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I have been trying to start exploring the Reactome Graph Database today following the instructions given at https://reactome.org/dev/graph-database#GetStarted

I have installed Neo4j Desktop 2 (version 2.0.5) I have installed Java Runtime Environment v.25 MacOS version 26.1

I have downloaded from Reactome the file: reactome.graphdb.dump

I have also a folder: graph.db

In Neo4j Desktop, I have created an instance called ‘Reactome', and opened/imported the database from the dump-file.

In a newly created Neo4j data folder, I have located the file ’neo4j.conf’ and added the following lines there:

dbms.default_database=reactome.graphdb

dbms.recovery.fail_on_missing_files=false

unsupported.dbms.tx_log.fail_on_corrupted_log_files=false

I have made sure that both the dump-file and the folder graph.db are in the subfolder 'path/to/neo4j/data/databases/'

When I try to explore the Reactome Graph Database in Neo4j Desktop App, I get the following error:

Please reload the application, if the problem persist please contact Neo4j Support. Error: {"type":"ERROR.NODATABASEACCESS”}

image.png

I have also tried the Web Browser (Safari) by going to the link: http://localhost:7474/browser/

The Reactome.graphdb seems to have been recognized as judged from the top bar of the page, where I can also see the version of Cypher (v.5):

image.png

Here is the screenshot of the upper half of the browser page, where the error can be seen too when trying to run a Cypher query:

image.png enter image description here

I am writing to you because essentially I am not sure what else I can try, and therefore heavily relying on your support.

Any input would be appreciated.

1 Answer 1

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The solution:

Neo4j Desktop version 2 is only compatible with Neo4j v5 and newer.

Neo4j Desktop version 1 should be instead downloaded from https://neo4j.com/deployment-center/?desktop-gdb . Then creating a project with a DBMS with version 4.3.6 solved the issue.

More details here: https://reactome.org/dev/graph-database/neo4j-desktop

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