Check Ancestry Relation Between Go Terms

Question

[Michi]

Hi

Does somebody know of a tool that takes as input a pair or a group of GO terms and then shows me who is the ancestor of who in in this group?

Let's say I have a 100+ different GO terms and want to know which are "fathers" of others. To verify all manually on the gene ontology website is a tedious job, and until now I haven't found an easy solution.

Cheers!

Michi

Answer 1

[Pierre Lindenbaum]

You can use a public mysql server for GO.

for example, you could use a variation of the following query ( http://wiki.geneontology.org/index.php/Example_Queries#Find_ancestors_of_the_node_.27nucleus.27) 'Find ancestors of the node 'nucleus'"

 SELECT DISTINCT
        ancestor.*, 
        graph_path.distance,
        graph_path.term1_id AS ancestor_id
 FROM 
  term
  INNER JOIN graph_path ON term.id=graph_path.term2_id)
  INNER JOIN term AS ancestor ON ancestor.id=graph_path.term1_id)
 WHERE term.name='nucleus';

[Michi]

In the end this was the best option for me. I created a script that recreates the ontology-hierarchy using this query. See for yourself: http://bg.upf.edu/blog/2011/04/understanding-the-hierarchy-of-your-go-terms-subset/

[Michi]

oh, nice. I haven't stumbled upon these queries. They will sure serve me in the near future, but regarding my question i just found something quite nice (QuickGo on ebi.ac.uk)

Answer 2

[Michi]

Ok, I found something!

Go here http://www.ebi.ac.uk/QuickGO/GMultiTerm#a=&tab=choose-terms

There you can enter a list of GO IDs, and then you can click on the "add to graph" symbol. Very easy to check the relation between GO-Terms!

Answer 3

[Ketil]

Download the gene_ontology.obo file, and search for the is_a: fields of the relevant records. The file is a simple text format, and easy to parse.