1. 1 Foundations V: Infrastructure and Architecture, Middleware Deborah McGuinness TA Weijing Chen Semantic eScience Week 10, November 7, 2011

2. Contents Review of reading, questions, comments Technology and how to use it Summary Next week 2

3. 3 Semantic Web Methodology and Technology Development Process Establish and improve a well-defined methodology vision for Semantic Technology based application development Leverage controlled vocabularies, et c. Use Case Small Team, mixed skills Analysis Adopt Technology Approach Leverage Technology Infrastructure Rapid Prototype Open World: Evolve, Iterate, Redesign, Redeploy Use Tools Science/Expert Review & Iteration Develop model/ ontology Evaluation

4. Architecture Importance of state –Grids –Web Existing infrastructure –Catalogs –Data sources –User interfaces –Services Wrapping these syntactic interface 4

5. Inventory Refer to the Resources –Files –Databases –Catalogs –Existing UI –Services –User database/ security –Logging –Backup/ archive 5

6. … … Geo App 1 Geo App 2 App 3 DB 2 DB 3 DB n DB 1  WSCommo n  Web Coverage Service  Web Feature Service  Web Mapping Service Limited interoperability

7. Fox WHOI: Semantic Data Frameworks March 20, 2008 7 The Astronomy approach; data- types as a service … … VO App 1 VO App 2 VO App 3 DB 2 DB 3 DB n DB 1  VOTable  Simple Image Access Protocol  Simple Spectrum Access Protocol  Simple Time Access Protocol VO layer Limited interoperability Lightweight semantics Limited meaning, hard coded Limited extensibility Under review

8. … … Web Portal Web Serv. API DB 2 DB 3 DB … DB 1 Semantic mediation layer: Ontology - capturing concepts of Parameters, Instruments, Date/Time, Space, Event, Feature, Data Product (and associated classes, properties) and Service Classes. Maps queries to underlying data. Generates access requests for metadata, data. Allows queries, reasoning, analysis, new hypothesis generation, testing, explanation, etc. Semantic mediation layer - mid- upper-level Education, clearinghouses, other services, disciplines, etc. Metadata, schema, data Query, access and use of data Semantic query, hypothesis and inference Semantic interoperability Data as Service

9. Implementing Let’s take an example –VSTO –Representative but does not exercise all semantic web capabilities 9

10. Fox RPI: Semantic Data Frameworks May 14, 2008 10 Web Service

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17. Additional Middleware Web server, Tomcat are essential (Axis) MySQL (or similar) is very handy to have OPeNDAP – for data access and transport 17

18. Fox RPI: Semantic Data Frameworks May 14, 2008 18 Web Service

20. 20 Infrastructure Protégé-OWL-API –http://protege.stanford.edu/plugins/owl/api/index.htmlhttp://protege.stanford.edu/plugins/owl/api/index.html –http://protege.stanford.edu/plugins/owl/api/guide.htmlhttp://protege.stanford.edu/plugins/owl/api/guide.html Jena (Java API for RDF and OWL) –http://protege.stanford.edu/plugins/owl/jena-integration.htmlhttp://protege.stanford.edu/plugins/owl/jena-integration.html –http://jena.sourceforge.net/http://jena.sourceforge.net/ –Migrate to other triple stores when needed

21. Using Protégé Load VSTO into Protégé 3.4 Generate Java-OWL classes from Tool menu Review other tools for generating code stubs –E.g. ELMO (http://www.openrdf.org/doc/elmo/1.3/user- guide/x463.html and http://www.openrdf.org/download.jsp )http://www.openrdf.org/doc/elmo/1.3/user- guide/x463.html http://www.openrdf.org/download.jsp 21

22. Examine some of the code Java Factory class Code stubs and ‘myclass’ VSTO code base can be made available for browsing 22

23. Jena 23

24. Infrastructure Reasoner – DIG/Pellet –http://protegewiki.stanford.edu/index.php/Protege ReasonerAPIhttp://protegewiki.stanford.edu/index.php/Protege ReasonerAPI SPARQL –http://www.w3.org/2001/sw/DataAccess/tests/imp lementationshttp://www.w3.org/2001/sw/DataAccess/tests/imp lementations Spring (Application Framework - optional) –http://www.springframework.org/http://www.springframework.org/ Eclipse (IDE) –http://www.eclipse.org/http://www.eclipse.org/ 24

25. Infrastructure Rules –OWL-2 RL –SWRL – plug-in for Protégé –Jena rules –Jess rules –Jess rules engine - http://herzberg.ca.sandia.gov/jess/ http://herzberg.ca.sandia.gov/jess/ 25

26. Software development Junit (generated in Eclipse) –http://smi- protege.stanford.edu/repos/protege/owl/trun k/junit.properties.templatehttp://smi- protege.stanford.edu/repos/protege/owl/trun k/junit.properties.template Faceted browsing – mspace 26

27. Metadata Migrate metadata into ontologies – instances, choose how you will populate them –Manual – okay to start with sufficient annotation –Scripted – preferred –rdfs_comment: essential Choose what you will not, cannot move 27

28. Services If you are going to put up services, include an end-point and a link to your WSDL (or SAWSDL) At this point, developing a full services ontology, e.g. in OWL-S may be beyond the initial implementation 28

29. Fox RPI: Semantic Data Frameworks May 14, 2008 29 Semantic Web Services

30. Fox RPI: Semantic Data Frameworks May 14, 2008 30 Semantic Web Services OWL document returned using VSTO ontology - can be used both syntactically or semantically

31. Result/ outcome Refer to the use case document Check the expected outcome and see if the test (to verify outcome) is complete Document all variations, note alternate flows Document in sufficient detail that someone else could come along and re-produce your work Include URLs for access, etc. 31

32. Summary Architectural design needs to take into account existing resources that you will leverage Keeping it simple is also very important as you begin to implement Take time to learn the tools and the supporting APIs; look at existing examples and working code Being prepared to iterate is really essential 32