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I see that Cytoscape.js has many of the great features of Cytoscape Web. But I don't see XGMML support in Cytoscape.js. Is that correct? Is XGMML graph support on the roadmap or is there some simple way to convert XGMML files into a format that Cytoscape.js can read XGMML in ?

What are the plans for plans for stable document formats?

Thanks Ted

Ted Goldstein, Ph.D. UC Santa Cruz Genomics Institute

Bayesian
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  • This question appears to be off-topic because what are someone's plans is not answerable question. This question should be asked at cytoscape.js support at https://github.com/cytoscape/cytoscape.js/issues – xmojmr Jan 03 '15 at 06:33

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xmojmr makes a good point that this isn't really a concrete code help question.

In any case -- in my opinion, formats like that ought not to be in the scope of the Cytoscape.js project. Cytoscape.js is a graph library for JS, and file parsing should be a separate library. Such a library would not even need to support the particular Cytoscape.js JSON "format", because it's very simple to map one array of objects (resultant from the parse) to the hierarchy expected by Cytoscape.js.

The XGMML format itself isn't very good in my opinion, and that's another strike against including it. Many people do have legacy data in that format though, so you may find a generic JS XML parsing lib useful. If you just need the graph data from the XGMML, then using a JS XML parsing lib should make it fairly straightforward to map to whatever JSON format you like.

maxkfranz
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