


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


Summary of PO

∆P is the domain of all package, ∆ S is the set of terms


Outline



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)


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


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


The PPO Editor

The PPO Editor


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


Other Package-based Ontologies

P-DL: package-extended

description logics


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


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


The Story about the Semantic Web

Berners-Lee, T., Hendler, J., and Lassila, O. (2001).The semantic web. Scientific American, 284(5):34-43.


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


Example from programming language (Java)

Organizational structure Semantic structure

Why – Organizational vs Semantic Structure


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.-

collaborative package-based ontology building and usage

Technology

ontology packages

ontology view

ontology languages

package package r

collaborative ontology

ontology modules

ontology term t

partial ontology reuse