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Merge pull request #25 from geneontology/issue-24-remove-downloads
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draft attempt at functionally removing downloads
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kltm authored Nov 17, 2022
2 parents d64d187 + 80b62ab commit cf22479
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12 changes: 6 additions & 6 deletions src/app/app.component.html
Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,16 @@

<aside style="margin: 0 10px; max-width: 400px;">

<!-- download section -->
<section>
<app-downloads></app-downloads>
</section>
<!-- <\!-- download section -\-> -->
<!-- <section> -->
<!-- <app-downloads></app-downloads> -->
<!-- </section> -->

<!-- documentation section -->
<section>
<app-documentations></app-documentations>
</section>

<!-- tools & api section -->
<section>
<app-api></app-api>
Expand All @@ -57,4 +57,4 @@
<!-- footer section -->
<footer>
<app-footer></app-footer>
</footer>
</footer>
106 changes: 53 additions & 53 deletions src/app/documentation/introduction/introduction.component.html
Original file line number Diff line number Diff line change
Expand Up @@ -145,60 +145,60 @@ <h3 class="heading-tertiary">Software</h3>
</p>
</section>

<section class="u-margin-bottom-small">
<h2 class="heading-secondary">Converting GO-CAMs to Simple Interaction Format (SIF)</h2>
<p>
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
<a href="https://cytoscape.org" target="blank">Cytoscape</a>.
</p>

<h3 class="heading-tertiary">go-cam-complete-sif</h3>
<p>
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.).
<!-- &nbsp; <button mat-raised-button (click)="download(dtype.sif)">
Download
<mat-icon>get_app</mat-icon>
</button> -->
</p>

<h3 class="heading-tertiary">go-cam-activity-sif</h3>
<p>
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.
</p>

<h3 class="heading-tertiary">Visualization in Cytoscape</h3>
<p>
We provide a Cytoscape styling to visualize GO-CAMs:
<a href="https://s3.amazonaws.com/geneontology-public/gocam/gocam-styles.xml" target="blank">gocam-styles.xml</a>.
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:
</p>

<p>
<span class="u-vertical-bar-left"></span>
File > Import > Network from File
</p>

<h3 class="heading-tertiary">Software</h3>
<p>
The GitHub repository to create the SIF exports is
<a href="https://github.com/geneontology/gocam-sif-pyexport" target="blank">https://github.com/geneontology/gocam-sif-pyexport</a>

You can use this SIF export program with alternate parameters to create other SIF exports from the Turtle files of GO-CAMs
available on
<a href="https://github.com/geneontology/noctua-models/tree/master/models" target="blank">GitHub</a>.
</p>
</section>
<!-- <section class="u-margin-bottom-small"> -->
<!-- <h2 class="heading-secondary">Converting GO-CAMs to Simple Interaction Format (SIF)</h2> -->
<!-- <p> -->
<!-- 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 -->
<!-- <a href="https://cytoscape.org" target="blank">Cytoscape</a>. -->
<!-- </p> -->

<!-- <h3 class="heading-tertiary">go-cam-complete-sif</h3> -->
<!-- <p> -->
<!-- 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.). -->
<!-- <\!-- &nbsp; <button mat-raised-button (click)="download(dtype.sif)"> -->
<!-- Download -->
<!-- <mat-icon>get_app</mat-icon> -->
<!-- </button> -\-> -->
<!-- </p> -->

<!-- <h3 class="heading-tertiary">go-cam-activity-sif</h3> -->
<!-- <p> -->
<!-- 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. -->
<!-- </p> -->

<!-- <h3 class="heading-tertiary">Visualization in Cytoscape</h3> -->
<!-- <p> -->
<!-- We provide a Cytoscape styling to visualize GO-CAMs: -->
<!-- <a href="https://s3.amazonaws.com/geneontology-public/gocam/gocam-styles.xml" target="blank">gocam-styles.xml</a>. -->
<!-- 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: -->
<!-- </p> -->

<!-- <p> -->
<!-- <span class="u-vertical-bar-left"></span> -->
<!-- File > Import > Network from File -->
<!-- </p> -->


<!-- <h3 class="heading-tertiary">Software</h3> -->
<!-- <p> -->
<!-- The GitHub repository to create the SIF exports is -->
<!-- <a href="https://github.com/geneontology/gocam-sif-pyexport" target="blank">https://github.com/geneontology/gocam-sif-pyexport</a> -->

<!-- You can use this SIF export program with alternate parameters to create other SIF exports from the Turtle files of GO-CAMs -->
<!-- available on -->
<!-- <a href="https://github.com/geneontology/noctua-models/tree/master/models" target="blank">GitHub</a>. -->
<!-- </p> -->
<!-- </section> -->

<br>

</mat-card-content>
</mat-card>
</mat-card>

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