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Export GO-CAMs to SIF (Python)
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README.md

GOCAM export to SIF

Export GO-CAMs to SIF in Python

Usage

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

Example

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

Parameters

  • 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

SIF files

View SIF in Cytoscape

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.

CURIEs vs Labels

In the following example, the -l parameter was used trying to show the labels of each entity: GO-CAM-SIF in CytoScape with labeled entities

And without the l parameter: GO-CAM-SIF in CytoScape with at unlabeled entity

Multiple vs single instance of an entity

In the following example, the -d parameter was used, hence the two instances of the gene Pear1 Mmus appears as two separate nodes: GO-CAM-SIF in CytoScape with multiple instances of an entity

Whereas in this same example, all instances of a same entity (e.g. Pear 1 Mmus) have been merged in a single node: GO-CAM-SIF in CytoScape with at most one instance of an entity

Gene Product - Gene Product relationships

The original GO-CAM graph: GO-CAM-SIF in CytoScape

can be simplified to highlight only GP-GP relationships using the g parameter: GO-CAM-SIF in CytoScape

Additional Notes

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