Gephi 101
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Gephi 101. Dan Ryan Mills College Spring 2012. What is XML?. Circa 1997/9 E x tensible M arkup L anguage  a  markup language for encoding/transmitting/storing data both  human-readable and machine-readable.  A “schema” says “this kind of data has this format”

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Gephi 101

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Gephi 101

Gephi 101

Dan Ryan Mills College Spring 2012


What is xml

What is XML?

  • Circa 1997/9

  • Extensible Markup Language 

    • a markup language

    • for encoding/transmitting/storing data

    • both human-readable and machine-readable. 

  • A “schema” says “this kind of data has this format”

  • THEN: anyone can write code to put data into that format or take data from that format


Gexf graph exchange xml format

GEXF (Graph Exchange XML Format)

http://gexf.net/format/

  • circa 2007, GEPHI project

  • Specifically intended as interchange format

    <?xml version="1.0" encoding="UTF-8"?>

    <gexfxmlns="http://www.gexf.net/1.2draft" version="1.2">

    <meta lastmodifieddate="2009-03-20">

    <creator>Gexf.net</creator>

    <description>A hello world! file</description>

    </meta>

    <graph mode="static" defaultedgetype="directed">

    <nodes>

    <node id="0" label="Hello" />

    <node id="1" label="Word" />

    </nodes>

    <edges>

    <edge id="0" source="0" target="1" />

    </edges>

    </graph>

    </gexf>


Graphml format

GraphML Format

http://graphml.graphdrawing.org/

  • Circa 2000/2001

  • An XML specification for network data

    <?xml version="1.0" encoding="UTF-8"?>

    <graphmlxmlns=http://graphml.graphdrawing.org/xmlnsxmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">

    <graph id="G" edgedefault="undirected">

    <node id="n0"/>

    <node id="n1"/>

    <node id="n2"/>

    <node id="n3"/>

    <node id="n4"/>

    <edge source="n0" target="n2"/>

    <edge source="n1" target="n2"/>

    <edge source="n2" target="n3"/>

    <edge source="n3" target="n4"/>

    </graph>

    </graphml>


Pajek net format

Pajek.net Format

Vertex Attributes

*Vertices 6

1 "1" 0.3034 0.7561

2 "2" 0.4565 0.6039

3 "3" 0.4887 0.8188

4 "4" 0.5687 0.4184

5 "5" 0.3574 0.4180

6 "6" 0.7347 0.2678

*Arcs

*Edges

1 2 1

1 3 1

2 3 1

2 4 1

2 5 1

4 5 1

4 6 1

  • Pajek is a free networkanalysis software tool

  • Circa 1990s

  • Simple text files

  • Lots of features beyond simple adjacency, attributes and weights

Edge Weights


Gephi 101

GDF

  • Used by GUESS (an open source Graph Exploration System

nodedef> name

a

b

c

d

edgedef> node1,node2

a,b

a,c

a,d

http://graphexploration.cond.org/index.html


Gml graph modelling language

GML: Graph Modelling Language

graph[  node  [   id A  ]  node  [   id B  ]  node  [   id C  ]   edge  [   source B   target A  ]  edge  [   source C   target A  ]]

  • Circa 2000s

  • text file format

  • University Passau?


Gephi 101

TLP

  • C. 2007

  • “Tulip is an information visualization framework dedicated to the analysis and visualization of relational data.”

  • (tlp "2.0“

    • (nodes id_node1 id_node2 ...)

  • (edge id id_sourceid_target)

  • )


The gephi gui

The GEPHI GUI

  • Intended to be flexible


Gephi import

GEPHI > IMPORT


Gephi 101

Select vertex and show its edges

Select vertices in a square

Drag a vertex


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