Quick Start Guide¶

What’s in this document?

Run GraphDB as a Desktop Installation¶

The easiest way to set up and run GraphDB is to use the native installations provided for the GraphDB Free edition. This kind of installation is the best option for your laptop/desktop computer, and does not require the use of a console, as it works in a graphic user interface (GUI). For this distribution, you do not need to download Java, as it comes preconfigured.

Go to GraphDB Free and request your GraphDB copy. You will receive an email with the download link. According to your OS, proceed as follows:

On Windows¶

Download your GraphDB .exe file.
Double-click the application file and follow the on-screen installer prompts.
Locate the GraphDB application in the Windows Start menu and start the database. The GraphDB Server and Workbench open at http://localhost:7200/.

On MacOS¶

Download the GraphDB .dmg file.
Double-click it and get a virtual disk on your desktop. Copy the program from the virtual disk to your hard disk Applications folder, and you’re set.
Start the database by clicking the application icon. The GraphDB Server and Workbench open at http://localhost:7200/.

On Linux¶

Download the GraphDB .rpm or .deb file.
Install the package with sudo rpm -i or sudo dpkg -i and the name of the downloaded package. Alternatively, you can double-click the package name.
Start the database by clicking the application icon. The GraphDB Server and Workbench open at http://localhost:7200/.

Configuring GraphDB¶

Once the GraphDB database is running, a small icon appears in the Status/Menu bar (varying depending on OS). It allows you to check whether the database is running, as well as to stop it or change the configuration settings. Additionally, an application window is also opened, where you can go to the GraphDB Free documentation, configure settings such as change the port on which the instance runs, and see all log files.

Configuring JVM properties¶

You can add and edit the Java Virtual Machine settings of the GraphDB native app from the GraphDB Free config file containing some basic configuration properties. It is located at:

On Mac: /Applications/GraphDB Free.app/Contents/Java/GraphDB Free.cfg
On Windows: \Users\<username>\AppData\Local\GraphDB Free\app\GraphDB Free.cfg
On Linux and other Unixes: /opt/graphdb-free/app/graphdb-free.cfg

Stopping GraphDB¶

To stop the database, simply quit it from the status/menu icon, or close the GraphDB Free application window.

Run GraphDB as a Standalone Server ¶

The default way of running GraphDB is as a standalone server. The server is platform-independent, and includes all recommended JVM (Java virtual machine) parameters for immediate use.

Note

Before downloading and running GraphDB, please make sure to have JDK (Java Development Kit) or JRE (Java Runtime Environment) installed.

Running GraphDB ¶

Download your GraphDB distribution file and unzip it.
Start the GraphDB Server and Workbench interface by executing the graphdb startup script located in the $graphdb_home/bin folder:

A message appears in the console telling you that GraphDB has been started in Workbench mode. To access the Workbench, open http://localhost:7200/ in your browser.

Options ¶

The startup script supports the following options:

Option	Description
-d	daemonize (run in background), not available on Windows
-s	run in server-only mode (no Workbench UI)
-p pidfile	write PID to `pidfile`
-h --help	print command line options
-v	print GraphDB version, then exit
-Dprop	set Java system property
-Xprop	set non-standard Java system property

Note

Run graphdb -s to start GraphDB in server-only mode without the web interface (no Workbench). A remote Workbench can still be attached to the instance.

Configuring GraphDB ¶

Paths and network settings ¶

The configuration of all GraphDB directory paths and network settings is read from the conf/graphdb.properties file. It controls where to store the database data, log files, and internal data. To assign a new value, modify the file or override the setting by adding -D<property>=<new-value> as a parameter to the startup script. For example, to change the database port number:

graphdb -Dgraphdb.connector.port=<your-port>

The configuration properties can also be set in the environment variable GDB_JAVA_OPTS, using the same -D<property>=<new-value> syntax.

Note

The order of precedence for GraphDB configuration properties is as follows: command line supplied arguments > GDB_JAVA_OPTS > config file.

The GraphDB home directory¶

The GraphDB home defines the root directory where GraphDB stores all of its data. The home can be set through the system or config file property graphdb.home.

The default value for the GraphDB home directory depends on how you run GraphDB:

Running as a standalone server: the default is the same as the distribution directory.
All other types of installations: OS-dependent directory.
- On Mac: ~/Library/Application Support/GraphDB.
- On Windows: \Users\<username>\AppData\Roaming\GraphDB.
- On Linux and other Unixes: ~/.graphdb.

GraphDB does not store any files directly in the home directory, but uses several subdirectories for data or configuration.

Java Virtual Machine settings ¶

We strongly recommend setting explicit values for the Java heap space. You can control the heap size by supplying an explicit value to the startup script such as graphdb -Xms10g -Xmx10g or setting one of the following environment variables:

GDB_HEAP_SIZE: environment variable to set both the minimum and the maximum heap size (recommended);
GDB_MIN_MEM: environment variable to set only the minimum heap size;
GDB_MAX_MEM: environment variable to set only the maximum heap size.

For more information on how to change the default Java settings, check the instructions in the $graphdb_home/bin/graphdb file.

Note

The order of precedence for JVM options is as follows: command line supplied arguments > GDB_JAVA_OPTS > GDB_HEAP_SIZE > GDB_MIN_MEM/GDB_MAX_MEM.

Tip

Every JDK package contains a default garbage collector (GC) that can potentially affect performance. We benchmarked GraphDB’s performance against the LDBC SPB and BSBM benchmarks with JDK 8 and 11. With JDK 8, the recommended GC is Parallel Garbage Collector (ParallelGC). With JDK 11, the most optimal performance can be achieved with either G1 GC or ParallelGC.

Stopping the database ¶

To stop the database, find the GraphDB process identifier and send kill <process-id>. This sends a shutdown signal and the database stops. If the database is run in non-daemon mode, you can also send Ctrl+C interrupt to stop it.

Set up Your License ¶

GraphDB Free is free to use and does not require a license file. It is, however, not open source.

Create a Repository ¶

Now let’s create your first repository.

Hint

When started, GraphDB creates GraphDB-HOME/data directory as an active location. To change the directory, see Configuring GraphDB Data Directory.

Go to Setup ‣ Repositories.
Click Create new repository.
Select GraphDB Free repository.
For Repository ID, enter myrepo and leave all other optional configuration settings at their default values.

Tip

For repositories with over several tens of millions of statements, see Configuring a Repository.
Click the Connect button to set the newly created repository as the repository for this location.
Use the pin to select it as the default repository.

Note

Make sure the location where you want to create the repository is active.

Tip

You can also use cURL command to perform basic location and repository management through the Workbench REST API.

Load Your Data ¶

All examples given below are based on the News sample dataset provided in the distribution folder.

Tip

You can also use public datasets such as the w3.org Wine ontology by pasting its data URL - https://www.w3.org/TR/owl-guide/wine.rdf - in Import ‣ User data ‣ Get RDF data from a URL.

Load data through the GraphDB Workbench ¶

Let’s load your data from a local file:

Go to Import ‣ RDF.
Open the User data tab and click the Upload RDF files to upload the files from the News sample dataset provided in the $graphdb_home/examples/data/news folder.
Click Import.
Enter the Import settings in the pop-up window.

Import Settings

Base URI: the default prefix for all local names in the file;
Target graphs: imports the data into one or more graphs.

For more details, see Loading data using the Workbench.

Click Import.

Note

You can also import data from files on the server where the Workbench is located, from a remote URL (with a format extension or by specifying the data format), from a SPARQL construct query directly, or by typing or pasting the RDF data in a text area.

Import execution

Imports are executed in the background while you continue working on other things.
Interrupt is supported only when the location is local.
Parser config options are not available for remote locations.

Load data through SPARQL or RDF4J API ¶

The GraphDB database also supports a very powerful API with a standard SPARQL or RDF4J endpoint, to which data can be posted with cURL, a local Java client API, or an RDF4J console. It is compliant with all standards, and allows every database operation to be executed via an HTTP client request.

Locate the correct GraphDB URL endpoint:
- select Setup ‣ Repositories
- click the link icon next to the repository name
- copy the repository URL.
Go to the folder where your local data files are.
Execute the script:
```
curl -X POST -H "Content-Type:application/x-turtle" -T <localfilename.ttl> \
  http://localhost:7200/repositories/repository-id/statements
```
where localfilename.ttl is the data file you want to import, and http://localhost:7200/repositories/repository-id/statements is the GraphDB URL endpoint of your repository.

Tip

Alternatively, use the full path to your local file.

Load data through the GraphDB LoadRDF tool ¶

LoadRDF is a low level bulk load tool that writes directly in the database index structures. It is ultra fast and supports parallel inference. For more information, see the Loading data using the LoadRDF tool.

Note

Loading data through the GraphDB LoadRDF tool can be performed only if the repository is empty, e.g., the initial loading after the database has been inactive.

Explore Your Data and Class Relationships ¶

Explore instances ¶

To explore instances and their relationships, first enable the Autocomplete index from Setup ‣ Autocomplete, which makes the lookup of IRIs easier. Then navigate to Explore ‣ Visual graph, and find an instance of interest through the Easy graph search box. You can also do it from the View resource search field in GraphDB’s home page - search for the name of your graph, and press the Visual button.

The graph of the instance and its relationships are shown. The example here is from the w3.org wine ontology that we mentioned earlier.

Hover over a node to see a menu for the following actions:

Expand a node to show its relationships or collapse to hide them if already expanded. You can also expand the node by double-clicking on it.
Copy a node’s IRI to the clipboard.
Focus on a node to restart the graph with this instance as the central one. Note that you will lose the current state of your graph.
Delete a node to hide its relationships and hide it from the graph.

Click on a node to see more info about it: a side panel opens on the right, including a short description (rdfs:comment), labels (rdfs:label), RDF rank, image (foaf:depiction) if present, and all DataType properties. You can also search by DataType property if you are interested in its value. Click on the node again if you want to hide the side panel.

You can switch between nodes without closing the side panel. Just click on the new node about which you want to see more, and the side panel will automatically show the information about it.

Click on the settings icon on the top right for advanced graph settings. Control number of links, types, and predicates to hide and show.

A side panel opens with the available settings:

Create your own visual graph ¶

Control the SPARQL queries behind the visual graph by creating your own visual graph configuration. To make one, go to Explore ‣ Visual graph ‣ Create graph config. Use the sample queries to guide you in the configuration.

The following parts of the graph can be configured:

Starting point - this is the initial state of your graph.
- Search box: start with a search box to choose a different start resource each time;
- Fixed node: you may want to start exploration with the same resource each time;
- Query results: the initial config state may be the visual representation of a Graph SPARQL query result.
Graph expansion: determines how new nodes and links are added to the visual graph when the user expands an existing node. The ?node variable is required and will be replaced with the IRI of the expanded node.
Node basics: this SELECT query controls how the type, label, comment and rank are obtained for the nodes in the graph. Node types correspond to different colors. Node rank is a number between 0 and 1 and determines the size of a node. The label is the text over each node, and if empty, IRI local name is used. Again, ?node binding is replaced with node IRI.
Predicate label: defines what text to show for each edge IRI. The query should have ?edge variable to replace it with the edge IRI.
Node extra: Click on the info icon to see additional node properties. Control what to see in the side panel. ?node variable is replaced with node IRI.
Save your config and reload it to explore your data the way you wish to visualize it.

Class hierarchy ¶

To explore your data, navigate to Explore ‣ Class hierarchy. You can see a diagram depicting the hierarchy of the imported RDF classes by number of instances. The biggest circles are the parent classes and the nested ones are their children.

Note

If your data has no ontology (hierarchy), the RDF classes will be visualized as separate circles instead of nested ones.

_images/rdf-class-hierarchy-diagram-news.png

Various actions for exploring your data:

To see what classes each parent has, hover over the nested circles.
To explore a given class, click its circle. The selected class is highlighted with a dashed line, and a side panel with its instances opens for further exploration. For each RDF class you can see its local name, URI, and a list of its first 1,000 class instances. The class instances are represented by their URIs, which, when clicked, lead to another view where you can further explore their metadata.
The side panel includes the following:
- Local name;
- URI (Press Ctrl+C / Cmd+C to copy to clipboard and Enter to close);
- Domain-Range Graph button;
- Class instances count;
- Scrollable list of the first 1,000 class instances;
- View Instances in SPARQL View button. It redirects to the SPARQL view and executes an auto-generated query that lists all class instances without LIMIT.
To go to the Domain-Range Graph diagram, double-click a class circle or the Domain-Range Graph button from the side panel.
To explore an instance, click its URI from the side panel.
To adjust the number of classes displayed, drag the slider on the left-hand side of the screen. Classes are sorted by the maximum instance count and the diagram displays only the current slider value.
To administrate your data view, use the toolbar options on the right-hand side of the screen.
- To see only the class labels, click Hide/Show Prefixes. You can still view the prefixes when you hover over the class that interests you.
- To zoom out of a particular class, click the Focus diagram home icon.
- To reload the data on the diagram, click the Reload diagram icon. This is recommended when you have updated the data in your repository, or when you are experiencing some strange behavior, for example you cannot see a given class.
- To export the diagram as an .svg image, click the Export Diagram download icon.
You can also filter the hierarchy by graph when there is more than one named graph in your repository. Just expand the All graphs drop-down menu next to the toolbar options and select the graph you want to explore.

_images/rdf-class-hierarchy-filter-by-graph.png

Domain-Range graph ¶

To explore the connectedness of a given class, double-click the class circle or the Domain-Range Graph button from the side panel. You can see a diagram that shows this class and its properties with their domain and range, where domain refers to all subject resources and range - to all object resources. For example, if you start from class pub:Company, you see something like: <pub-old:Mention pub-old:hasInstance pub:Company> <pub:Company pub:description xsd:string>.

You can also further explore the class connectedness by clicking:

the green nodes (object property class);
the labels - they lead to the View resource page, where you can find more information about the current class or property;
the slider Show collapsed predicates to hide all edges sharing the same source and target nodes;

_images/rdf-domain-range-graph-diagram-collapsed-news.png

To see all predicate labels contained in a collapsed edge, click the collapsed edge count label, which is always in the format <count> predicates. A side panel opens with the target node label, a list of the collapsed predicate labels and the type of the property (explicit or implicit). You can click these labels to see the resource in the View resource page.

_images/rdf-domain-range-graph-diagram-collapsed-side-panel-news.png

Administrating the diagram view

To administrate your diagram view, use the toolbar options on the right-hand side of the screen.

To go back to your class in the Class hierarchy, click the Back to Class hierarchy diagram button.
To collapse edges with common source/target nodes, in order to see the diagram more clearly, click the Show all predicate/Show collapsed predicates button. The default is collapsed.
To export the diagram as an .svg image, click the Export Diagram download icon.

Class relationships ¶

To explore the relationships between the classes, navigate to Explore ‣ Class relationships. You can see a complicated diagram showing only the top relationships, where each of them is a bundle of links between the individual instances of two classes. Each link is an RDF statement, where the subject is an instance of one class, the object is an instance of another class, and the link is the predicate. Depending on the number of links between the instances of two classes, the bundle can be thicker or thinner and gets the color of the class with more incoming links. These links can be in both directions.

In the example below, you can see the relationships between the classes of the News sample dataset provided in the distribution folder. You can observe that the class with the biggest number of links (the thickest bundle) is pub-old:Document.

To remove all classes, use the X icon.

To control which classes to display in the diagram, use the add/remove icon next to each class.

To see how many annotations (mentions) there are in the documents, click on the blue bundle representing the relationship between the classes pub-old:Document and pub-old:TextMention. The tooltip shows that there are 6,197 annotations linked by the pub-old:containsMention predicate.

_images/news-scenario-class-document.png

To see how many of these annotations are about people, click on light purple bundle representing the relationship between the classes pub-old:TextMention and pub:Person. The tooltip shows that 274 annotations are about people linked by the pub-old:hasInstance predicate.

Just like in the Class hierarchy view, you can also filter the class relationships by graph when there is more than one named graph in the repository. Expand the All graphs drop-down menu next to the toolbar options and select the graph you want to explore.

Query Your Data ¶

Query data through the Workbench ¶

Hint

SPARQL is a SQL-like query language for RDF graph databases with the following types:

SELECT: returns tabular results;
CONSTRUCT: creates a new RDF graph based on query results;
ASK: returns YES if the query has a solution, otherwise “NO”;
DESCRIBE: returns RDF data about a resource; useful when you do not know the RDF data structure in the data source;
INSERT: inserts triples into a graph;
DELETE: deletes triples from a graph.

For more information, see the Additional resources section.

Now it is time to delve into your data. The following is one possible scenario for querying it.

Select the repository you want to work with, in this example News, and click the SPARQL menu tab.

Let’s say you are interested in people. Paste the query below into the query field, and click Run to find all people mentioned in the documents from this news articles dataset.

PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
select distinct ?x ?Person  where {
?x a pub:Person .
?x pub:preferredLabel ?Person .
?doc pub-old:containsMention / pub-old:hasInstance ?x .
}

Run a query to calculate the RDF rank of the instances based on their interconnectedness.

PREFIX rank: <http://www.ontotext.com/owlim/RDFRank#>
INSERT DATA { _:b1 rank:compute _:b2. }

Find all people mentioned in the documents, ordered by popularity in the repository.

PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
PREFIX rank: <http://www.ontotext.com/owlim/RDFRank#>
select distinct ?x ?PersonLabel ?rank where {
    ?x a pub:Person .
    ?x pub:preferredLabel ?PersonLabel .
    ?doc pub-old:containsMention / pub-old:hasInstance ?x .
    ?x rank:hasRDFRank ?rank .
} ORDER by DESC (?rank)

_images/news-scenario-ordred-by-popularity.png

Find all people who are mentioned together with their political parties.

PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
select distinct ?personLabel ?partyLabel where {
    ?document pub-old:containsMention ?mention .
    ?mention pub-old:hasInstance ?person .
    ?person pub:preferredLabel ?personLabel .
    ?person pub:memberOfPoliticalParty ?party .
    ?party pub:hasValue ?value .
    ?value pub:preferredLabel ?partyLabel .
}

_images/news-scenario-people-and-political-parites.png

Did you know that Marlon Brando was from the Democratic Party? Find what other mentions occur together with Marlon Brando in the given news article.

PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
select distinct ?Mentions where {
<http://www.reuters.com/article/2014/10/06/us-art-auction-idUSKCN0HV21B20141006> pub-old:containsMention / pub-old:hasInstance ?x .
?x pub:preferredLabel ?Mentions .

}

_images/news-scenario-MB-and-other-mentions.png

Find everything available about Marlon Brando in the database.

PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
select distinct ?p ?objectLabel where {
<http://ontology.ontotext.com/resource/tsk78dfdet4w> ?p ?o .
    {
?o pub:hasValue ?value .
    ?value pub:preferredLabel ?objectLabel .
    } union {
        ?o pub:hasValue ?objectLabel .
        filter (isLiteral(?objectLabel)) .
     }
}

Find all documents that mention members of the Democratic Party and the names of these people.

PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
select distinct ?document ?personLabel where {
    ?document pub-old:containsMention ?mention .
    ?mention pub-old:hasInstance ?person .
    ?person pub:preferredLabel ?personLabel .
    ?person pub:memberOfPoliticalParty ?party .
    ?party pub:hasValue ?value .
    ?value pub:preferredLabel "Democratic Party"@en .
}

_images/news-scenario-all-DP-members-and-names.png

Find when these people were born and died.

PREFIX pub-old: <http://ontology.ontotext.com/publishing#>
PREFIX pub: <http://ontology.ontotext.com/taxonomy/>
select distinct ?person ?personLabel ?dateOfbirth ?dateOfDeath where {
    ?document pub-old:containsMention / pub-old:hasInstance ?person .
    ?person pub:preferredLabel ?personLabel .
    OPTIONAL {
       ?person pub:dateOfBirth / pub:hasValue ?dateOfbirth .
    }
    OPTIONAL {
       ?person pub:dateOfDeath / pub:hasValue ?dateOfDeath .
    }
    ?person pub:memberOfPoliticalParty / pub:hasValue / pub:preferredLabel "Democratic Party"@en .
} order by ?dateOfbirth

Tip

You can play with more example queries from the Example_queries.rtf file provided in the $graphdb_home/examples/data/news folder.

Query data programmatically ¶

SPARQL is not only a standard query language, but also a protocol for communicating with RDF databases. GraphDB stays compliant with the protocol specification, and allows querying data with standard HTTP requests.

Execute the example query with an HTTP GET request:

curl -G -H "Accept:application/x-trig" \
  -d query=CONSTRUCT+%7B%3Fs+%3Fp+%3Fo%7D+WHERE+%7B%3Fs+%3Fp+%3Fo%7D+LIMIT+10 \
  http://localhost:7200/repositories/yourrepository

Execute the example query with a POST operation:

curl -X POST --data-binary @file.sparql -H "Accept: application/rdf+xml" \
  -H "Content-type: application/x-www-form-urlencoded" \
  http://localhost:7200/repositories/worker-node

where file.sparql contains an encoded query:

query=CONSTRUCT+%7B%3Fs+%3Fp+%3Fo%7D+WHERE+%7B%3Fs+%3Fp+%3Fo%7D+LIMIT+10

Tip

For more information on how to interact with GraphDB APIs, refer to the RDF4J and SPARQL protocols or the Linked Data Platform specifications.

Additional Resources ¶

SPARQL, OWL, and RDF:: RDF: http://www.w3.org/TR/rdf11-concepts/

RDFS: http://www.w3.org/TR/rdf-schema/

SPARQL Overview: http://www.w3.org/TR/sparql11-overview/

SPARQL Query: http://www.w3.org/TR/sparql11-query/

SPARQL Update: http://www.w3.org/TR/sparql11-update