Next Generation of Metadata Registries and Open Ontology Registries

Transcription

1 WUH-ROS-004 Next Generation of Metadata Registries and Open Ontology Registries Workshop on ROR, On-Demand Model Selection and Semantic Metadata Mapping Process SKLSE (State Key Laboratory of Software Engineering), Wuhan University, Wuhan, China, September 4-6, 2008 Bruce Bargmeyer Lawrence Berkeley National Laboratory University of California, Berkeley Tel: g 1

2 Notions Useful for This Workshop Issues for WG 2 (from Horiuchi-san) NCI advances linking terminology to data (metadata) ISO/IEC11179 Edition 3 Open Ontology Repository BioPortal and XMDR 2

3 Issues for WG2 Consolidation of MDR & MFI Service Interfaces From presentation given by Prof. Hajime Horiuchi at Sydney y OFMR, May

4 Overview of MDR Metamodel MDR Metamodel describe describe describe Naming data element owner Identification & Classification Stewardship Registration Authority 4 From presentation given by Prof. Hajime Horiuchi at Sydney OFMR, May 2008

5 Overview of MFI Metamodel MFI Metamodel describe describe describ e Naming Models owner Identification & Classification Stewardship Registration Authority 5 From presentation given by Prof. Hajime Horiuchi at Sydney OFMR, May 2008

6 Expected Evolution of MDR & MFI (1) Common Administration Information Common Facility for both MDR & MFI Metadata Registration ISO/IEC11179 Edition 3 ISO/IEC11179 Edition 2 ISO/IEC11179 Edition 1 Model Registration ISO/IEC19763 MOF (ISO/IEC19502) MOF (OMG) 6 Dt Data Elements SC14 From presentation given by Prof. Hajime Horiuchi at Sydney OFMR, May 2008 IRDS (ISO/IEC 10728)

7 Expected Evolution of MDR & MFI (2) Registration Procedure ISO/IEC ISO/IEC MDR+MFI Registration & Maintenance Procedure ISO/IEC ; Formulation of data ISO Directive JTC1 Directive IEC Common Database Procedure IEC ISO From presentation given by Prof. Hajime Horiuchi at Sydney OFMR, May 2008

8 ISO/IEC & and OOR Common Facility for MDR/MMF ISO/IEC11179 (MDR) ISO/IEC19502(MOF) ISO/IEC (MMF) Ontology Evolution Metamodels for Basic Ontology Constructs Registration Metamodel Content Management Normative Basic Elements Terminology Basic Classes Basic Relationship Analysis and Extraction ODM Metamodel f ODM or Metamodel CL for OWL Ontologies Registering i XMDR Registry Query Service From Prof. Hajime Horiuchi

9 NCI enhancements: with Enterprise Vocabulary Services (EVS) Concepts Unite NCI MDR Object Class Chemopreventive Agent Conceptual Domain Agent Classification Schemes cadsrtr aining Property NSCNumber Data Element Concept Chemopreventive Agent NSC Number Data Element Chemopreventive Agent Name Value Domain NSC Code Representation Code Valid Values Cyclooxygenase Inhibitor Doxercalciferol Eflornithine Ursodiol Context cacore Source: Denise Warzel, National Cancer Institute 9

10 NCI cagrid Production Environment

11 Overview A framework which enables fast and easy creation of Globus based grid services Provide easy to use graphical service authoring tool Hide all grid-ness from the developer Integration with other core grid services and architecture components GAARDS Security Infrastructure (Dorian, GridGrouper, CSM) Globus Index Service Global Model Exchange (GME) Cancer Data Standards Repository (cadsr) Extension framework for integrating with other architecture components

12 Metadata Services Cancer Data Standards Repository (cadsr) cabig projects register their data models as Common Data Elements (CDEs) which are semantically harmonized and then centrally stored and managed the cadsr The cadsr grid service provides: Model discovery and traversal cagrid standard metadata generation capabilities Enterprise Vocabulary Services (EVS) EVS is set of services and resources that address the need for controlled vocabulary The EVS grid service provides: Query access to the data semantics and controlled vocabulary managed dby the EVS

13 Metadata Services cont. Global Model Exchange (GME) GME is a DNS-like data definition registry and exchange service that is responsible for storing and linking together structural data models in the form of XML schema. The GME grid service provides: Access to the authoritative structural representation of data types on the grid Globus Information Services: Index Service The Globus Information Services infrastructure provides a generic framework for aggregation g of service metadata,, a registry of running Grid services, and a dynamic data-generating and indexing node, suitable for use in a hierarchy or federation of services The Index grid service provides: Yellow and white pages for the grid

14 cagrid Data Description Infrastructure Client and service APIs are object oriented, and operate over well-defined and curated data types Objects are defined in UML and converted into ISO/IEC Administered Components, which are in turn registered in the Cancer Data Standards Repository (cadsr) Core Services Cancer Data Standards Repository Registered In Object Definitions Semantically Described In WSDL Enterprise Vocabulary Services Data Type Definitions Registered In XSD Client GME Global Model Exchange Object definitions draw from controlled terminology and vocabulary registered in the Enterprise Vocabulary Services (EVS), and their relationships are thus semantically described XML serialization of objects adhere to XML schemas registered in the Global Model Exchange (GME) Service Service API Object Definitions Objects Service Definition Grid Service Objects Serialize To Validates Against XML Grid Client Objects Client Uses Client API

15 Ontology Summit NIST, NSF, MITRE, National Center for Ontological Research (NCOR), and others organized an Ontology Summit meeting in April The theme of the 2008 Ontology Summit was the vision for an Open Ontology Repository. This vision forms the basis of the international Open Ontology Repository community. The summit participants p supported the idea to produce such a repository (or set of repositories). An OOR-Forum will serve as a venue - both virtual and face-to-face - in which many of the issues relating to the design, implementation, ti and ongoing use of an ontology repository can be discussed and ultimately resolved. This was the third in a series of Ontology Summit meetings There are bi-weekly OOR telecons all are invited 15

16 Two Thrusts The theoretical aspects discussed in Ontology Summit Forum See: See: The practical aspects of building an Open Ontology Repository. This is pursued in the OOR- Forum. See: bin/wiki.pl?openontologyrepository iki l i 16

17 OOR Charter Promote the global use and sharing of ontologies by: 1. establishing a hosted registry-repository; y; 2. enabling and facilitating open, federated, collaborative ontology repositories; 3. establishing best practices for expressing interoperable ontology and dtaxonomy work kin registryrepositories. 17

18 Key Issues OpenOntologyRepository_Scope - documentation related to this OOR initiative's mission, charter, objectives, goals, terms of reference, definitions, scope,... etc. OpenOntologyRepository_Requirement - documentation related to the requirements of the "open ontology repository" we are planning to implement through this OOR initiative. OpenOntologyRepository_UseCases OpenOntologyRepository_Approach - documentation related to this OOR initiative's approach, and the process we will be using. OpenOntologyRepository_Architecture - documentation related to the architecture of the "open ontology repository" we are planning to implement through this OOR initiative. OpenOntologyRepository_Plan - documentation related to this OOR initiative's deliverables, timeline, milestones & deadlines, project plans, etc. 18

19 Scope An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed. 19

20 Message from Leo Obrst (MITRE) I'd advise folks to look over xmdr.org (extended Metadata Registry) )before they re-invent 95% of the wheels, including definitions, architecture, requirements, use cases, etc. Although h XMDR, like the ISO Metadata Registry standard, is concerned with more than an ontology registry/repository, their notions are extremely salient to our effort. And no, I am not involved in XMDR, and am only interested in seeing that good work is recognized, 20 and possible duplication of effort is avoided.

21 BioPortal and XMDR Demo BioPortal here Demo XMDR here 21

22 What XMDR Brings to the Table Use cases - semantics challenges - and Requirements Proposed specifications for ISO/IEC Edition 3 Model, definitions, ontology Modular d l software architecture and open source software modules Open Source XMDR software Test T tcontent t 22

23 XMDR Use Cases OOR - what do we want to construct? XMDR contributed use cases to the OOR web site. It would be good to update and flesh out the use cases. The XMDR use cases are based on proposals for ISO/IEC Edition 3. The intent is to use semantic artifacts, such as ontologies, to help manage data. The core OOR functionality may be registering and disseminating ontologies. Do we want to extend our effort to the linkage of concept systems (e.g., ontologies) to metadata that describes data? Do we want to be able to reason across the content of an OOR? XMDR enables this. 23

24 Use Case: Combine Data, Metadata & Concept Systems Inference Search Query: find water bodies downstream from Fletcher Creek where chemical contamination was over 10 micrograms per liter between December 2001 and March 2003 Data: ID Date Temp Hg A B X Concept system: Contamination Biological Radioactive Chemical mercury lead cadmium Metadata: Name Datatype Definition Units ID text Monitoring Station Identifier not applicable Date date Date yy-mm-dd Temp number Temperature (to 0.1 degree C) degrees Celcius micrograms per Hg number Mercury contamination ti liter 24

25 Use Case: Gain Common Understanding of meaning between Data Creators and Data Users A common interpretation of what the data represents EEA text data ambiente agricultura tiempo salud hunano industria turismo tierra agua aero USGS text data environ agriculture climate human health industry tourism soil water air DoD text data environ agriculture climate human health industry tourism soil water air EPA text environ agriculture climate human health industry tourism soil water air data ambiente text data agricultura tiempo salud huno industria turismo tierra agua aero 308 Others... Users Information systems Data Creation 25

26 Use Case: Find and process non-explicit data For example Analgesic Agent Patient data on drugs contains brand names (e.g. Tylenol, Anacin-3, Datril, ); However, want to study patients taking analgesic agents Non-Narcotic Analgesic Analgesic and Antipyretic Nonsteroidal Antiinflammatory Drug Acetominophen Tylenol Anacin-3 Datril 26

27 Model Ontology Region 27

28 Model Registration Region 28

29 Model: XMI from ed3 UML is transformed to RDF/OWL for XML metamodel specification XMDR OPEN SOURC CE TOOLS ABSTRA ACT STEP Poseidon Human compare / hand editing XSLT Protege Swoop Jena Pellet scripts ) FILES (AN ND TYPES) XMDR Metamodel (UML) XMDR Metamodel (XMI) XMDR Metamodel (preliminary RDF/OWL) XMDR Metamodel (final RDF/OWL) XMDR Metamodel asserted logic index XMDR Metamodel inferred l i i d RDF/OWL) RDF/OWL) logic index POSS SIBLE ALTER RNATE TOO OLS Rational Rose? MagicDraw? Sandpiper Visual Ontology Modeler? page 29 of xxx CMWR July 8, v2.ppt Others?

30 XMDR Architecture & Open Source Software Metadata Sources concept systems, data elements USERS Web Browsers..Client Software Content Loading & Transformation (LexGrid & custom) Validation (XML Schema) Human User Interface (XML pages & javascript) Application Program Interface (REST) Authentication Service Metamodel specs (UML & Editing) (Poseidon, Protege) XMDR data model & exchange format XML, RDF, OWL Registry Store (Subversion) XMDR metamodel (OWL & xml schema) page 30 of xxx Mapping Engine standard XMDR files standard XMDR files standard XMDR files Inferred standard XMDR files CMWR July 8, v2.ppt LogicIndex Search & Inference Queries (Jena, SPARQL) Reasoner Text Search (Pellet) (Lucene) Asserted LogicIndex Full Text Index

31 Content loading, with XMDR metamodel used for inferred indexing and validation CONTENT TRANSFORMATION VALIDATION REGISTRY INFORMATION INDEXING Terminology A Terminology B Thesaurus C LexGrid Subversion XMDR Files A XMDR Files B XMDR Files C Reasoner (Pellet) Inferred LogicIndex Terminology D Data Element Source E XSLT script E XMDR metamodel In XML schema XMDR Files D XMDR Files E Search & Inference Framework (Jena) Assesed Lo ogicindex Terminology Source F XSLT script F XMDR Files F Ontology Source G External Source H page 31 of xxx XSLT script G XSLT script G XMDR Files G XMDR Files H (virtual) Text Indexing (Lucene) Fu ull Text Log gicindex

32 An Approach Use BioPortal Use LexGrid Extend with XMDR 32

33 Concept System Store Metadata Registry Structured Metadata Concept System Thesaurus Themes Ontology GEMET Data Standards Concept systems: Keywords Controlled Vocabularies Thesauri Taxonomies Ontologies Axiomatized Ontologies (Essentially graphs: node- relation-node + axioms) 33

34 Management of Concept Systems Metadata Registry Concept system: Structured Metadata Concept System Thesaurus Themes Ontology GEMET Data Standards } Registration Harmonization i Standardization Acceptance (vetting) Mapping (correspondences) 34

35 Life Cycle Management Metadata Registry Structured Metadata Concept System Thesaurus Themes Ontology GEMET Data Standards Life cycle management: Data and Concept systems (ontologies) 35

36 Grounding Semantics Metadata Registry Structured Metadata Concept System Thesaurus Themes Ontology GEMET Metadata Registries Semantic Web RDF Triples Data Standards Subject (node URI) Verb (relation URI) Object (node URI) Ontologies 36

37 Another Application: GEO/GEOSS/GMES The work addresses information challenges identified by major initiatives including the Intergovernmental Group on Earth Observations (GEO), Global Earth Observation System of Systems (GEOSS), and Global Monitoring for Environment and Security (GMES). The techniques and technologies developed will be useful for GEO/GEOSS/GMES. In particular, this work addresses priority challenges identified by the GEOSS Architecture & Data Management (ADM) committee to enable increased interoperability across existing data management systems: Identify & address integration gaps in data management systems Utilize community standards for data & metadata Enable integrated measurements, data, products & predictive models Examine the need for future data management requirements. Architecture & Data Management (ADM) Working Group Report February 22, See: 37

38 Thanks & Acknowledgements John McCarthy, LBNL Kevin Keck, LBNL Fred Gey, UCB Hajime Horiuchi, Tokyo International University Leo Obrst, MITRE Frank Olken, LBNL Anirban Sen, UCB Harold Solbrig, Mayo Clinic Denise Warzel, NCI INCITS L8 and ISO/IEC JTC1/SC 32/WG 2 Standards Committees Major XMDR Project Sponsors and Collaborators National Science Foundation (Grant # ) National Cancer Institute t U.S. Environmental Protection Agency Department of Defense U.S. Geological Survey And others!

39 Acknowledgement This material is based upon work supported by the National Science Foundation under Grant No , and USEPA. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, USEPA or USDOD. For more information see XMDR.org 3