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Database of graphs(networks) arising in bioinformatics

Hello!

I apologize if my question is too broad and vague. My research field is not directly linked to bioinformatics.

I would like to study the (abstract) structure of graphs (networks) arising from bioinformatics. It seems that there is a overwhelming number of problems in bioinformatics that are modelled with a graph. Since I have no overview of this field I am not sure I am looking for data in the right places.

I was able to find the following two sites

The later one does not offer datasets for direct download while the former does not seem to have much from the field of bioinformatics.

Hence I am wondering

What are some other good sites offering graphs arising from bioinformatics? Is there any other way to obtain such graphs?

Edit. Ideally I would like to get access to really large and dense graphs in a easy to understand format such as for example this protein interaction graph. I'd like the graphs to have from 1000 to ~50k vertices.

network graphs dataset
• 3,649 views • link
updated by Ram Ram • written by azi • azi

4 answers

Hello. Thanks for the links. I am having troubles understanding the first link. How is the e underlying graph (pairs of adjacent vertices) modeled from the format described on the first link?

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written by azi • azi

Hm.. I am still failing to see, how to use the xml file to obtain a graph. Do you happen to have a trivial example how the format of the xml translates into a list (x_1,y_1),..,(x_n,y_n) of edges between some vertices? I apologize for this but I am really clueless about gene ontology and would only like to see the underlying graphs.

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written by azi • azi 
GO:term2 ---is_a_subclass_of---> GO:term1
GO:term3 ---is_a_subclass_of---> GO:term2

etc...

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

You can try these resources: http://www.pathwaycommons.org/ http://string.embl.de, http://www.genemania.org. Add as a general resource, this might be of interest: http://www.pathguide.org

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updated by Ram Ram • written by jeffk8900 jeffk8900

The go:term stanzas in the example would be nodes, they contains various properties/attributes including elements that contain <... rdf:resource ...> which are edges to other nodes.

All the nodes are identified with URIs (they look just like URLs but need not lead to a page)

You might be more comfortable converting the XML RDF to to a triple format such as turtle

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updated by Ram Ram • written by tomc tomc

I found these graphs to be really impressive and detailed: http://www.virtuallyimmune.org/pathways/

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updated by Ram Ram • written by Mary Mary

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