Add cBioPortal page (#83)

* Add page for #82, update refs accordingly

* Lint

* change color and small text edits

* Update cBioPortal.md

* Update cBioPortal.md

* Remove directSubmission path

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Co-authored-by: Christina Conrad <[email protected]>

docs/onboarding/data-analysis.md

@@ -28,6 +28,6 @@ Below, we provide more details on analysis apps and which data types are targete
 #### External Viewers
 
 - [cBioPortal](https://docs.cbioportal.org/) for Cancer Genomics was originally developed at Memorial Sloan Kettering Cancer Center (MSK) for sharing genomic data. We provide a custom instance for the Gray Foundation.
-Sage and MSK teams will assist in the transfer of data to cBioportal. To learn more about the behind the scenes curation process [see here](https://github.com/cBioPortal/datahub/blob/master/docs/curation-process.md).
+Sage and MSK teams will assist in the transfer of data to cBioportal. Refer to the workflow [here](/docs/workflows/cBioPortal).
 
-- [CELLxGENE](https://github.com/chanzuckerberg/cellxgene) ("cell-by-gene") is an interactive data explorer specifically designed for analyzing single-cell datasets. 
+- [CELLxGENE](https://github.com/chanzuckerberg/cellxgene) ("cell-by-gene") is an interactive data explorer specifically designed for analyzing single-cell datasets. (TO DO: Link to workflow.)

docs/workflows/_category_.json

@@ -0,0 +1,14 @@
+{
+  "label": "Workflows and SOPs",
+  "position": 2,
+  "collapsible": true,
+  "collapsed": false,
+  "link": {
+    "type": "generated-index",
+    "description": "Workflows and Standard Operating Procedures"
+  },
+  "customProps": {
+    "description": "This description can be used in the swizzled DocCard"
+  }
+
+}

docs/workflows/cBioPortal.md

@@ -0,0 +1,42 @@
+---
+sidebar_position: 6
+---
+
+# cBioPortal
+
+This is the workflow for submitting data into cBioPortal for sharing and visualization. 
+The steps for contribution are [detailed here](https://github.com/cBioPortal/datahub/blob/master/docs/curation-process.md).
+
+```mermaid
+
+
+
+flowchart TB
+
+    classDef Sage fill:#1A7DBB,color:white,stroke:#333,stroke-width:2px;
+    classDef MSKCC fill:lightgray,stroke:#333,stroke-width:2px;
+    classDef Contributor fill:#E6F7E7,color:green,stroke:#333,stroke-width:2px;
+    classDef Decision fill:white,stroke:#333,stroke-width:2px;
+
+    communicate["CONTRIBUTOR: Communicates about in-progress data to SAGE"]:::Contributor --> checkDataType["SAGE: Tracks data types and confirms potential for cBioPortal"]:::Sage
+    checkDataType --> potentialDev["MSKCC: Informed and works on new features for incoming data as needed"]:::MSKCC
+    communicate --> uploadsData:::Contributor
+    uploadsData["CONTRIBUTOR: Uploads data to Synapse"] --> annotatesDCA["CONTRIBUTOR: Annotates data files using Data Curator App (DCA)"]:::Contributor
+    annotatesDCA --> reviewData["SAGE: Reviews data/metadata for completeness <br>and correctness with Gray Foundation data model"]:::Sage
+    reviewData --> reviewResult["CONTRIBUTOR: Receives confirmation of data completeness<br>or receives requests for additional data or corrections"]:::Contributor
+    reviewResult --> decidePrep1
+    decidePrep1{{"Does the contributor have the expertise and resources<br>to independently manage and prepare data submissions for cBioPortal<br>or is intervention from Sage required to facilitate this process?"}}:::Decision
+    reviewResult -.-> uploadsData
+    reviewResult -.-> annotatesDCA
+    decidePrep1 -->|no| fallbackToSage["SAGE: Handles preparation of<br>data to be submitted to cBioPortal"]:::Sage
+    fallbackToSage --> uploadscBioData:::Sage
+    uploadscBioData --> validated["SAGE: Validates dataset and hands off to MSKCC Team"]:::Sage
+    validated --> loadData["MSKCC: Loads data to cBioPortal private instance to be accessible in phase 2 (data can be viewed by consortium)"]:::MSKCC
+    loadData --> informContributor["MSKCC: Informs the Contributor about loaded/updated dataset and provides access for review"]:::MSKCC
+    informContributor --> contributorReviews["CONTRIBUTOR: Reviews and corrects data as needed"]:::Contributor -.-> uploadscBioData
+    informContributor --> updateGFPortal["MSKCC: Updates GF Data Portal with accession to share with funders/other teams"]:::MSKCC
+    updateGFPortal --> moveToPhaseIII["CONTRIBUTOR: Confirms moving to data to <br> phase 3 (data can be viewed by public)"]:::Contributor
+    moveToPhaseIII --> copiesDataPublic["MSKCC: Makes data available in public cBioPortal"]:::MSKCC
+
+
+```