usage-examples.md

Usage examples

Loading the data

Loading the data graph depends on it's implementation, Tinkerpop3 supports these graph types:

• TinkerGraph
• Neo4j
• Giraph

Bio4j's DSL

We've created a DSL that is respective of the semantics of the GeneOntology module. GoTraversal extends Traversal, it can now be used as follows:

gremlin> g.of(GoTraversal.class).goTerms()

It iterates over all the GoTerms in a Gene Ontology graph g.

GoTraversal provides other methods:

• goTerms()
• goTerm(int)
• in(Relationship)
• in()
• inE()
• inE(Relationship)
• out(Relationship)
• out()
• outE()
• outE(Relationship)
• id()
• synonyms()
• name()
• definition()
• comment()

For more info about the DSL, see the Bio4j DSL section.

The :bio4j command

For example

• Save to /home/andre/bio4j.json:

  gremlin> :bio4j graphson /home/andre g.of(GoTraversal.class).goTerms()

• Save to bio4j.json in the current folder:

  gremlin> :bio4j graphson g.of(GoTraversal.class).goTerms()

• Save to /home/andre/out.json:

  gremlin> :bio4j graphson /home/andre/out.json g.of(GoTraversal.class).goTerms()

Generalizing:

gremlin> :bio4j format path query or simply gremlin> :bio4j format query to save to current location.

On the possible export formats, see the Supported formats section.