Neo4j unmanaged extension for retrieving relationships and metrics from biological nodes
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docker/centos/neo4j-install
scripts
src/main/java/cat/cau/neo4j/biorelation/rest
LICENSE
README.md
pom.xml

README.md

Biorelation Neo4j unmanaged extension

DOI

This is an unmanaged extension. Details at: http://neo4j.com/docs/stable/server-unmanaged-extensions.html

REQUIREMENTS

You would need to import NCBI taxonomy, Gene Ontology and UniProt into your Neo4j Database. The scripts and instructions can be found at scripts directory in this repository.

  • Java 1.8
  • Maven >= 3.1
  • Compatible with Neo4j 3.1.0

INSTALL

  1. Build it:

    mvn clean package

  2. Copy target/neo4j-biorelation-0.2.x.jar to the plugins/ directory of your Neo4j server.

  3. Configure Neo4j by adding a line to conf/neo4j.conf:

    dbms.unmanaged_extension_classes=cat.cau.neo4j.biorelation.rest=/biodb

In this case, queries will need biodb prepended.

You likely need to add further packages. For instance, copying minimal-json to system/lib Neo4j directory.

  1. Start Neo4j server.

  2. Query it over HTTP:

TODO

  • Simplify functions

  • Restrict a bit more path finding

    • Allow different GO options relations (is_a, part_of, etc.)

    MATCH (n:TAXID { id:9604 })<-[r*]-(m:TAXID) where not(()-->m) return distinct m;

  • Make tests work.

  • root working in all cases

  • Dealing with exceptions