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Update gocam-overview.md
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eliminating sif for #570
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suzialeksander authored Jul 24, 2024
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Expand Up @@ -43,33 +43,3 @@ GO-CAMs can be “decomposed” into the standard GO annotations (connecting a g
### Software

Code handling the export of standard GO annotations from a GO-CAM model is provided by the open source [Minerva software](https://github.com/geneontology/minerva/){:target="blank"}, which is the data handling backend for Noctua. This code extracts an initial set of proposed standard GO annotations from a model, and then applies filters ensuring that appropriate metadata, such as an [ECO evidence code](http://www.evidenceontology.org/){:target="blank"}, is obtained for each annotation.

### 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](https://cytoscape.org/){:target="blank"}.

#### 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](https://s3.amazonaws.com/geneontology-public/gocam/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
Example of a GO-CAM rendered by cytoscape using the [gocam-styles.xml](https://s3.amazonaws.com/geneontology-public/gocam/gocam-styles.xml):

<p align="center">
<img width="800" src="/assets/GO-CAM-SIF-cytoscape-d.png" alt="GO-CAM visualized with Cytoscape">
</p>


#### Software
GitHub repository to create the SIF exports: [https://github.com/geneontology/gocam-sif-pyexport](https://github.com/geneontology/gocam-sif-pyexport){:target="blank"}.

You can use this SIF export program with alternate parameters to create variations of the SIF exports from the Turtle files of GO-CAMs available on [GitHub](https://github.com/geneontology/noctua-models/tree/master/models){:target="blank"}.

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