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TopBraid Composer: Features Overview TBC 3.5

August 23, 2011

© Copyright 2007-2011 TopQuadrant Inc. Slide 2

Overview q  The Composer User Interface q  Opening Ontologies with TopBraid Composer q  Adding Exis<ng Data to the TBC Workspace q  Viewing and Edi<ng Ontologies with Composer q  TBC Naviga<on Aids q  Namespaces q  The Base URI q  Expor<ng Data q  Refactoring Ontologies q  Customiza<ons q  Data Integra<on q  Other TopBraid Suite Features q  Other Resources


The Composer User Interface


Eclipse Basics Within TBC

q  Eclipse is an Integrated Development Environment (IDE) Ø a panel-‐based interface with mul<ple views per panel Ø named perspec<ve define a set of panes and views

Ø Composer defines the “TopBraid” perspec<ve

Movable, configurable Panes

Navigator shows contents of the workspace. Roots of the Navigator are Eclipse projects.


Show View

q View Window -‐> Show View …for other panes

Associa<ons View

Error Log View


Context Menu for View

q Each view has a context menu Ø list of opera<ons specific to that view

Context menu for view


Error Messages

q Highlight where error(s) occur q Error message on boXom


Help Files

q Help > Help Contents Ø opens a Web browser to localhost files

Where applicable, addi<onal help content in: Help > Help Contents > TopBraid Composer will be iden<fied with the following: see Help > [topic name]


Help Files

q Tip for searching Help Ø set search scope to TBC Choose “TBC” as search scope to search

only TBC Help files for keywords


Projects

q Projects encapsulate a set of files & folders Ø Navigator tab Ø choose New… Project Ø then Next

General Project, click ‘next’ to name project

Tip: Name project with a Java-style package name. i.e. “www.topbraid.org”

Supports creation of namespaces for new files…

see Help > Ge_ng Started > Workspaces, Projects, Folders and Files


Files

q  Files belong to projects Ø Composer supports many file types Ø place file in Workspace and double-‐click to open Ø File > New to create new files

q Many file types have context-‐sensi<ve editors

JSP file


Workspace

q Workspaces contain a set of projects Ø a workspace is a folder in the system directory

Ø can switch workspace

Ø File > Switch Workspace

see Help > Ge_ng Started > Workspaces, Projects, Folders and Files


Navigator Icon Reference

q  Icons in Navigator View indicate status/type Ø indicates non-‐primary files Ø currently loaded and imported Ø etc…

Ontology file

currently loaded model

non-‐primary base URI

locked (read-‐only) file (can be read by impor<ng)

File from remote server (SVN/CVS/…)

File imported into currently loaded model

text file

base URI not found (also empty file, remote server unavailable, etc)

Oracle ontology

Allegro ontology


Opening Ontologies with TopBraid Composer


TBC Library Examples

q Example Ontologies provided in installa<on

Double-‐click to open any of the examples

TBC folder holds system ontologies necessary for some Composer features (to refresh, click on Project Import… RDF/OWL Library from the Web)

see Help > Import and Export > Import external informa<on > Import ontology libraries and examples


TopBraid Composer (TBC)

Ontology Ontology Namespaces & Prefixes Ontology home


Exploring Ontologies

q Use kennedy ontology to explore models in TBC Ø double-‐click on resource label Ø  -‐ or – single-‐click on icon (to the right of label)

select class

select property

select instance of selected class sort property list by

name or by namespace

sort class list by name or by namespace


Creating a New Model

q Create an OWL file Ø New -‐> OWL/RDFS file



q Edit your base namespace Ø this will be the namespace for the file being created

Change this name to: 1. specify a file name 2. specify a baseURI (file namespace)

File extension specified here…

also determines serialization format

Note that project name (using Java package style) creates a valid URI



q Ontology Overview Ø shows namespaces, imports, etc. Ø more later…

see Help > How to? > Create a new ontology


Opening an Existing Model

Ø RDF/XML is the W3C standard Ø  Turtle (.Xl) is default op<on in TBC dialogs. It is more readable and less verbose than RDF/XML. Now being standardized by the RDF Working Group at W3C and quickly becoming a preferred serializa<on for RDF.

q To get a file into a project Ø drag & drop from file system -‐ or – Ø get from local file system

•  in this case choose File System •  and choose kennedys.rdf

q Composer can read many RDF file formats


Opening a File From a URL

q  Import… to get a OWL/RDFS file from a Web source


Label View

q  “Human readable” labels Ø displays rdfs:label and subproper<es thereof Ø SKOS-‐friendly Ø renders unique labels (conflict resolu<on)

toggle label view


Adding ExisGng Data to the TBC Workspace


TBC and Workspace Files

q Composer requires all files it opens to be in workspace Ø workspace acts like a server space Ø when opening a file for import, scripts, etc. Composer first searches workspace •  if not found, will use base URI as a URL to “search for missing imports”

q Two kinds of workspace files Ø projects – container for files, can be opened & closed in Navigator, controlling whether data is available to workspace • must use Import > General > Existing Project into workspace •  project must contain a .project Hile with project metadata

Ø folders and files •  see next slides


Importing Existing Files into Workspace (1)

q Drag/drop into Navigator view



q Perform a copy on the file in your file system Ø right-‐click on a folder and choose paste



q  Copy the file through the Eclipse Import... > General > File System wizard. 1.  Right-‐click on a folder and

choose Import... 2.  Open 'General' in the

wizard (see circled '1' below) and choose File system.

3.  Choose the files you wish to import into the workspace (see circled '2' below).


Viewing and EdiGng Ontologies with Composer


Text Serialization Formats

q An RDF Text serializa<on is a representa<on of RDF triples in text format Ø Composer parses the text and creates an internal RDF graph structure

q Composer supports a number of text serializa<ons Ø RDF, RDFS, OWL (XML serializa<ons) Ø Turtle, N-‐Triple

q  Files in any of these formats can be opened directly Ø place in workspace Ø double-‐click to open


Multiple Ontologies in TBC

q Example: two ontologies open in Composer Ø click on a tab in the Form view Ø chosen ontology becomes the current ontology

•  other tabs, etc. all refer to this ontology


RDF Triples

q Two main subject-‐predicate-‐object profiles: Ø  <URI> <URI> <URI> Ø <URI> <URI> Literal Ø subject can be a bnode (blank node – an unnamed node)

City subclass of

type

Cairns label

Text serializa<on (nt) <hXp://example.org#City> <hXp://www.w3.org/2000/01/rdf-‐schema#subClassOf> <hXp:// #UrbanArea> <hXp://example.org#Cairns> <hXp://www.w3.org/1999/02/22-‐rdf-‐syntax-‐ns#type> <hXp://example.org.City> <hXp://example.org#Cairns> <hXp://www.w3.org/2000/01/rdf-‐schema#label> “Cairns”

Text serializa<on (Turtle) @prefix geotravel: <http://example.org#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . geotravel:City rdfs:subClassOf geotravel:UrbanArea . geotravel:Cairns rdfs:type geotravel:City ; rdfs:label “Cairns” .

UrbanArea

Cairns


owl:imports

q Ontologies can easily be merged Ø RDF triples and URIs are designed for merge Ø if URIs are the same, data is merged

q Merge by impor<ng file into your ontology Ø adds an owl:imports statement to the ontology Ø imports triples so they are available

No current imports

see Help > User Interface Overview > Imports View and Help > Import and Export


RDF Graph Merging

q  Triples and URIs combine to make file merges easy and powerful Ø two URIs with the same value are the same thing

rdfs:subClassOf

rdf:type

Cairns rdfs:label

hXp://example.org#UrbanArea

hXp://example.org#Cairns

hXp://example.org#City

graphA

hXp://example.org#hasAccomoda<on

142,001 hXp://example.org#popula<on


hXp://example.org#AllSeasonsSunshineTower

graphB

rdfs:subClassOf

rdf:type Cairns rdfs:label

hXp://example.org#UrbanArea


http://example.org#City

Merge of graphA and graphB

hXp://example.org#hasAccomoda<on

142,001

hXp://example.org#popula<on

hXp://example.org#AllSeasonsSunshineTower

Either import one into the other {:graphA owl:imports :graphB} -‐ or – Import both into an aggregator graph {:aggGraph owl:imports :graphA . :aggGraph owl:imports :graphB}


owl:imports

q  Imports tab in TBC Ø drag-‐and-‐drop into Imports tab Ø from workspace, drag-‐and-‐drop

- or – click “Import from local file” - or – “Import from URL”

see Help > User Interface Overview > Imports View and Help > Import and Export


owl:imports new data added to the ontology (from import)

faded icons indicate imported resources This namespace represents the graph we imported;

“kennedy:” is the prefix defined in the imported graph


Finding Triple Locations

q  Imported triples indicated in interface

Mouse-‐over icons to get a tool<p describing where the triple is defined

Local resources shown in

saturated color

De-‐saturated color and arrow indicate the triple is defined elsewhere and imported into this model


Triples View

q Viewing all triples in model Ø …in Subject Predicate Object (SPO) form

Choose file(s) to display

see Help > User Interface Overview > Triples View


Exploring Triples

q Use the form to browse rela<onships (triples) :JosephKennedy :Harvard

:almaMater

:College true

:ivyLeague rdf:type

1888

:EdwardKennedy

:birthYear

:child

Mouse-‐over icon to get '+' character, click to show resource informa<on

see Help > User Interface Overview > Resource Editor


Resource Editor Views

q Resource Editor has mul<ple views Ø see tabs on boXom of pane

View source code (in various formats)

see Help > User Interface Overview > Resource Editor > Source Code Panel


Graph View

q Can view triples directly in Composer Ø on Form, click on "Graph Tab” (subtab)

Represents an RDF node (currently selected in form)

Look at the “outgoing” nodes (right-click)

see Help > User Interface Overview > Resource Editor > Graph Panel


Graph View

q  Star<ng point is current selec<on in form Ø lex-‐click: open all Ø right-‐click: choose property


Diagram View q View selected class and rela<onships to others

Ø on Form, click on “Diagram” (subtab) Save diagram as image file

see Help > User Interface Overview > Resource Editor > Diagram

Save diagram as a snapshot in .diagram file for future re-display in TBC


Incoming References

q  Form also show things referring to this resource Ø i.e. resources using this resource as the object


TBC NavigaGon Aids


Hyperlinked Resources

control-‐mouse over click to navigate to resource

previous/next page

see Help > User Interface Overview


Find References

q Where is “ivy-‐league” used? Ø use “Find references” icon

Finds all triples in which selected resource is used (as predicate or object of triple)


Association View

q Not all data is based on class/subclass rela<onships

Shows all: <rsc1> :parent <rsc2> relationships

root nodes are any <rsc2> that do not have a parent

see Help > Interface Overview > Associa<ons View


Basket

•  Can hold any resource •  Useful as a clipboard to hold several resources for easy access and batch opera<ons •  Double-‐click to view basket resource in its form •  Drag-‐drop into form, etc. •  Can be used across any domain (although namespace may differ)

see Help > Interface Overview > Basket View


Basket Operations

q  Find all individuals for a selected class Ø a resource in the basket (whose type is ‘class’)

q Add all unreferenced resources Ø With respect to the current ontology

see Help > Interface Overview > Basket View and Help > How to? > Refactor ontologies > Perform batch opera<ons


Using Basket to add triples to multiple Resources

q  Use Shift or Ctrl key to select multiple resources

q  Drag statement(s) from a form’s property widget Ø  In case of OWL axioms

statements can contain several triples

q  Drop into the basket Ø Select “Add” option in the

popup dialog Ø Note that you can also

replace existing values for this property


Command Completion

q Command comple<on available throughout Composer Ø type in a character Ø then ctl-‐space

More than a convenience – prevents misspellings and other errors

Displays type and rdfs:comment (if exists) for chosen value


Search for Resources

q Classes and Proper<es Ø can become quite large… Ø hard to find what you need

Highlights match in tab or pops up a list if multiple matches are found

Show available completions


TBC Icons


Namespaces


Name/URI

q All names in Composer are URIs Ø names (qname) displayed by default

Click to show full URI

Can also display using the rdfs:label instead of qname

see Help > User Interface Overview


Namespace Prefix

q Resource URIs can be long Ø and difficult to discern with the human eye

q Create an abbrevia<on Ø for the common part of the URI (the namespace) Ø borrowed from XML

Ø example: define prefix ‘kennedy’ for: hXp://topbraid.org/examples/kennedys#

http://topbraid.org/examples/kennedys#EdwardKennedy …becomes… kennedy:EdwardKennedy

a ‘qname,’ or ‘qualified name’


qnames

q Prefixed resource name known as a qname Ø define prefixes:

q qnames for these resources are:

bank for http://www.example.org/path/banking# psych for http://www.example.org/path/psychology/

bank:interest psych:interest

http://www.example.org/path/finance#interest http://www.example.org/path/psych/interest

Note that namespace ends in a '/' or '#’


Namespace Prefixes

q Ontology “home” page in Composer shows all prefixes

Imported prefixes in gray

Define new prefixes see Help > How to? > Modify namespaces and Help > User Interface Overview > Resource Editor > Ontology Overview


Default Namespace q  Default namespace iden<fies a namespace that is assumed for any

unprefixed qualified names

ForeignBorn's URI is http://topbraid.org/MyHandsOn#ForeignBorn

see Help > Developing Ontologies > TopSAIL Methodology > Naming Conven<ons and Namespaces


Managing Prefixes

q  Best prac<ce: do not rely on the use of a default namespace —explicitly define prefixes for model’s base URI Ø  then when a file is imported into another ontology, prefix for its resources is already defined

Click to break link between base URI and default namespace

prefix defined for all URIs defined in this file


Defining Prefixes

q Can define prefix for selected resource


The Base URI


Base URI

q All resources have a URI Ø i.e. a unique iden<fier for the resource

q Base URI -‐ two uses Ø the URI by which a file is known in TBC Ø in XML, a mechanism for resolving rela<ve URIs

q Base URI and Default namespace Ø base URI refers to the file

• U R I for the Hile Ø default namespace completes the named items

• …for those that do not specify a preHix


Base URI & Default Namespace

q  Composer default couples base URI and default namespace Ø changing one changes the other

q Changing base/default Ø all URIs in the file change to the new base URI Ø you change what resources you are referring to!


“Primary” Files

q Base URI is used to iden<fy a file Ø Last file opened with a par<cular URI is the primary file

If the file is not primary and you want to change to this file, click “Yes”

Can’t open another file with the same base URI (the equivalent of opening the same file twice)

see Help > Import and Export > Working with imported ontologies


File Registry

q At any point in <me there can be only one valid mapping of a file to a base URI Ø otherwise owl:import’s would not be able to func<on

q  File Registry shows the current mapping Ø Window > Show View > File Registry Sort by Base URI

see Help > User Interface Overview > File Registry View


ExporGng Data


File Export

q TBC supports many file formats Ø Export…

•  exports currently selected ontology into a Hile Ø in general, export the triples (full graph) to some file format

see Help > How to? > Refactor ontologies > Export / Merge / Convert RDF Graphs


Export and Merge

q Note that data can be merged into a common file Ø suppose you'd like to save the current ontology into a single file

Ø "merge" the triples into a single file

Merge these files into one file

Best prac<ce: one base URI per file If merging/copying, then a new file is created Hence it should have a new “iden<fier” (base URI)


Refactoring Ontologies


Refactoring Ontologies - Basket

q Batch opera<ons using Basket

some<mes an indicator of “orphans”

add all instances from ontology…

see Help > How to? > Refactor ontologies


Refactoring Ontologies – Basket Batch

q Once in basket, can perform opera<ons on contents Ø note that basket can have any resource

•  classes, individuals, properties

see Help > How to? > Refactor ontologies > Perform batch opera<ons


Refactoring Ontologies – Move Between Files

q Move a resource and associated triple Ø drag/drop onto file in Navigator Ø can also use Basket or SPARQL tab to perform on mul<ple resources

note this will not, for example, move the resources type i.e. only copies S -‐> P -‐> O triples

see Help > How to? > Refactor ontologies > Move resources between files


Refactoring Ontologies – Move Between Files

q Moving triples between imported files Ø more on owl:imports in a bit…

the chosen namespace

drag/drop to des<na<on namespace

e.g. proper<es associated with a resource


CustomizaGons


Preferences

q Class browser Ø start Hierarchy with owl:Thing

context menu

all owl:Class defini<ons are subclasses of owl:Thing Best Practice: make all defined classes a subclass of owl:Thing

Preferences for displaying instance count

see Help > User Interface Overview > Preferences


Preferences

q Composer-‐specific preferences Ø Window > Preferences Ø max number of instances, values displayed (UI efHiciency)

e.g. max number of instances displayed in instance view (including SPARQL queries)

Automa<cally chooses label for a language • labels must have language tag

e.g. number of proper<es displayed in form


Setting Preferred Language

q  Se_ng the preferred language Ø in label mode

Preferences:


Form Layout

q Customizing display of form for class instances

modify Form Layout for class

see Help > User Interface Overview > Resource Editor > Form Layout Panel


Form Layout

q Customizing display of form for class instances

Design View Preview


Data IntegraGon


Data Integration RelaGonal

XML

RDF (TopBraid Suite)

Spreadsheet UML RSS

Text SerializaGons

RDF/XML

Turtle

N-‐Triples

Other Formats

Jena TDB

Jena SDB

RDF Data Back-‐ends •  Oracle RDF •  Sesame •  AllegroGraph


Importing External Data

q TBC can import many data forms and convert into ontologies Ø XML Ø UML Ø Spreadsheets Ø Rela<onal Databases Ø RDFa Ø GRDLL

Different sense of “import” – here means importing into a TBC project

see Help > Import and Export > Import external informa<on


File Import

q Wizards to support data imports Ø XML, Spreadsheets, RSS, UML, RDFa, etc.


Accessing non-RDF Data Sources

q Composer automa<cally converts many non-‐RDF sources to RDF:

Ø XML and Excel (.xls, .csv and .tsv) files can be opened and auto-‐converted by double clicking (Maestro Edi<on only) • Done using Semantic XML and Semantic Tables features • On the Hly conversion only, no persistent RDF Hiles are created •  If you need to permanently save these in RDF, use Export>Export/Merge/Convert RDF Graphs

Ø Other data sources are converted by using right click and Import: •  RDBMs, XML Schemas, UML, RSS, tab-‐delimited text and more …


Database Connections q Connec<ons to RDF databases are established by using:

Ø File > New, then select the appropriate connec<on Ø In the Create dialog specify required parameters

•  The same dialog is used to create a brand new database and connect to an existing one

q Connec<ons to Rela<onal data are established by using: Ø Import > Create Mapping Files for D2RQ Rela<onal Database Interface

Ø Four files are created; connec<on file has extension d2rq

q Connec<ons are dynamic Ø Data remains in the databases, accessed by Composer on the fly

q Connec<ons can be OWL imported Ø Drag and drop into Import view as any RDF graph


Other TopBraid Suite Features



q  SPARQL query language support Ø hXp://www.topquadrant.com/products/SPARQLMo<on.html Ø User Interface Overview > SPARQL View

q Configurable Inferencing Ø Help > How to? > Run and Configure Inference Engines

q Data Back-‐Ends Ø Help > Advanced Topics > Working with RDF Databases Ø Help > Import and Export > Import external informa<on > Impor<ng Rela<onal Databases with D2RQ

q  SPIN (SPARQL Inferencing Nota<on) Ø hXp://www.topquadrant.com/products/SPIN.html Ø Help > SPIN > SPIN Inferencing

q Web Service Scripts Ø Help > SPARQLMo<on Scripts (ME) > Overview of Web Services



q  Seman<c XML Ø Help > Import and Export > Crea<ng, Impor<ng, Querying, Saving XML documents with Seman<c XML

q  Seman<c JSP Ø Help > Import and Export > Genera<ng XML/HTML documents with Seman<c Java Server Pages

q  Seman<c Tables Ø Help > Import and Export > Impor<ng, Querying, Saving Table documents with Seman<c Tables

q Web Applica<ons with TopBraid Ensemble Ø hXp://www.topquadrant.com/products/TB_Ensemble.html

q  Seman<c Web server – TopBraid Live Ø hXp://www.topquadrant.com/products/TB_Live.html


Semantic XML

q Converts arbitrary XML to RDF Ø maintains all informa<on from the original Ø …some<mes in annota<ons

q Uses default RDF mapping Ø each element name becomes a class Ø each aXribute becomes datatype property Ø nes<ng is mapped into a dedicated object property (composite:child)

q Use SPARQL to find paXerns in XML q Round-‐trip: Can create XML files from RDF

see Help > Import and Export > Handling XML documents with Seman<c XML


Semantic XML q Open XML files directly

Ø Double click to open or Ø Right click and select Open With > TopBraid (Seman<c XML Documents)


Other Resources


q Available from TopBraid Web site Ø  hXp://www.topquadrant.com/dics/marcom/TBC-‐Ge_ng-‐Started-‐Guide.pdf

q Hands-‐on exercises Ø create, import, export, edit ontologies

Getting Started Guide


TopQuadrant Web Site

q Key informa<on on products Ø downloads, training, resources, support, etc.

q  Links to tutorials and other informa<on

Links to Composer tutorials and other informa<on