Visualization result of a set of GO terms in DOT file format?

[cytrix1]

The currently working amigo visualization tool for GO terms only provides results as PNG and SVG format? http://amigo.geneontology.org/visualize?mode=client_amigo

According to Tang's blog, DOT format was also available, but the link to the service is broken. https://davetang.org/muse/2012/12/27/gene-ontology-graph-visualisation/

How can I get results as DOT format?

Thanks in advance.

Young Soo

[kltm]

@cytrix1

Unfortunately, the blog entry is talking about a version of AmiGO a decade old and a lot of the exposed interfaces have changed in that time, with the current version being a very major release increment since then.

That said, if you're willing to work with unsupported code paths that could technically break at any time, some things are still possible if you're will to play with the URL and inserting dot some places; e.g.:

http://amigo.geneontology.org/visualize?mode=amigo&inline=false&term_data=GO%3A0007272&format=dot&term_data_type=string

For a more supported path forward for ontology visualization, I would suggest taking a look at https://github.com/INCATools/obographviz, which would give you a lot more flexibility than what AmiGO would have been able to offer.

[cytrix1]

http://amigo.geneontology.org/visualize?mode=amigo&inline=false&term_data=GO%3A0007272&format=dot&term_data_type=string

That would be quite useful if only more than one term_data is allowed. Is it possible to submit GO:0007272 and GO:99536 and get an entire GO graph including all the submitted GO terms?

Young Soo

[kltm]

@cytrix1 I'd go ahead with playing with the visualize client and changing the output manually; e.g.: http://amigo.geneontology.org/visualize?term_data_type=string&mode=amigo&term_data=GO%3A0007272%0D%20GO%3A0099536&inline=false&format=png and http://amigo.geneontology.org/visualize?term_data_type=string&mode=amigo&term_data=GO%3A0007272%0D%20GO%3A0099536&inline=false&format=dot Again, this is an unsupported hack and the current "official" solution would be to look at the obographviz software.