The Arachne Graph Database server

To Install

go get github.com/bmeg/arachne

If you have defined $GOPATH the application will be installed at $GOPATH/bin/arachne otherwise it will be $HOME/go/bin/arachne

To Turn on server

arachne server

To Run Larger 'Amazon Data Test'

Turn on local arachne server

Download test data

curl -O http://snap.stanford.edu/data/bigdata/amazon/amazon-meta.txt.gz

Convert the data

python $GOPATH/src/github.com/bmeg/arachne/example/amazon_convert.py amazon-meta.txt.gz test.data

Create Amazon Graph

arachne create amazon

List the Graphs

arachne list

Load data

arachne load --edge test.data.edge --vertex test.data.vertex --graph amazon

Example queries: Command line

arachne query amazon 'O.query().V().groupCount("group")'

Python

import aql
import json

conn = aql.Connection("http://localhost:8201")

O = conn.graph("amazon")

#Count the Vertices
print list(O.query().V().count())
#Count the Edges
print list(O.query().E().count())

#Try simple traveral
print list(O.query().V("B00000I06U").outEdge())


#Do a group count of the different 'group's in the graph
print list(O.query().V().groupCount("group"))

#use graph to find every Book that is similar to a DVD
for a in O.query().V().has("group", "Book").mark("a").outgoing("similar").has("group", "DVD").mark("b").select(["a", "b"]):
    print a

Matrix Data Loading Example

Create the graph

arachne create test-data

Add aql.py Python Library to PYTHONPATH

export PYTHONPATH=`pwd`

Install Pandas if you don't already have it

pip install pandas

Load Pathway information

curl -O http://www.pathwaycommons.org/archives/PC2/v9/PathwayCommons9.All.hgnc.sif.gz
gunzip PathwayCommons9.All.hgnc.sif.gz
python $GOPATH/src/github.com/bmeg/arachne/example/load_sif.py PathwayCommons9.All.hgnc.sif

Load Matrix data

curl -O https://tcga.xenahubs.net/download/TCGA.BRCA.sampleMap/HiSeqV2.gz
gunzip HiSeqV2.gz
python $GOPATH/src/github.com/bmeg/arachne/example/load_matrix.py HiSeqV2

Load clinical information

curl -O https://tcga.xenahubs.net/download/TCGA.BRCA.sampleMap/BRCA_clinicalMatrix.gz
gunzip BRCA_clinicalMatrix.gz
python $GOPATH/src/github.com/bmeg/arachne/example/load_property_matrix.py BRCA_clinicalMatrix

Python Query: Open Connection

import aql
conn = aql.Connection("http://localhost:8201")
O = conn.graph("test-data")

Print out expression data of all Stage IIA samples

for row in O.query().V().hasLabel("Sample").has("pathologic_stage", "Stage IIA").outgoing("has").hasLabel("Data:expression").outgoingBundle("value"):
  print row

GraphQL Example

./bin/arachne example

Get Types:

{__schema{types{name}}}

{__type(name:"Human"){fields{name}}}

query {Human(id:"1000"){name,friend{name}}}