Networks: persist them - Samuel Thiriot

How, where to save graphs and networks ?
The classical solution is to store graphs into files using formats as interoperable as possible; yet more and more databases are proposed to store and explore networks.

File formats for storing networks

see many formats described in the gephi website.

Pajek

First case without weights for a mixed network

/* comment one */
/* another comment */
*Vertices      3
0 "first vertice"
1 "second vertice"
2 "third one"
*Arcs
1 2
*Edges
0 2
0 1

Second case without weights for a mixed network

/* comment one */
/* another comment */
*Vertices      3
0 "first vertice"
1 "second vertice"
2 "third one"
*Arcs
1 2 20 
*edgeslist
0 1 2

Thrid case with weights for a mixed network

/* comment one */
/* another comment */
*Vertices      3
0 "first vertice"
1 "second vertice"
2 "third one"
*Arcs
1 2 20 
*Edges
0 2 12
0 1 160

Source: https://gephi.org/users/supported-g...

Compact

The graph6 and sparse6 file formats (http://cs.anu.edu.au/~bdm/data/form...), proposed by Brendan McKay, are very efficient for large networks (dense resp. sparse). The result is not human-readable, and requires a tool to "unflat" the network (see showg from the nauty package above).

Databases

Neo4j

Neo4j was specially designed for storing networks: http://neo4j.org/
a NoSQL database, Java,
* Wikipedia page: http://en.wikipedia.org/wiki/Neo4j
see: http://en.wikipedia.org/wiki/Graph_database

Neo4j databases can be viewed with Gephi, or online (http://linkurio.us/)

less famous

FlockDB was developped by Twitter for storing networks: https://github.com/twitter/flockdb

AllegroGraph
** official link: http://www.franz.com/agraph/allegrograph/
** wikipedia page: http://www.franz.com/agraph/allegrograph/

Bigdata
CloudGraph
Cytoscape
DEX
Filament
GraphBase
Graphd
Horton
HyperGraphDB
InfiniteGraph
InfoGrid
OrientDB
OQGRAPH
sones GraphDB
VertexDB
Virtuoso Universal Server
R2DF
GiraffeDB