Export GO-CAMs to SIF in Python

python ttl2sif.py -i <input:directory> [-o <output:directory> -a <output:archive> -l -d -g]

python ttl2sif.py -i /data/noctua-models/models/ -a gocam-sif.zip -l -d

• i: input directory containing GO-CAM TTL files
• o: output directory to save the GO-CAM SIF files
• a: zip filename to store all the GO-CAM SIF files
• l: when specified, try to convert URIs in human readable labels
• d: when specified, if a given entity (e.g. GO term) has multiple instances, the entity name will also be duplicated _2, _3, etc, so that it appears as different nodes in the SIF format
• g: when specified, only extract basic Gene Product - Gene Product relationships from the GO-CAMs

• Documentation about the SIF Format
• SIF files can be viewed with Cytoscape
• They can also be exported with Cytoscape as a web application as in the cytocam example

We advise using our styling in Cytoscape for a better rendering of the GO-CAM graphs. You can import GO-CAM styles in Cytoscape by going to File -> Import -> Styles from file. When viewing your GO-CAM graph in Cytoscape, go in the "Style" tab of your control panel and select any of the GO-CAM style.

In the following example, the -l parameter was used trying to show the labels of each entity:

And without the l parameter:

In the following example, the -d parameter was used, hence the two instances of the gene Pear1 Mmus appears as two separate nodes:

Whereas in this same example, all instances of a same entity (e.g. Pear 1 Mmus) have been merged in a single node:

The original GO-CAM graph:

can be simplified to highlight only GP-GP relationships using the g parameter:

• GO-CAM TTL files made from Noctua can be retrieved here: https://github.com/geneontology/noctua-models/tree/master/models.
• Other GO-CAM TTL files can be retrieved from the Gene Ontology current release