Roland Roller, Gaurav Vashisth, Philippe Thomas, He Wang, Michael Mikhailov and Mark Stevenson [To appear] Proceedings of the International Semantic Web Conference 2019.

Graph-KD is a general graph exploring tool, which has following functionalities:

1. Finding K-shortest path between two nodes.
2. Exploring paths around a given node.
3. Infering relations between source and target node of a given path.

The knowledge-graph that is used to build this tool is the UMLS (Unified Medical Language System) dataset which is freely available at UMLS website

In order to use Graph-Kb you should have:

• Neo4j
• JVM
• Python 3.x

The following tutorial supports only Unix-Systems

• echo "deb http://httpredir.debian.org/debian jessie-backports main" | sudo tee -a /etc/apt/sources.list.d/jessie-backports.list
• sudo apt-get update
• sudo add-apt-repository ppa:webupd8team/java
• sudo apt-get update
• sudo apt-get install oracle-java8-installer

• wget -O - https://debian.neo4j.org/neotechnology.gpg.key | sudo apt-key add -
• echo 'deb http://debian.neo4j.org/repo stable/' | sudo tee -a /etc/apt/sources.list.d/neo4j.list
• sudo apt-get update

• sudo apt-get install neo4j=3.2.2

• systemctl start neo4j to start Neo4j.
• systemctl status neo4j to check the status whether Neo4j is running.
• systemctl stop neo4j (After testing whether Neo4j is running, please disconnect the Neo4j service).

• After starting the Neo4j service (systemctl start neo4j) please open http://localhost:7474/browser/ on your local browser.

• Username: neo4j Password: neo4j this will redirect you to set a new password.

• Stop the Neo4j instance before performing following steps (systemctl stop neo4j)
• cp com.dfki.LT.OntologyExplorer-1.0-SNAPSHOT.jar /var/lib/neo4j/plugins/

• The default Neo4j function was used to create the DB.
• In order to create DB for Neo4j we need 4 files (2 header files and 2 content files)

Content: :ID,ConceptID,ConceptName

• :ID ==> Node IDbiomedical-dfki
• ConceptID,ConceptName ==> Properties of the node

Content: :START_ID,:END_ID,:TYPE,RelationLabel,weight

• :START_ID,:END_ID ==> Node ID
• :Type ==> Vocabulary
• RelationLable ==> Relation Name
• weight ==> Edge weight

This file contains data for node in 3 columns comma separated, without header.

This file contains data for relation in 4 columns comma separated, without header.

neo4j-import --into graph.db --nodes:<Node label> "nheader.txt,node.txt" --relationships "rheader.txt,relation.txt" --skip-duplicate-node true

• --into Name of the generated database
  • graph.db Recommended name
• --nodes:UMLSConcepts Node label Note: When you have one label only you provide it via this command, but when you have too many labels you must provide them via a file.
  • "nheader,node" Name of the Node-Header-File (nheader.txt) and the Node-Content-File (nodefile)
• --relationships
  • "rheader,relation" Name of the Relation-Header-File (rheader.txt) and the Relation-Content-File (relationfile)
• --skip-duplicate-node
  • true Skip duplicate nodes

After running this command a graph.db folder will be generated in the present directory, you need to move this file into the following folder /var/lib/neo4j/data/databases/

Default location of the folder is: /var/lib/neo4j/data/databases/

To change the path of the folder:

• Open neo4j.conf by typing gedit /etc/neo4j/neo4j.conf

• Replace line dbms.directories.data=/var/lib/neo4j/data with dbms.directories.data=<folder of your choice>

• Copy the graph.db into <folder of your choice>/databases/

• cp -r graph.db /var/lib/neo4j/data/databases/

• CREATE INDEX ON :<Node label>(<Node property>)
• CREATE INDEX ON :UMLSConcepts(ConceptID)

• cd to UI/biomedical-dfki-0.1/bin
• Run ./biomedical-dfki
• Open the browser and type http://localhost:9000/graph-kd