Database of graphs(networks) arising in bioinformatics

Question

[azi]

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 Koblenz Network Collection http://konect.uni-koblenz.de/
• RI datasets http://ferrolab.dmi.unict.it/ri/datasets.html

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.

Answer 1

[Pierre Lindenbaum]

GO: http://geneontology.org/page/go-rdfxml-file-format

uniprot: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/

http://bio2rdf.org/

etc...

[azi]

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?

[Pierre Lindenbaum]

RDF is a formal description of a graph. For GO, there's a link to the files: http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz

[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.

[Pierre Lindenbaum]

GO:term2 ---is_a_subclass_of---> GO:term1
GO:term3 ---is_a_subclass_of---> GO:term2

etc...

Answer 2

[jeffk8900]

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

Answer 3

[tomc]

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

Answer 4

[Mary]

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