README.md

Biorelation Neo4j unmanaged extension

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 3.5.x

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.

4. Start Neo4j server.

5. 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

Docker

• CentOS version

Data population scripts

We provide data population scripts at population directory for sake of convenience. They are compatible with provided Docker versions.

TODO

• Simplify functions

• Add Molecular interaction controlled vocabulary https://www.ebi.ac.uk/ols/ontologies/mi

• 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

  (m:MOL)-[has_annotation]-(a:annotation)-[has_go]-(g:GO_TERM) (a:annotation)-[has_evidence]-(e:ECO_TERM) (a:annotation)-[has_goref]-(r:GOREF_TERM)

  • ECO: https://www.ebi.ac.uk/ols/ontologies/eco
  • GO_REF: http://www.geneontology.org/cgi-bin/references.cgi