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Set Up Pathway Database

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Luis Francisco Hernández Sánchez edited this page Mar 22, 2022 · 2 revisions

An example of manual installation could follow these steps:

  • Install Neo4j Community Server following the instructions.

    • From the Current Releases select Community Server.
    • Download Neo4j Community Edition
    • Extract to the desired location, for example: C:\Program Files\
    • This directory will be the Neo4j home, i.e. C:\Program Files\neo4j-community-4.4.4\

  • Download Reactome Graph database from downloads page.

  • Extract the compressed reactome.graphdb.tgz graph database file to the databases directory in the Neo4j home: i.e. C:\Program Files\neo4j-community-4.4.4\data\databases\ If the file is doubly compressed, decompress also the file reactome.graphdb.tar to the same directory to finally obtain a folder called graph.db. It should contain the ".db" files with the database content.

  • Rename the folder graph.db to the desired name according to the version: i.e. reactome.graph.db.v79. The resulting directory structure should look like: C:\Program Files\neo4j-community-4.4.4\data\databases\reactome.graph.db.v79\

  • Modify the Neo4j configuration file "C:\Program Files\neo4j-community-4.4.4\conf\neo4j.conf":

    • For easy access to the data, disable the authentication by uncommenting the line:
    #dbms.security.auth_enabled=false

    Remove the '#' character at the beginning of the line:

    dbms.security.auth_enabled=false
    • In a simmilar way, allow Neo4j to upgrade the database if needed:
    #dbms.allow_upgrade=true --> dbms.allow_upgrade=true
    • Finally, set the correct name of the database for the default. Uncomment the dbms.default_database line and replace with the name of the directory of the database downloaded from Reactome:
    #dbms.default_database=neo4j --> dbms.active_database=reactome.graph.db.v79

Run the Neo4j Browser

  • From a command window located at: "C:\Program Files\neo4j-community-4.4.4\bin", run the command: 
    neo4j console
  • Open a browser at http://localhost:7474/
  • It may be necessary to install Java 11 to run Neo4j. It can be downloaded here.
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