- Converting GO-CAMs to Simple Interaction Format (SIF)
-
- The GO-CAM format allows representation of details that may be of little interest for certain applications. To enable the
- simple reuse and visualization of GO-CAMs, we provide two SIF exports that can easily be loaded for instance in
- Cytoscape.
-
-
- go-cam-complete-sif
-
- All molecular functions, biological processes and cellular components as well as their relationships are included in this
- export. This version essentially contains all the biological facts described in the GO-CAM but does not include any
- meta-data (e.g. describing evidence, xrefs, contributors, etc.).
-
-
-
- go-cam-activity-sif
-
- This export highlights the causal relationships between molecular functions (activities) and the genes carrying out these
- functions. In essence, they represent a protein-protein interaction network highlighting the positive and negative
- regulation relationships between activities.
-
-
- Visualization in Cytoscape
-
- We provide a Cytoscape styling to visualize GO-CAMs:
- gocam-styles.xml.
- To import this style in Cytoscape: File > Import > Styles from File and select the gocam-styles.xml
- you downloaded. In the left Control Panel, select the “Style” tab and in the list, select the “GO-CAMs” style. From
- now on, any GO-CAM imported from a SIF file will be displayed using our recommended styling.
- To load a GO-CAM SIF export, select in the menu:
-
-
-
-
- File > Import > Network from File
-
-
-
- Software
-
- The GitHub repository to create the SIF exports is
- https://github.com/geneontology/gocam-sif-pyexport
-
- You can use this SIF export program with alternate parameters to create other SIF exports from the Turtle files of GO-CAMs
- available on
- GitHub.
-
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