How to visualize a large number of GO terms in directed acyclic graphs

Question

[oussumenten]

Hi,

I have a list of about 500 GO terms that I want to visualize in directed acyclic graphs so as to figure out their relationships.

Is there a tool that would let me input my list of GO terms and gives me directed acyclic graphs of the GO terms as output?

I tried EBI QuickGO tool, but it does not work with a lot of GO terms.

I am open to alternative strategies/suggestions.

Let me know if you have any questions.

Thanks.

Answer 1

[Pierre Lindenbaum]

I wrote a XSLT stylesheet transforming GO to XML+GEXF . See https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/go/go2gexf.xsl

The resulting graph can then be visualized using http://gephi.org

$ curl "http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz" |\
gunzip -c |\
xsltproc --novalid go2gexf.xsl -

output:

<gexf xmlns="&lt;a href=" http:="" www.gexf.net="" 1.2draft"="" rel="nofollow">http://www.gexf.net/1.2draft" xmlns:g="http://www.gexf.net/1.2draft" xmlns:go="http://w
ww.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:viz=
"http://www.gexf.net/1.1draft/viz" version="1.2">
  <meta>
    <creator>Pierre Lindenbaum</creator>
    <description>Gene Ontology</description>
  </meta>
  <attributes class="node">
    <attribute id="0" title="definition" type="string"/>
  </attributes>
  <graph mode="static" defaultedgetype="directed">
    <nodes>
      <node id="GO:0000001" label="mitochondrion inheritance">
        <attvalues>
          <attvalue for="0" value="The distribution of mitochondria, including the mitochondrial gen
ome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and
 the cytoskeleton."/>
        </attvalues>
      </node>
      <node id="GO:0000002" label="mitochondrial genome maintenance">

(...)

[oussumenten]

Hi Pierre,

Thanks for your help. So how do I input GO terms of interest? Can you clarify this code:

$ curl "http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz" |\
gunzip -c |\
xsltproc --novalid go2gexf.xsl -

Answer 2

[andrew.j.skelton73]

Try out the RamiGO package in Bioconductor

It allows you to produce Amigo Trees which shows the relationship between GO terms

[oussumenten]

I have looked at RamiGO but it does not support a large number of GO terms. Thanks though.