Tag / import

by Mathieu Jacomy

Gephi 0.9.2 : a new CSV importer

A new version of Gephi has been released! Thanks to Eduardo’s relentless issue fixing, Gephi’s overall stability has been improved. Eduardo is the author of the Data Laboratory, and at this occasion he revamped its CSV importer for a more flexible and straightforward user experience.

The new CSV/spreadsheet importer

Did you know that Gephi can export and import just the table of nodes or the table of edges? This feature is useful in many situations, for instance to produce charts in Excel or to clean data in Open Refine. Below we will showcase the new features and more generally explain how to import a spreadsheet as a list of nodes.

To import a spreadsheet you have to reach the Data Laboratory and click on Import Spreadsheet. In the example below a network is already loaded: we will decide later whether the imported nodes will be merged into the existing ones or not.

Tuto01

Gephi is now able to recognize the type of file you upload, and the support of Excel files has been added. Choosing the right separator is crucial since improperly separated columns would compromise the data. In the example below Gephi recognized that the separator is the Comma (as in a properly formatted CSV file).

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The encoding of the file is a common issue, notably with languages using accents and special characters. Gephi can guess the encoding and you can manually edit it if necessary. In the example below Gephi correctly guessed the UTF-8 encoding.

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Selecting a different encoding would produce errors. Fortunately the Preview table allows you to see them and fix the encoding. In the screenshot below, see how the wrong encoding produces exotic characters in the data.

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When you validate these settings, Gephi now opens the exact same panel as when you open a new network. I personally love this addition since it brings more consistency to the user experience. It allows Gephi to provide a number of useful informations like the number of nodes detected or the issues found during the import process.

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Do not miss an important feature here: in this panel you decide either to create a new workspace with the imported data or to merge the new nodes with the old ones. This very useful feature was already present at the opening of a new network, but many users still ignore it exists. Mind to select the Append option if you intend to merge the nodes. In that case when an imported node has the same Id than an already present one, the new node data will override the old one.

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More info

Take a look at the full list of improvements there:
https://github.com/gephi/gephi/releases/tag/v0.9.2

How do I get this release?

  • If you have a recent Gephi, the update will be automatically proposed to you
  • If you have an older version (0.8 or before) you have to download and install manually
  • This update can be downloaded from http://gephi.org
by Sébastien Heymann

Import graph files

application_x_lhaThis article discusses graph file format and introduce a new support page about graph import, which explain a bit of each format and gives tips about current Importer’s specificities.

Gephi supports major graph file format and GEXF, which is our own creation. These file format come from different editors and therefore none is really a standard. Needless to say Gephi supports them for enable previous work to be imported but it is not always easy, due to differences between them. Some standardization efforts exist but they are difficult to apply anyway, due to very different features within graph editors, for instance mixed diagrams and graphs editors.

Our approach when building the GEXF format is slightly different. Instead being specific to our software focus is made on what may be common to all network editors. In addition it will be the first standard dynamic, yet easy format. You can follow the process of specification and see some samples on this page. It recently reached a 1.1 version.

Gephi’s domain of application are networks only, this tends to clarify which data shall be imported. Although these (old) formats can have sometimes complicated functionalities, only few are essential to import a graph structure in Gephi, in sum topology and attributes.

See below current and future status about file import. Note that graph file format export is so far not a priority, as long as we have GEXF export, but we may perhaps consider it more in the future. Note that as PDF is not a graph format, export feature is set at high priority for 0.7.

Import Implementation status (Gephi 0.6 beta2)

* GEXF Implement GEXF 1.0 Specification.
* GDF Implemented, but some rare bugs remains.
* GraphML Support basic node, edge and attribute. Don’t currently support hierarchy but planned for 0.7.
* Pajek Implemented, works fine.
* XGMML As for GraphML, hierarchy is not yet supported.

More details and compare on Supported Graph Formats.

Future

* GML Needs to be done, planned for 0.7 version.
* Excel/CSV We are thinking how to do this.
* Database In the 2009 roadmap.