Neo4j unmanaged extension for retrieving relationships and metrics from biological nodes
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src/main/java/cat/cau/neo4j/biorelation/rest
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README.md upgrade scripts for 3.1.0 version, removed multi in python for now Jan 13, 2017
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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:

    • curl http://localhost:7474/biodb/helloworld -> Dummy
    • curl http://localhost:7474/biodb/distance/tax/9606/10114 -> Distance (hops) between human and guinea pig
    • curl http://localhost:7474/biodb/path/tax/9606/10114 -> Path between human and guinea pig
    • curl http://localhost:7474/biodb/common/tax/9606-10114 -> LCA between human and guinea pig. Many values allowed
    • curl http://localhost:7474/biodb/distance/go/GO:0004180/GO:0004866 -> Distance (hops) between carboxypeptidase and endopeptidase GOs
    • curl http://localhost:7474/biodb/path/go/GO:0004180/GO:0004866 -> Path between carboxypeptidase and endopeptidase GOs
    • curl http://localhost:7474/biodb/common/go/GO:0004180-GO:0004866 LCA between carboxypeptidase and endopeptidase GOs
    • curl http://localhost:7474/biodb/rels/go/Q96IY4 -> GO information about Q96IY4
    • curl http://localhost:7474/biodb/rels/tax/Q96IY4 -> Taxon information about Q96IY4

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