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 fileso: output directory to save the GO-CAM SIF filesa: zip filename to store all the GO-CAM SIF filesl: when specified, try to convert URIs in human readable labelsd: 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 formatg: 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