Collaborative Package-based Ontology Building and Usage


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  • Collaborative Package-based Ontology Building and Usage

    1. 1. Collaborative Package-based Ontology Building and Usage Jie Bao and Vasant Honavar Artificial Intelligence Research Laboratory Computer Science Department Iowa State University Ames IA USA 50010 {baojie,honavar} 2005 Nov 27 Houston. IEEE Workshop on Knowledge Acquisition from Distributed, Autonomous, Semantically Heterogeneous Data and Knowledge Sources, in ICDM2005.
    2. 2. What is it about? <ul><li>Package-based Ontology (PO), a modular approach for cooperative and scalable building and reuse of large-scale ontologies </li></ul><ul><li>The motivations of PO </li></ul><ul><li>The basic definitions of PO </li></ul><ul><li>Example language: Package-based Hierarchy </li></ul>
    3. 3. Outline <ul><li>Why package-based ontology </li></ul><ul><li>What is package-based ontology </li></ul><ul><li>Example of package-based ontology </li></ul>
    4. 4. Why – Local vs Global Semantics <ul><li>Ontologies represent local views of its producers </li></ul><ul><ul><li>Biologist: dog species only eats animal </li></ul></ul><ul><ul><li>Pet owner: my dog eats food from the supermarket </li></ul></ul><ul><li>Global semantics could lead to semantic conflicts </li></ul><ul><ul><li>Dog is Carnivore and Carnivore only eats Animal </li></ul></ul><ul><ul><li>PetDog is Dog and some PetDog eats DogFood ; DogFood is CannedFood and not Animal </li></ul></ul><ul><ul><li> some dog food is both animal and not animal </li></ul></ul><ul><li>Terms and semantics should have its ‘scope’ </li></ul><ul><ul><li>Don’t make everything global </li></ul></ul>
    5. 5. Why – Partial vs All Or None Reuse <ul><li>Lack of modularity: all or none </li></ul><ul><ul><li>Eg: how to import part of WordNet? </li></ul></ul><ul><li>Modular ontologies : more flexible and efficient reuse </li></ul><ul><ul><li>Less communication </li></ul></ul><ul><ul><li>Less memory </li></ul></ul><ul><ul><li>Less parsing time. </li></ul></ul><ul><ul><li>Less junk! </li></ul></ul>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 ontology Legend :
    6. 6. Why – Organizational vs Semantic Structure <ul><li>Organizational structure: how to arrange terms for better usage and understanding </li></ul><ul><ul><li>Eg: Computer Science Dictionary and Biology Dictionary </li></ul></ul><ul><li>Semantic structure: how meanings of terms are related </li></ul><ul><ul><li>Eg: ‘Mouse’ is a kind of ‘Animal’ or ‘Mouse’ is part of ‘PC’ </li></ul></ul>Animal is a part of
    7. 7. Why – Hiding vs Sharing <ul><li>Ontology reflects shared knowledge </li></ul><ul><li>However, the provider may be willing to expose not the entire ontology but only part of it. </li></ul><ul><ul><li>Copyright, Privacy, Security </li></ul></ul><ul><li>Hiding definition details of an ontology module helps safer ontology organization </li></ul><ul><ul><li>Reduce unexpected coupling </li></ul></ul><ul><ul><li>Separate “implementation” and “interface” </li></ul></ul>Locally visible: Has personal date Globally visible: Has activity schedule
    8. 8. Ontology Languages Today <ul><li>DL, RDF(S) and OWL, OBO (for hierarchies) </li></ul><ul><li>However, the state of art in ontology languages is reminiscent of the early programming languages </li></ul><ul><ul><li>Uncontrolled use of global terms </li></ul></ul><ul><ul><li>Unwanted and uncontrolled interactions between fragments </li></ul></ul><ul><ul><li>Difficult to reuse: all or none </li></ul></ul>
    9. 9. Ontology Languages Needed <ul><li>Modularity </li></ul><ul><ul><li>Enables collaborative and scaleable tools </li></ul></ul><ul><ul><li>Has localized terminology and semantics </li></ul></ul><ul><ul><li>Allows partial ontology reuse </li></ul></ul><ul><ul><li>Utilizes both organization and semantic structure </li></ul></ul><ul><li>Knowledge Hiding </li></ul><ul><ul><li>Copyright, Privacy, Security concerns </li></ul></ul><ul><ul><li>Controls term access in collaborative ontology building </li></ul></ul><ul><ul><li>Semantic encapsulation: hide details of module </li></ul></ul>
    10. 10. Outline <ul><li>Why package-based ontology </li></ul><ul><li>What is package-based ontology </li></ul><ul><li>Example of package-based ontology </li></ul>
    11. 11. PO: Overview P 3 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
    12. 12. Package <ul><li>A package is an ontology module with clearly defined access interface; </li></ul><ul><li>Each package is defined with certain ontology language and </li></ul><ul><ul><li>Import: a set of terms that is imported from other ontologies </li></ul></ul><ul><ul><li>Interface: a set of terms that is visible to other ontologies </li></ul></ul>1. Whole ontology consists of a set of packages General Pet Poultry Livestock
    13. 13. Nested Package <ul><li>A nested package is part of another package </li></ul><ul><li>Could be used to represent organizational structure </li></ul><ul><li>Transitive nesting: packages are organized in a tree </li></ul>2. Packages are organized in hierarchies Animal Pet Animal Ontology (Package-extended) Dog
    14. 14. Scope Limitation Modifier <ul><li>SLM of an ontology term t </li></ul><ul><ul><li>is a boolean function V(t,r), where r is a package </li></ul></ul><ul><ul><li>Package r could access t if and only if V(t,r) = True. </li></ul></ul><ul><li>Predefined SLMs </li></ul><ul><ul><li>Public (t,r): t is accessible from anywhere </li></ul></ul><ul><ul><li>Private (t,r): t is only available in the home package </li></ul></ul><ul><ul><li>Protected(t,r): t is accessible from the home package and its descendants in the package hierarchy. </li></ul></ul><ul><li>Term Scope is the set of packages from which t is visible </li></ul>3. Terms has scope limitation
    15. 15. SLM: example The schedule ontology(In description logics) Hidden: details of the activity Visible: there is an activity
    16. 16. View and Interface <ul><li>View and interface serve as a ‘digest’ of the ontology </li></ul><ul><ul><li>View is a selected subset of terms in one or more ontology packages. </li></ul></ul><ul><ul><li>Interface is view defined on a single package </li></ul></ul><ul><li>Usage </li></ul><ul><ul><li>fine-grained organization for efficiency or convenience. eg: GO Slim </li></ul></ul><ul><ul><li>Customization of the ontology: same ontology, different interfaces. </li></ul></ul><ul><ul><li>Reusable integration of modules </li></ul></ul>4. Ontology modules can be partially reused and connected with views and interfaces
    17. 17. View and Interface - example <ul><li>Packages: </li></ul><ul><ul><li>P Animal : Dog, Cat, Carnivore,… </li></ul></ul><ul><ul><li>P plant : Tree, Grass, Flower… </li></ul></ul><ul><li>Partially reuse package by interface </li></ul><ul><ul><li>I american over: P animal terms: Bison; Turkey;Coyote; PrairieHog... </li></ul></ul><ul><ul><li>I asian over: P animal terms: AsianBuffalo; Panda; Tiger; ChineseAlligator. </li></ul></ul><ul><li>Integrate package by view </li></ul><ul><ul><li>V YellowStoneWildLife over: P animal ; P plant terms: Bison;Elk; GrizzlyBear; LodgeP olePine; Sagebrush </li></ul></ul>A Package with multiple interfaces P 1 P 2 P 3 A View can be built upon multiple packages and can be referred to by multiple modules P 1 P 3 P 4 P 2
    18. 18. Summary of PO ∆ P is the domain of all package, ∆ S is the set of terms
    19. 19. Outline <ul><li>Why package-based ontology </li></ul><ul><li>What is package-based ontology </li></ul><ul><li>Example of package-based ontology </li></ul>
    20. 20. Package-based Partial-order Ontology <ul><li>Based on partial-order ontology </li></ul><ul><ul><li>Partial-order ≤ over a set S is a relation over S×S such that ≤ is transitive, self-reflexive, anti-symmetric. </li></ul></ul><ul><ul><li>Eg. is-a, part-of </li></ul></ul><ul><li>An ontology language for modular hierarchies </li></ul><ul><ul><li>Trees and DAGs </li></ul></ul><ul><ul><li>Hierarchy example: Yahoo directory, Gene Ontology (GO) </li></ul></ul>
    21. 21. PPO <ul><li>Branch Packages : A big hierarchy may be divided into smaller branches each is a package. </li></ul><ul><ul><li>Example 1: in a library ontology, Q is for science, QA76 is the branch for computer science </li></ul></ul><ul><ul><li>Example 2: metabolism is a branch of biological process in GO </li></ul></ul><ul><li>Aspect Packages : An ontology may use multiple hierarchies to describe different aspects of data </li></ul><ul><ul><li>Example 1, the library ontology contains both topic hierarchy and media type hierarchy </li></ul></ul><ul><ul><li>Example 2: GO has 3 ‘ domains ’ </li></ul></ul>branches Aspects
    22. 22. Collaborative Building of PPO <ul><li>The modularity of PPO facilitates collaborative ontology building </li></ul><ul><li>Each package can be autonomously developed </li></ul><ul><li>Different curators can concurrently edit the ontology on different packages </li></ul><ul><li>Ontology can be only partially loaded to save memory </li></ul><ul><li>Unwanted coupling is minimized by limiting term visibility </li></ul><ul><li>Module access privileges is controlled by the package hierarchy </li></ul>
    23. 23. The PPO Editor The PPO Editor
    24. 24. Features of the Editor <ul><li>Collaborative </li></ul><ul><li>Scaleable database storage </li></ul><ul><li>Multiple hierarchies e.g. both is-a and part-of </li></ul><ul><li>User profile management e.g. as ontology admin or package admin </li></ul><ul><li>I/O from/to OWL and OBO format </li></ul><ul><li>Communication among people </li></ul><ul><li>Handy GUI </li></ul>Download:
    25. 25. Other Package-based Ontologies P-DL: package-extended description logics
    26. 26. Ongoing work <ul><li>Formal description for package-based description logics </li></ul><ul><li>Distributed reasoning for package-based ontologies </li></ul><ul><li>Inconsistency detecting and reconciliation in PO </li></ul><ul><li>Reasoning with knowledge hiding </li></ul><ul><li>Improve existing tools </li></ul>
    27. 27. Acknowledgements <ul><li>Grants </li></ul><ul><li>National Science Foundation (0219699) </li></ul><ul><li>National Institutes of Health (GM 066387) Grant </li></ul><ul><li>USDA </li></ul><ul><li>Discussions </li></ul><ul><li>Zhiliang Hu and Jame Reecy of ISU, the Animal Science Department </li></ul><ul><li>Members of ISU AI Lab </li></ul>
    28. 29. The Story about the Semantic Web Berners-Lee, T., Hendler, J., and Lassila, O. (2001).The semantic web. Scientific American, 284(5):34-43.
    29. 30. More Stories about the Semantic Web <ul><li>Distributed </li></ul><ul><li>Possibly Inconsistent </li></ul><ul><li>Partially Hidden </li></ul>Lucy Lucy's agent asks the hospital agent for available doctors Lucy‘s agent 1 Hospital agent Dr. Smith‘s agent Dr. Black‘s agent 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
    30. 31. Why – Organizational vs Semantic Structure Example from programming language (Java) Organizational structure Semantic structure
    31. 32. PPO Embedded in OBO <ul><li>[Term] </li></ul><ul><li>id: GO:0000009 </li></ul><ul><li>name: alpha-1,6-mannosyltransferase activity </li></ul><ul><li>![attribute]author: baojie </li></ul><ul><li>![attribute]modified: </li></ul><ul><li>![attribute]package: molecular_function </li></ul><ul><li>![attribute]slm: public </li></ul><ul><li>def: Catalysis of the transfer of … </li></ul><ul><li>def_xref: PMID:2644248, SGD:mcc </li></ul><ul><li>xref_analog: EC:2.4.1.- </li></ul>