OntoBrowse: A World of Knowledge - ePrints Soton
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1. 4 D A Countries with 15 Airports Armenian Armenia Map Yerevan untitled2 O narrowing rdf label Armenia 3store pling net 7 3store pling net Afghanistan Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Arctic Ocean Argentina Armenia Aruba Ashmore and Cartier Islands Atlantic Ocean Australia Austria Azerbaijan Bahamas The Bahrain Baker Island Bangladesh Barbados Bassas da India Belarus Belgium Belize Benin gt factbook Administrativedivisions factbook Agestructure 0 14years factbook Agestructure 15 64years factbook Agestructure 65yearsandover factbook Agriculture products factbook Airports factbook Airports withpavedrunways 1524to2437m factbook Airports withpavedrunways 2438to3047 factbook Airports withpavedrunways 914to1523m factbook Airports withpavedrunways over3047m factbook Airports withpavedrunways total factbook Airports withunpavedrunways 1524to2437m factbook Airports withunpavedrunways 914to1523m factbook Airports withunpavedrunways over3047m factbook Airports withunpavedrunways total factbook Airports withunpavedrunways under914m factbook Area comparative factbook Area land factbook Area total factbook Area water factbook Background factbook Birthrate factbook Budget expenditures factbook Budget revenues factbook Capital factbook Climate factbook Coastline En foo d ai SELECT y WHERE2. e Java using Swing for the GUI e C C with a cross platform windowing toolkit such as GTK or wxWin dows for the GUI e PHP with extensive use of JavaScript for a web based system Highlighted in the above list is an important design consideration Whether the system be a desktop application or a web based application World wide web browsers exist for virtually all platforms and thus a web based solution would be ideal for this constraint however in order to create a viable web based solution that would act as dynamically as a desktop application i e without a visible page refresh one would have to employ complicated JavaScript on the client side While possible the development time on such as project is not feasible for the time contraints put upon this project Leaving a choice between C C and Java for creating a desktop application solution the differences come in the form of the following Chapter 2 Technology Choices 9 e Level of personal experience with either language e Amount of time required to produce high quality application e Ease of debugging e Performance While my own personal experience with both is enough to choose either I have written more applications in Java in terms of quantity as well as complexity Java also boasts much easier debugging as well as a centralised API documenta tion In terms of the available Integrated Development Environments IDEs Java was once lacking t
3. Armenia Guinea Marshall Islands Sri Lanka SELECT y WHERE x lt factbook Airports gt 15 x lt rdf label gt y FIGURE 3 5 Five Column Screenshot Note that when an alias is used the octothorpe symbol is changed to a colon this is the standard and is required in this case so that the RDQL queries are aware this is an alias The RDQL operator USING is used to state aliases and this is automatically appended to the query where necessary 3 6 Query Generation One of the main abilities of ontoBrowse is to automatically generate and execute RDQL Seaborne 2004 queries on behalf of the user There is of course no need for the user to even know what RDQL is The very first query is generated from an entry point predicate chosen by the user All objects referenced by this predicate are listed in a new column The initial query is generated as thus SELECT x WHERE z lt rdf label gt x USING rdf FOR lt http www w3 org 1999 02 22 rdf syntax ns gt Chapter 3 Development 17 This is one of the simplest forms of query with only one triple and indeed only one values The triplestore will return an XML formatted table of results containing the value of rdf label for all objects which are referenced by this predicate In this example the pretty names i e rdf labels of all objects that have them are displayed The second query is generated when the user selects one of th
4. 2 3 Knowledge Acquisition 2 e tedte 2 dees ea T 2 4 Software Development Language 8 3 Development 10 Sos RDE E Oe eR ct LA ga ek Ee ate 10 3 2 The CIA World Factbook 3 0 0 54 2 5 5 6 a ee 4h A ere BO 11 Dial a ote hn IR oe he EEN 11 A e E eh A O 12 A 6 ech ted fe ee th IR OR Bed le ag 12 3 4 Multiple Ke aaa ea ep ee Ser ps dor 13 3 5 Namespace CACHING e io aa grp e Seep a Ge Ste 13 3 6 Query Generation a a A a A 16 Out Bookmarks ds oe ka ee Ee es ae aes o a A 17 3 8 Rendezvous Sharing of Bookmarks 19 O00 Renderer Panel ye e ea a tn hn Yee a Go Sd on aaa oat Uy 20 3 10 Docked Panels and State o o 21 3 11 URIs nd Literals VE E E ee e as de pa 21 Se laa da ot og he Boe a eye eas la ea 23 Jal sia BEN Boa is See Sone E are E 23 Glee e s g 3 6 ran lt a Gua ra ee aoe Ge ws Ge BS 24 4 3Store 26 Ah Producida ea e Le Oh hae IE Bale a 26 425 Installation oat aS a id as E aaa e eae BOT 26 AND ACCESS IO hid dee Ree a e 27 AA Oe EIKES ae O ae EE 27 4 5 Possible Improvements ab aD wa Sb koe a AA Ser CONTENTS 3 A User Manual 28 A 1 The Features of OntoBrowse 0 2 00 28 A 1 1 What is OntoBrowse for ia aa e dde 28 A 1 2 What else can OntoBrowse do 28 A 1 3 Why is OntoBrowse easy to use 29 A 1 4 Does OntoBrowse utilise any advanced technology 29 A 1 5 Does OntoBrowse only show results 30 A 2 Basi
5. Atlantic Ocean Australia Austria Azerbaijan Bahamas The Bahrain Baker Island Bangladesh Barbados Bassas da India Belarus Belgium Belize A ai E d 3store pling net factbook Administratived factbook Agestructure 0 factbook Agestructure 1 factbook Agestructure 6 factbook Agriculture pro factbook Airports factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withun factbook Airports withun factbook Airports withun factbook Airports withun factbook Airports withun factbook Area comparati factbook Area land factbook Area total factbook Area water factbook Background factbook Birthrate factbook Budget expendi factbook Coastline iv GP llanas D 3store pling net 15 3store pling net E factbook Administratived 4 factbook Agestructure 0 factbook Agestructure 1 factbook Agestructure 6 factbook Agriculture pro factbook Airports factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withpa factbook Airports withun factbook Airports withun factbook Airports withun factbook Airports withun factbook Airports withun factbook Area comparati factbook Area land factbook Area land in s factbook Area note factbook Area total factbook Area total in s_ factbook Area water factbook Area wa
6. D Beckett Rdf xml syntax specification revised 2004 http www w3 org TR 2004 REC rdf syntax grammar 20040210 National Technical Information Service CIA The CIA World Factbook US Gov ernment Printing Office 2003 M Dixon An overview of document mining technology 1997 URL citeseer ist psu edu dixon97overview html H Glaser H Alani L Carr S Chapman F Ciravegna A Dingli N Gibbins S Harris m c schraefel and N Shadbolt Cs aktive space Building a semantic web application Proceedings of European Semantic Web Symposium 2004 2004 T Leonard and H Glaser Large scale acquisition and maintenance from the web without source access In Proceedings of Workshop 4 Knowledge Markup and Semantic Annotation pages 97 101 2001 D McGuinness and van Harmelen F Owl web ontology language overview http www w3 org TR owl features 2004 A Seaborne Rdql a query language for rdf 2004 http www w3 org Submission RDQL L Tauscher Supporting world wide web navigation through history mechanisms In CHI 96 Workshop HCI and the Web University of Calgary 1996 38
7. See Figure 3 3 Once the resultant objects are shown the user can then select one and since an object is also a subject the result is treated as a new subject and a query to result in a list of predicates is generated and executed See Figure 3 4 Utilising this mechanism it is possible for a user to quickly browse or surf through the contents of a triplestore indefinately See Figure 3 5 3 4 Multiple Triplestores Using the browsing metaphor of a step by step branching choice it can should be possible to choose at any branch the triplestore to which the resultant query is to be sent for execution Preferably in the form of a drop down combobox ref pre populated with known triplestores These would be saved from the users previous queries An option to clear the saved servers should be available 3 5 Namespace Caching In RDF every non literal resource and object must be referenced by a properly formatted URI In order that the interface is not clogged up with these often very long URIs ontoBrowse stores a cache of aliases Once an alias is set the user never needs to see the original URI again for example the aktors org triplestore may reference a person as http www ecs soton ac uk info person 02686 An alias can be set for the namespace http www ecs soton ac uk info as ecs so that the above URI would therefore show as ecs person 02686 Chapter 3 Development 14 Onto
8. x lt factbook Name gt Armenia x y z FIGURE 3 2 Two Column Screenshot Chapter 3 Development 15 OntoBrowse lt das301 ecs soton ac uk gt gt SN RIB K Columns per row Vi a Ww Bookmarks x Lo Yerevan 7 Armenia Map gt gt 3store pling ne 2 Airports Y gt 3store pling ne gt gt factbook N factbook Ai 2 Countries with 154 Y 3store pling ne gt factbookiN Y gt factbook Ai Dis rgilabel 1 Armenian a gt Renderer x Countries with 15 Airports Armenian Armenia Map Yerevan untitled2 1 narrowing rdf label Armenia factbook Airports 3store pling net 3store pling net Afghanistan Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Arctic Ocean Argentina Armenia Aruba Ashmore and Cartier Islands Atlantic Ocean Australia Austria Azerbaijan Bahamas The Bahrain Baker Island Bangladesh Barbados Bassas da India Belarus Belgium Belize Nani aS 2 D factbook Administrativedivisions factbook Agestructure 0 14years factbook Agestructure 15 64years factbook Agestructure 65yearsand factbook Agriculture products factbook Airports factbook Airports withpavedrunway factbook Airports withpavedrunway factbook Airports withpavedrunway factbook Airports withpavedrunway fact
9. Aruba Ashmore and Cartier Islands Atlantic Ocean Australia Austria Azerbaijan Bahamas The Bahrain Baker Island Bangladesh Barbados Bassas da India Belarus Belgium Belize Benin FIGURE A 5 All Country Names A 2 2 Using Bookmarks If there is not a panel shown entitled Bookmarks you will need to open it using the bookmarks toolbar button which looks like two green bookmarks overlaid at 45 degrees See Figure A 6 Click this icon to toggle the bookmarks panel FIGURE A 6 Bookmarks Toolbar Toggle Button To save all or a portion of the current query as a bookmark simply right click on the required column and choose one of the bookmark options as in Figure A 7 Appendix A User Manual 32 ctbook Airports ctbookybisnos ithpavedcun ctboo Bookmark Entire Tree ctboo Bookmark Upto This Node ctboo Bookmark From This Node gi Image Render in New Window bel Web Render in New Window rhel Airnorte owithtinnavadrii FIGURE A 7 Bookmark Options When an option is chosen a dialog will prompt for a name for the bookmark See Figure A 8 enter then name you wish to use Enter a name for this bookmark Egypt Cancel Co i FIGURE A 8 Bookmark Name Prompt In the bookmarks panel the new bookmark will be shown as in Figure A 9 Bookmarks x T PP E O Daniel Smith s Bookmarks Armenia Map LA Armenian Lo Countries with 15 Airpor
10. database tables for use with the 3store server software Taken from 3store release v2 2 8 USE rdf CREATE TABLE models hash bigint 20 NOT NULL default 0 model text NOT NULL PRIMARY KEY hash TYPE MyISAM CREATE TABLE literals hash bigint 20 NOT NULL default 0 literal text NOT NULL PRIMARY KEY hash TYPE MyISAM CREATE TABLE resources hash bigint 20 NOT NULL default 0 uri varchar 255 NOT NULL default PRIMARY KEY hash KEY uri TYPE MyISAM 36 Appendix C 3Store SQL 37 CREATE TABLE triples model bigint 20 NOT NULL default 0 subject bigint 20 NOT NULL default 0 predicate bigint 20 NOT NULL default 0 object bigint 20 NOT NULL default 0 literal tinyint 1 NOT NULL default 07 inferred tinyint 1 NOT NULL default 0 UNIQUE KEY spo subject predicate object KEY o object KEY po predicate object TYPE MyISAM CREATE TABLE taxonomy class bigint 20 NOT NULL default 0 superclass bigint 20 NOT NULL default 0 KEY class class KEY superclass superclass TYPE MyISAM CREATE TABLE cache_state taxonomy int 11 NOT NULL default 0 sia int 11 NOT NULL default 0 TYPE MyISAM INSERT INTO cache_state VALUES Bibliography
11. either at initialisation of the Rendezvous layer or during running the system connects to the specified IP and Chapter 3 Development 20 port When a connection is made the serving program sends an XML formatted stream of all bookmarks as such lt messagestream gt lt bookmark gt lt name gt Armenia Map lt name gt lt server gt 3store pling net lt server gt lt type gt 1 lt type gt lt entry type uri gt factbook Name lt entry gt lt entry type literal gt Armenia lt entry gt lt entry type uri gt factbook has map lt entry gt lt bookmark gt lt bookmark gt lt name gt Armenian lt name gt lt server gt 3store pling net lt server gt lt type gt 1 lt type gt lt entry type uri gt factbook Name lt entry gt lt entry type literal gt Armenia lt entry gt lt bookmark gt lt messagestream gt The connecting client decodes this stream and displays it to the user via the bookmark panel If the user decides to stop sharing bookmarks or when the program is closed the Rendezvous service notification is expired and removed 3 9 Renderer Panel When results are shown the rendering panel parses them for any literal URIs that reference any document types that that renderer knows how to display which is currently PNG JPEG and GIF images The renderer will scale them retaining correct aspect ratio to the width of the panel stacking them vertically with a scroll facility when required a
12. gt NumericExpression lt GT gt NumericExpression lt LE gt NumericExpression lt GE gt NumericExpression NumericExpression ShiftExpression ShiftExpression AdditiveExpression lt LSHIFT gt AdditiveExpression lt RSIGNEDSHIFT gt AdditiveExpression lt RUNSIGNEDSHIFT gt AdditiveExpression AdditiveExpression MultiplicativeExpression lt PLUS gt MultiplicativeExpression lt MINUS gt MultiplicativeExpression MultiplicativeExpression UnaryExpression lt STAR gt UnaryExpression lt SLASH gt UnaryExpression lt REM gt UnaryExpression UnaryExpression UnaryExpressionNotPlusMinus lt PLUS gt UnaryExpression lt MINUS gt UnaryExpression UnaryExpressionNotPlusMinus lt TILDE gt lt BANG gt UnaryExpression PrimaryExpression PrimaryExpression Var Literal FunctionCall lt LPAREN gt Expression lt RPAREN gt FunctionCall Identifier lt LPAREN gt ArgList lt RPAREN gt ArgList VarOrLiteral VarOrLiteral Literal URI NumericLiteral TextLiteral BooleanLiteral NullLiteral NumericLiteral lt INTEGER_LITERAL gt lt FLOATING_POINT_LITERAL gt TextLiteral lt STRING_LITERAL gt BooleanLiteral lt BOOLEAN_LITERAL gt NullLiteral lt NULL_LITERAL gt URL URI URI lt lt URI gt gt Identifier lt IDENTIFIER gt Appendix C 3Store SQL The following SQL creates properly formatted empty
13. produced the maps The Hoover Commission s Clark Committee set up in 1954 to study the structure and administration of the CIA reported to Congress in 1955 that The National Chapter 3 Development 12 Intelligence Survey is an invaluable publication which provides the essential el ements of basic intelligence on all areas of the world There will always be a continuing requirement for keeping the Survey up to date The Factbook was created as an annual summary and update to the encyclopedic NIS studies The first classified Factbook was published in August 1962 and the first unclassified version was published in June 1971 The NIS program was terminated in 1973 except for the Factbook map and gazetteer components The 1975 Factbook was the first to be made available to the public with sales through the US Government Printing Office GPO The Factbook was first made available on the Internet in June 1997 The year 2003 marks the 56th anniversary of the establishment of the Central Intelligence Agency and the 60th year of continuous basic intelligence support to the US Government by The World Factbook and its two predecessor programs CIA 2003 3 2 2 Parsing The process followed for the parsing of the CIA World Factbook was to first exam ine the web documents to ensure that the required data fields could be extracted and to formulate a basic strategy for this extraction As with a lot of data sources on the world wide web the
14. sesame aidministrator nl e 3Store at http sourceforge net projects threestore RDFStore and Jena are both backend systems for local query of RDF data and as such are not suitable for this application other similar systems also exist in the form of PHP and Perl libraries for the query of RDF data which do not provide the server capability that this project requires Sesame and 3Store however both run as server applications centrally storing and indexing RDF data accepting RDQL queries and returning results In terms of ability Sesame and 3Store are very capable of the job 3Store offers the benefit of a speedier core engine thanks to the choice of C over Sesame s Java Interfacing with 3Store also offers the benefit that it is being used by a number of publically accessible ontologies run by AKT and as such these will be usable immediately 3Store also has the advantage of local development i e it is being developed in this department whereas Sesame is being developed primarily in the Netherlands This allows for easier debugging of any potential server issues as well as solving troubleshooting issues Given these advantages 3Store shall be used for RDF storage on this project 2 3 Knowledge Acquisition I have chosen to parse the data using the scripting language perl Perl has very strong regular expression pattern matching and as such is very powerful tool when parsing large volumes of data Another option
15. Browse lt das301 ecs soton ac uk gt NS 0 0 d 0 wo i Columns per row 4 Bookmarks x Lo Yerevan Armenia Map gt gt 3store pling ne 2 Airports Y 3store pling ne gt factbook Nz 7 factbook Ai 2 Countries with 15 4 Y 3store pling ne gt factbook Nz Y gt factbook Ai Dis gt rdf label gt Armenian E 7 Renderer x Countries with 15 Airports Armenian Armenia Map Yerevan untitled2 C narrowing rdf label 3store pling net 3 Afghanistan Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Arctic Ocean Argentina Armenia Aruba Ashmore and Cartier Islands Atlantic Ocean Australia Austria Azerbaijan Bahamas The Bahrain Baker Island Bangladesh Barbados Bassas da India Belarus Belgium Belize Benin A at SELECT y WHERE x lt factbook rports gt 1 2x Py 22 FIGURE 3 1 Single Column Screenshot eN9 OntoBrowse lt das301 ecs soton ac uk gt Gr ez Z g BIA 3 Columns per row 4 Bookmarks Lo Yerevan 2 Armenia Map gt 2 3store pling ne 2 Airports Y 3store pling ne gt factbook Nz gt factbook Ai Countries with 15 4 Y 3store pling ne gt 7 factbook Nz Y gt factbook Ai Ss rdf label Lo Armenian ED Renderer x
16. Chapter 3 Development 18 Egypt Y 3store pling net Y factbook Name Egypt y factbook has url http www cia c Airports FIGURE 3 6 Bookmarks are shown as a Tree in OntoBrowse When saved the bookmarks are stored permanently using the Java Preferences subsystem which provides a tree of nodes with key value pairs similar to that of the Microsoft Windows registry although the actual implementation differs on each platform There are several different choices of bookmarking the current session available to the user Upon right clicking any of the results columns the user has the choice of either bookmarking all columns bookmarking all columns from the current column or bookmarking all columns up to the current column This flexibility allows the user more control over what they save which is was found in usability testing to be especially useful when a lot of columns were shown and the user wished to backtrack without losing the current browsing point All saved bookmarks are shown in the bookmark panel and a right click context menu gives the user the following options Open in New Window Open in New Tab Remove Entire Bookmark Remove This Pair The above options allow the user to utilise the powerful multiple window and mul tiple tab interface as well as easy manage their bookmarks removing bookmarks that are no longer required as well as removing pairs that are no longer of interest Chapter 3 Dev
17. Entered newResults renderList repaint2 reRender v Vector selected String triplestore JComboBox myStatus JLabel jlb JList q2 RDOLEntry NARROWING int NON_NARROWING query String sp JScrollPane getName add remove getType get Server jp JPanel jtf JTextField jt 2 JTextField parent ontoPanel qe String saveMe popup JPopupMenu P_BOOKMARKALL String P_BOOKMARKTO String P_BOOKMARKFROM String P_IRENDER String P_WRENDER String resultListeners Vector entries Vector cellColor Color server treeString autoComp boolean name treeString TextCurrent String getName add remove getType removeTreeModelListener textToPut String queue PrioQueue listening boolean resetRemove String processQueue addTreeModelListener getRoot isLeaf getIndex0fChild getChild generateFromPrefs actionPerformed access 0 access 1 attachMenu focusJTF addResultListener removeResultListener getServer saveMe openRenderer makeTreeModelEvent getChildCount valueForPathChanged getAl1Children reQuery reDraw renderQuery setQuery changedUpdate insertUpdate autoComplete setAutoComp setListen getReset autoComplete2 removeUpdate FIGURE 3 11 Class Diagram RENDEZVOUS int ENTRYPOINT i
18. School of Electronics and Computer Science Faculty of Engineering Science and Mathematics University of Southampton Daniel Alexander Smith May 2004 OntoBrowse A World of Knowledge Project Supervisor Hugh Glaser Second Examiner Dr John N Carter A project submitted for the award of MEng Computer Science UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF ENGINEERING SCIENCE AND MATHEMATICS SCHOOL OF ELECTRONICS AND COMPUTER SCIENCE A project report submitted for the award of MEng Computer Science by Daniel Alexander Smith This paper describes the creation and function of OntoBrowse a domain independent ontology browser system that was developed to provide generic access to any triple store ontology without the need to create a bespoke interface It features support for accessing multiple triplestores in one query session book marks Rendezvous sharing of bookmarks multiple tabs multiple windows names pace caching and automatic generation of RDQL queries OntoBrowse automat ically loads images when referenced by URI and has a fully customisable user interface In addition the CIA World Factbook was asserted into a triplestore in order to gain a conceptual understanding of knowledge systems and for use as a controllable testing ground for the ontology browser Contents Abstract 1 Acknowledgements 4 1 Introduction 5 2 Technology Choices 6 2 1 Knowledge Representation 6 22 gt o AA De deh lt a 6
19. World Factbook triplestore will yield the following response lt xml version 1 0 encoding UTF 8 gt lt table gt lt row gt lt column name x type literal gt Cape Verde lt column gt lt row gt lt row gt lt column name x type literal gt Peru lt column gt lt row gt lt row gt lt column name x type literal gt Virgin Islands lt column gt lt row gt lt table gt Since only one variable x is requested there is only one column always named x containing the results In this case since the names of the countries are requested the results are all literals This indicates that the data is not a reference it is simply textual data provided as is Sometimes however the type is returned as uri This indicates that the data returned for that particular entry is in fact a reference This occurs when we pass a query such as SELECT y WHERE y lt http www ecs soton ac uk das301 factbook Name gt x to the same triplestore as above resulting in lt table gt lt row gt lt column name y type uri gt http www cia gov cia publications factbook print cv html Chapter 3 Development 23 lt column gt lt row gt lt row gt lt column name y type uri gt http www cia gov cia publications factbook print pe html lt column gt lt row gt lt row gt lt column name y type uri gt http www cia gov cia publications f
20. actbook print vq html lt column gt lt row gt lt table gt The data is clearly in the form of a URI and as the type attribute is set as uri this is enforced as a reference in this case the countries are being referenced by the URI of the CIA World Factbook pages The main reason that these must be carefully handled by ontoBrowse is that when performing an RDQL query any URI must be surrounded with greater than less than brackets as in the triple lt http www cia gov cia publications factbook print vq html gt x z OntoBrowse handles these properly with the type always being attached to the data through the use of a particular java class This is maintained throughout saving bookmarks sharing bookmarks and all queries 3 12 UML 3 12 1 Use Case A use case diagram showing the actors that interect with the browser are shown in Figure 3 10 namely the user and the triplestore server The user actor selects a subject or predicate whilst the triplestore server actor sends results back to the browser Chapter 3 Development 24 Browser Select Subject Predicate User TripleStore Server Receive Results FIGURE 3 10 Use Case Diagram 3 12 2 Class Diagrams For a breakdown of the important classes and links in the system see Figure 3 11 Most importantly in this diagram is the notion that the main application class OntoBrowse incorporates the ontoPanel which contains multi
21. book Airports withpavedrunway factbook Airports withunpavedrunw factbook Airports withunpavedrunw factbook Airports withunpavedrunw factbook Airports withunpavedrunw factbook Airports withunpavedrunw factbook Area comparative factbook Area land factbook Area total factbook Area water factbook Background factbook Birthrate factbook Budget expenditures factbook Budget revenues factbook Capital af E a a o o Lt E o D E GC 3 GP LEE Jr sey e 3 3store pling net 15 SELECT y WHERE x lt factbook Name gt Armenia x lt factbook Airports gt y FIGURE 3 3 Three Column Screenshot OntoBrowse lt das301 ecs soton ac uk gt B B s amp Vi CG Columns per row 4 wo SN Bookmarks x Lo Yerevan 7 Armenia Map gt gt 3store pling ne 2 Airports Y 3store pling ne gt 7 factbook Nz _ factbook Ai 2 Countries with 15 Y LF 3store pling ne gt factbook Ni Y gt factbook Ai Dis _ rdf label Armenian ED gt Renderer x Countries with 15 Airports Armenian Armenia Map Yerevan untitled2 narrowing rdf label Armenia factbook Airports 15 3store pling net Afghanistan Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Arctic Ocean Argentina Armenia Aruba Ashmore and Cartier Islan
22. c Usage of OntoBrowse 00 000002 ee 30 A 2 1 Create a New Query aci a Se Ge ee A 30 A 2 2 Using Bookmarks cr a Ge oe Se Gk ope a 31 A 2 3 The Image Renderer acu sd om BOR Ce en 33 B RDQL Grammar 34 C 3Store SQL 36 Acknowledgements Hugh Glaser for regular suggestions and support in a supervisory role Steve Harris for developing the triplestore software answering my queries and accepting my bug fix Nick Gibbins for providing me with the code for the aktors org web site peo ple ontology browser The Eclipse development team for creating a wonderful Java IDE Sun Microsystems for giving Java to the world Chapter 1 Introduction The consistent growth of the semantic web and the popularity in particular of the Resource Description Framework RDF in knowledge systems has revealed the need for an ontological browsing system Currently available systems for browsing ontological databases are often bespoke systems specific to the relevant information domains The CS AKTiveSpace Glaser et al 2004 is an example of such a system In order to gain an advanced understanding of knowledge systems a triplestore will be created and asserted with new data The CIA World Factbook has been chosen as the knowledge base to be asserted This requires the per country pages of the web site to be parsed all knowledge extracted and formatted as RDF data Once this RDF data has been asserted into a triplestore sys
23. data was laid out in a tabular format which allowed for an intelligent script to parse the data using standard methods Dixon 1997 Once parsed and formed into RDF using the field names as predicates the data was ready to be asserted into a triplestore 3 3 UI Design The starting point for any UI design is to understand the data being modelled In this case the data is in the form of RDF triples see 3 1 for specifics on RDF There exists no precursor example or requirements specification of how to display triples and concept relation to the user Development of the display to the user has been very much research based and incremental It has been discovered that the modelling of this data into the user interface should be in the form of lists of subjects then predicates and then the resulting objects as in Figure 3 3 Chapter 3 Development 13 Using this layout it is possible for the user to specify the subject they require from a list taken from the result of a query made to a triplestore See Figure 3 1 Upon choosing a subject another query is made to the triplestore returning and displaying in a new list the available predicates that describe the relationships between the subject they have chosen and resulting objects See Figure 3 2 As with the subjects the user selects a predicate a query is generated and sent to the server and the objects described by the chosen subject predicate relationship are displayed
24. ed specifically with the return of headers to the client which was affecting the correct behaviour of not only OntoBrowse but also the default query interface that ships with triplestore This was debugged by myself and fixed A patch was sent to the 3store developer Steve Harris and I was informed that this would be included in the next release of the software 4 5 Possible Improvements A more user friendly way to rebuild the database could be incorporated into 3store The method used for rebuilding the triplestore could be incorporated into the web interface via the Apache module As described above in order to rebuild the data the database must be manually cleared and default table structure created before data can be imported Appendix A User Manual A 1 The Features of OntoBrowse A 1 1 What is OntoBrowse for OntoBrowse provides an easy to use interface for browsing large ontological databases These databases known as triplestores are asserted with RDF formatted data The TripleStore software utilises a fast MySQL database backend to enable re sults of RDF Data Query Lanuage RDQL queries to be returned very quickly Queries are sent to the server using the HyperText Transfer Protocol HTTP and eXtensible Markup Language XML formatted data is returned A 1 2 What else can OntoBrowse do OntoBrowse is much more than a graphical user interface GUI for these RDQL queries It allows the user to migrate subseque
25. elopment 19 3 8 Rendezvous Sharing of Bookmarks OntoBrowse incorporates an implementation of the ZeroConf multicast DNS system also known as Apple Rendezvous When enabled by simply toggling the toolbar button shown in Figure 3 7 if not already saved the user is asked for their name The Rendezvous system then advertises that an ontoBrowse service is running at this machine s IP FIGURE 3 7 Rendezvous Toolbar toogle button Other users running ontoBrowse on the same network segment will have a node added to their bookmark panel such as Daniel Smith s bookmarks see Fig ure 3 8 which they can choose to traverse to access other users bookmarks Right clicking on this node offers a Refresh option to update the bookmarks Network users cannot alter other users bookmarks Bookmarks xx Daniel Smith s Bookmarks P akt P akt2 Y UK Map gt 3store pling net gt 2 akt3 Armenia Man FIGURE 3 8 Another user s bookmarks are shown To the user this process is extremely simple however the system behind this functionality is much less so When the user chooses to share their bookmarks by pressed the aforementioned toolbar button the system announces via Ren dezvous that a new ontoBrowse service is available at the user s IP and on a specific port it then starts a TCP server listening on that port Upon receiving a notification of a new ontoBrowse service being offered
26. enian Trinidad and Tobago factbook Railways standardgaug Countries with 15 Airports hash lang reset A pena Turkey factbook Sexratio 15 64years e Turkmenistan factbook Sexratio 65yearsandove Turks and Caicos Islands factbook Sexratio atbirth Tuvalu factbook Sexratio totalpopulatio Uganda factbook Sexratio underl 5years Ukraine factbook Suffrage a United Arab Emirates factbook Telephones mainlinesir Renderer x United Kingdom factbook Telephones mobilecellt Ss United States factbook Telephonesystem dome c Uruguay factbook Telephonesystem gene Uzbekistan factbook Telephonesystem interi Vanuatu factbook Televisionbroadcaststat Venezuela factbook Televisions in million Vietnam factbook Terrain Virgin Islands factbook Totalfertilityrate Wake Island factbook Unemploymentrate in Wallis and Futuna factbook Waterways West Bank factbook has flag A ama Western Sahara factbook has large flag e Ze Gent 2 World factbook has map maca Yemen factbook has url fm ee Zambia H rdf label D SELECT y WHERE x lt factbook Name gt United Kingdom x lt factbook has map gt y FIGURE A 1 Sharing Bookmarks with Rendezvous Appendix A User Manual 30 A 1 5 Does OntoBrowse only show results Ontologies often reference external documents and media via a literal URI Onto Browse detects when the results of a query contain such documents and renders them automatically in the rendering panel See Figure A 1 A 2 Basic Usa
27. ese objects from the list The algorithm used is designed to then show the user all predicates which apply from the selected object to other objects A query in the form of the following is generated SELECT x WHERE z lt rdf label gt choice z x y USING rdf FOR lt http www w3 org 1999 02 22 rdf syntax ns gt Thus for each object which has an rdf label of choice all predicates desig nated by x are returned and displayed in a list The remaining queries are generated in much the same way meaning that all even columns are predicates and all odd columns are subjects In order to help the user distinguish them the background colour of the predicate columns is slighty tinted The RDF Data Query Language RDQL was derived from SquishQL an RDF query language based upon the Structured Query Language SQL used for query ing databases See Appendix B for the complete RDQL grammar in Backus Naur form BNF 3 7 Bookmarks One of the most used features of a traditional web browsing environment is the use of bookmarks to save return to and share areas of interest Tauscher 1996 Given the pairing of predicates to subjects in the browsing of ontologies the bookmarks system in ontoBrowse stores these pairings visualising them to the user as a tree with first order parent nodes representing predicates and second order child nodes representing subject literals see Figure 3 6
28. feature which found particular favour in usability testing This feature is particularly useful when the user is browsing for an item and there is a predicate such as in the case of the CIA World Factbook has map which Chapter 3 Development 21 returns a the literal URI where a map image can be downloaded The user clicks on has map and as the result is shown the map is also automatically shown in the renderer see Figure 3 9 Renderer BAGHDAD Ki T 79 Karbala Al Kot zs An Najal An N siriyan y Al Basrah e r 4 Umm Qas Y j Y FIGURE 3 9 A map of Iraq has been rendered 3 10 Docked Panels and State The bookmarks and renderer panels are implemented using a generic panel archi tecture which means that not only is maintenance of the source code a lot simpler but also that the preference of the user is maintained quite gracefully OntoBrowse remembers which panels the user had open and opens only those as opened before retaining almost all state as when it was last closed If fully stateful operation was required this could be implemented quite easily by creating temporary bookmarks of all open windows and tabs 3 11 URIs and Literals Data returned by the triplestore in response to a query is formatted as an XML formatted table Passing the query Chapter 3 Development 22 SELECT x WHERE y lt http www ecs soton ac uk das301 factbook Name gt x to the CIA
29. ge of OntoBrowse A 2 1 Create a New Query To start a query click the second button on the toolbar that looks like a document with a symbol on it See Figure A 2 FIGURE A 2 New Tab Toolbar Button Once this button has been pressed a dialog will appear prompting for a server to be chosen See Figure A 3 Choose a server from the list or if you wish to enter the hostname of another server choose other and the prompt will allow you to enter any name you wish 1 d eN Enter Server Triplestore Server hostname d ez triplestore aktors org ES te al l D Cancel ancel CO E FIGURE A 3 Server Prompt Dialog Once a server has been chosen a dialog prompting for a start predicate will appear See Figure A 4 you should enter a start point predicate i e rdf label The main area of the window will show a column containing the result of all objects will are referenced by this predicate as in Figure A 5 where factbook Name has been entered into the CIA World Factbook and hence has returned all the names of countries Appendix A User Manual 31 AL 800 Enter Predicate l Start Predicate name e g factbook Name l U FIGURE A A Predicate Prompt Dialog Cuntitledi narrowing rdf labell 3store pling net F Afghanistan 2 Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua and Barbuda Arctic Ocean Argentina Armenia
30. he level of support to which was available for C C through products such as Microsoft s Visual Studio for example A new IBM sponsored product Eclipse now provides similar levels of development support to the Java programmer While the performance of a compiled C C program would be greater than that of running Java bytecode the performance of Java is adequate for this project Given my own level of experience with Java the comparatively shortened develop ment time ease of debugging and the benefits of the Java Swing GUI construction C C shows no advantages for this project The final decision has been taken to use Java with significant use of the Swing widget system for the GUI as well as the Simple API for XML SAX now included in the standard Java API for XML processing Chapter 3 Development 3 1 RDF The World Wide Web holds an amazing amount of information on many subjects While for humans this is simple to search through and use it is more difficult from a machine understandable perspective Given the volume of information the web contains it is not possible to manage it manually The idea behind RDF Beckett 2004 is to use metadata data about data to catalogue this information It must be understood however that the distinction between data and metadata in this context is application specific and not absolute RDF emphasizes facilities to enable automated processing of web resources in ma
31. inux Unstable branch 2 4 series kernel Although initial confusion was encountered regarding the correct install procedure for the Apache web server module and some de pendencies mainly due to the installation instructions assuming a RedHat Linux system the 3store was installed with few problems To assert RDF data into the 3store one has to first create the database and import the default table structure for the SQL See Appendix C Once this has been 26 Chapter 4 3Store 27 completed simply pass the RDF data one wishes to assert to the tstore_import utility which takes care of putting the RDF into the database 4 3 Access There are two methods of performing remote queries on the triplestore Open Knowledge Base Connectivity OKBC and HTTP RDQL OKBC uses a lisp like syntax and would take much longer to implement than the RDQL method which is what ontoBrowse uses When the Apache module is installed a handler is created on the web server defaultly located at rdql To send RDQL queries to the triplestore the client sends a GET request to the server with the server variable query holding the RDQL query The server will then return the XML formatted results 4 4 Bug Fixes While working with the triplestore server a bug was discovered in the included Apache module which is used by the server to allow access to the triplestore data via an HTTP RDQL query the method OntoBrowse uses The bug was concern
32. nt makeTreeModelEvent getAl1Children nonNarrowingBookmarkEntry bookmarkPanel popup bookmarkPopupMenu popup2 bookmarkPopupMenu popup3 bookmarkPopupMenu jt bookmarkTree parent ontoFrame P_REMOVE String P_REMOVENODE String P_OPENTAB String P_OPENWINDOW String P_REFRESHSERVER String actionPerformed attachMenu unspecificBookmarkEntry narrowingBookmarkEntry entries Vector server treeString name treeString getName add remove getType removeTreeModelListener addTreeModelListener getRoot isLeaf getIndex0fChild getChild generateFromPrefs getServer saveMe makeTreeModelEvent getChildCount valueForPathChanged getAl1Children Chapter 4 3Store 4 1 Introduction 3store is an RDF triplestore released under the GNU General Public Licence It is an infrastructure server for the Semantic Web Its purpose is to store large amounts of RDF data in a way that it can be queried quickly It is developed in the Intelligence Agents and Multimedia research group at Southampton University as part of the AKT Project 3store is a core C library that uses MySQL to store its raw RDF data and caches The library offers OKBC and RDQL query interfaces over HTTP via an Apache web server module or directly though the C library 4 2 Installation Installation of 3store was performed on a server running Debian L
33. nt queries through multiple dif ferent servers This could be used for example when a user wishes to find out about a subject referenced in triplestore A they can further explore the subject in triplestore B 28 Appendix A User Manual 29 A 1 3 Why is OntoBrowse easy to use One of the major features of OntoBrowse is the easy to use GUI OntoBrowse utilises many well known techniques to aid the cognitive use of the software On toBrowse features multiple windows multiple tabs toolbars and dock panels This allows anybody who has used web browsing software such as Netscape Navigator or Microsoft Internet Explorer to be able to simply jump in and use OntoBrowse without any specific training A 1 4 Does OntoBrowse utilise any advanced technology OntoBrowse also features a complete bookmarks solution including one click net work sharing of bookmarks using Apple Rendezvous ZeroConf See Figure A 1 e098 OntoBrowse lt das301 ecs soton ac uk gt j R E le 7 Columns per row 4 E Bookmarks x UK Map Daniel Smith s Bookmarks 1 7 narrowing rdf label gt ak gt akt2 United Kingdom factbook has map Y UK Map 3store pling net t 3store pling net iv 3store pling net 7 gt 3 3store pling net eege Ti pawo erreneren n FEED Pla Tokelau Factbook Radios ine million http www cia gov cia publication a Armenia Map Tonga factbook Railways broadgauge A Arm
34. ny ways For example in the cataloguing of web pages or describing collections of pages that may abstractly represent a single logical document At this stage RDF is known for using XML syntax however this is only one possible incantation of RDF and alternate ways to represent RDF may emerge In order to achieve complete domain neutrality one must make no assumptions about a particular application domain and RDF does this Through the use of an appropriate schema authored for a specific domain the data is given reason Schemata can be fully specific or one can make incremental updates to the base schema and indeed to any interim schemata The use of multiple inheritance is entirely supported allowing mixing of definitions as well as providing multiple views of data if required 10 Chapter 3 Development 11 Primarily RDF is simply a model for representing named properties and property values which can be modelled in an entity relationship diagram This basic data model consists of three object types Resources properties and statements Ev erything that is described by RDF expressions are called resources usually a web page or some other online resource accessible via a named URI A property is a specific aspect characteristic attribute or relation used to describe a resource A specific resource together with a named property plus the value of that property for that resource is an RDF statement These three individual parts
35. of a statement are called respectively the subject the predicate and the object The object of a statement can be another resource or it can be a literal A literal is allowed to have XML markup and is not evaluated by the RDF processor RDF has a basic legal abbreviated syntax which allows well formatted XML DTDs to be directly interpreted as RDF models This is achieved through the use of relaxed syntax definition and allowing multiple syntactic models to accurately model identical data Modelling containers is also defined quite specifically in RDF There are three container types a bag a sequence and alternative A bag is an unordered list a sequence is an ordered list and alternative is a list that represents alternatives for the single value of a property 3 2 The CIA World Factbook 3 2 1 History The Central Intelligence Agency was established on 26 July 1947 and officially began operating on 18 September 1947 On 13 January 1948 the National Se curity Council issued Intelligence Directive NSCID No 3 which authorized the National Intelligence Survey NIS program as a peacetime replacement for the wartime Joint Army Navy Intelligence Studies JANIS program Before ade quate NIS country sections could be produced government agencies had to develop more comprehensive gazetteers and better maps The US Board on Geographic Names BGN compiled the names the Department of the Interior produced the gazetteers and CIA
36. ple browsePanels The other part of the program incorporated through the pluginPanel is the rendererPanel and bookmarkPanel The bookmarkPanel contains multiple book mark entries which are implement the unspecificBookmarkEntry interface Chapter 3 Development 25 OntoBrowse Vector main removeCustomServers SetServerDefaults getServers getServerInt ontoPanel parentFrame ontoFrame bps Vector mainPanel JPanel jtb JToolBar narrowing boolean narrowingCB JCheckBox defaultRender JTextField serverCache String resultListeners Vector rowPanels Vector maxCols int actionPerformed focusJTF setMaxCols addResultListener removeResultListener getChildrenUpto isNarrowing removeBPFrom getDefaultRender getParentFrame bookmarkAl1 bookmarkAl1 bookmarkTo bookmarkFrom getq2At setNarrowing removeAl11BP addBP getMaxCols pluginPanel parent ontoFrame name String jt JToolBar BOOKMARKS int NOTEPAD int rendererPanel labels Vector RENDERER int jsp notifyScrollPane type int panel JPanel subpanel JPanel v Vector parent ontoFrame equals getType propertyChange getTitle actionPerformed class 0 Class mousePressed mouseRe leased mouseClicked getPanel mouseExited getSubPanel browsePanel number int mouse
37. t FROM gt SourceSelector SourceSelector URL TriplePatternClause lt WHERE gt TriplePattern TriplePattern ConstraintClause lt SUCHTHAT gt Expression lt SUCHTHAT gt Expression TriplePattern lt LPAREN gt VarOrURI VarOrURI VarOrLiteral lt RPAREN gt VarOrURI Var URI VarOrLiteral Var Literal Var Identifier PrefixesClause lt PREFIXES gt PrefixDecl PrefixDecl PrefixDecl Identifier lt FOR gt URI Expression Conditional0rExpression Conditional0rExpression ConditionalXorExpression lt SC_OR gt ConditionalXorExpression ConditionalXorExpression ConditionalAndExpression ConditionalAndExpression ValueLogical lt SC_AND gt ValueLogical ValueLogical StringEqualityExpression 34 Appendix B RDQL Grammar 35 StringEqualityExpression NumericalLogical lt STR_EQ gt NumericalLogical lt STR_NE gt NumericalLogical NumericalLogical InclusiveOrExpression InclusiveOrExpression ExclusiveOrExpression lt BIT_OR gt ExclusiveOrExpression ExclusiveOrExpression AndExpression lt BIT_XOR gt AndExpression AndExpression ArithmeticCondition lt BIT_AND gt ArithmeticCondition ArithmeticCondition EqualityExpression EqualityExpression RelationalExpression lt EQ gt RelationalExpression lt NEQ gt RelationalExpression RelationalExpression NumericExpression lt LT
38. tem an application will be created to allow the user to display and browse through the ontological knowledge of the triplestore The application should allow the user to browse through multiple triplestores bookmark entries and concepts view documents referenced by URI and preferably be cross platform Chapter 2 Technology Choices 2 1 Knowledge Representation There are two clear choices when it comes to deciding on how to represent knowl edge There is RDF a maturing technology widely used with a lot of support ing applications and OWL the Web Ontology Language McGuinness and van Harmelen F 2004 OWL is comparatively new and has an optionally rich feature set manifested in three different levels of complexity depending on whether OWL Lite OWL DL or OWL Full are used OWL is particularly useful when creating web content designed to be viewed by humans as well as machines Given that the data being used here is already in the form of a web site there is only a need to parse into a knowledge format with no real need to embrace the complexity of OWL for republication 2 2 RDF Storage One of the indicators of the maturity of RDF is number of storage solutions that exist for RDF data One of the following must be chosen to act as the server for the ontology e Jena at http www hpl hp com semweb jena htm e RDFStore at http rdfstore sourceforge net Chapter 2 Technology Choices 7 e Sesame at http
39. ter in lt factbook Background factbook Birthrate po ap EE mmm TS SELECT y WHERE x lt factbook Airports gt 15 2x y z FIGURE 3 4 Four Column Screenshot Chapter 3 Development 16 e09 OntoBrowse lt das301 ecs soton ac uk gt EA j Tes TY A DN EN IS di L7 Columns per row 4 Bookmarks x Countries with 15 Airports Armenian Armenia Map Yerevan Lo Yerevan a narrowing rdf label _ Armenia Map Fi 3store pling ne Armenia factbook Airports 15 rdf label 2 Airports 3store pling net el 3store pling net ei 3store pling net E 3store pling net x gt pepinos Afghanistan S factbook Administratived 4 15 Dit Galen ae eg Albania 0 factbook Agestructure 0 factbook Railways standz ESEeseN Algeria factbook Agestructure 1 EE A Countries with 15 4 American Samoa factbook Agestructure 6 factbook Reli ae Y w 3store pling ne Andorra factbook Agriculture prot peptic ae ed gt S factbookN Angola factbook Airports factbook Sexratio 6Syear Y 4 factbook Ai Anguilla factbook Airports withpa factbook Sexratio atbirth 15 Antarctica factbook Airports withpa A rdf label Antigua and Barbuda factbook Airports withpa factbook Sexratio under1f 2 Armenian Arctic Ocean factbook Airports withpa factbook Suffrage gt Argentina gt EE H factbook Telephones mai y SS D 6 K z Renderer x 3store pling net i
40. ts Lo Yerevan gt Egypt Y 3store pling net Y L factbook Name _ Egypt Y factbook has url http www cia c Lo Airports oo gt mi a FIGURE A 9 Bookmark Panel showing new bookmark Egypt To load a bookmark simply right click on the bookmark and select either Open in New Tab or Open in New Window as in Figure A 10 Appendix A User Manual 33 E tcrcvar Egyp oral Sea Islanc Open Bookmark in New Tab Open Bookmark in New Window Vi vi Remove Entire Bookmark Y Remove This Pair cia FIGURE A 10 Opening a bookmark A 2 3 The Image Renderer When a query results in URIs being returned in a column such as a map or flag see Figure A 12 the image is downloaded and shown in the Renderer Panel To toggle the visibility of the Image Renderer depress the renderer toolbar button which looks like a pair of binoculars over a globe see Figure A 11 FIGURE A 11 Image Renderer Toolbar Toggle Button 3store pling net http www cia gov cia publications factbook maps eg map gif FIGURE A 12 Image URI Returned Appendix B RDQL Grammar A Backus Naur Form BNF of the RDQL grammar CompilationUnit Query lt EOF gt Query SelectClause SourceClause TriplePatternClause ConstraintClause PrefixesClause SelectClause lt SELECT gt Var Var lt SELECT gt SourceClause lt SOURCE gt l
41. would have been to use a utility called Dome Leonard and Glaser 2001 Dome is a utility for harvesting external data into XML on a regular basis If the CIA World Factbook were updated regularly without format change Dome would be ideal The Factbook however is updated online once a year only often with a format and design change This would mean the Dome harvester would have to set up again to use the new design something which can be done much more quickly in Perl Chapter 2 Technology Choices 8 2 4 Software Development Language Before development can begin the decision of in which language to develop must be made In order to make the ideal choice for this project the following constraints and considerations were taken into account e Given the strict time contraints of this project the development language must not only be one which is known to deliver a good return on investment in terms of coding time but also one to which I am familiar e Due to the widespread use of different operating systems especially within this department and the knowledge technologies community as a whole it would be preferable if the end solution be cross platform or at the very least be easily portable e It should have available a simple to use XML parsing API e It should allow the straightforward creation of an intuitive GUI so that good HCI can be achieved Upon application of these considerations the following languages remain
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