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Add cBioPortal page #83

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Add page for #82, update refs accordingly
anngvu committed Mar 19, 2024
commit 3f4fb6e049f385913fe4dc2b2b2288418807db47
4 changes: 2 additions & 2 deletions docs/onboarding/data-analysis.md
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@@ -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.)
14 changes: 14 additions & 0 deletions docs/workflows/_category_.json
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{
"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"
}

}
41 changes: 41 additions & 0 deletions docs/workflows/cBioPortal.md
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---
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:blue,color:white,stroke:#333,stroke-width:2px;
classDef MSKCC fill:lightgray,stroke:#333,stroke-width:2px;
classDef Contributor fill:red,color:white,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 using DCA"]:::Contributor
annotatesDCA --> reviewData["SAGE: Review data/metadata for completeness <br>and correctness with Gray Foundation data model"]:::Sage
reviewData --> reviewResult["CONTRIBUTOR: Receives OK or requests for additional data or corrections"]:::Contributor
reviewResult --> decidePrep1
decidePrep1{{"Is Contributor able and willing<br>to do direct contribution?"}}:::Decision
reviewResult -.-> uploadsData
reviewResult -.-> annotatesDCA
decidePrep1 -->|yes| directSubmissionProcess["CONTRIBUTOR: Works directly with MSKCC on submission process"]:::Contributor
decidePrep1 -->|no| fallbackToSage["SAGE: handles submission to MSKCC"]:::Sage
directSubmissionProcess --> uploadscBioData["SAGE/CONTRIBUTOR: Add or update cBioPortal dataset in Synapse"]
fallbackToSage --> uploadscBioData:::Sage
uploadscBioData --> validated["SAGE: Validates dataset and hands off to MSKCC Team"]:::Sage
validated --> loadData["MSKCC: Loads data to GF private instance"]:::MSKCC
loadData --> informContributor["MSKCC: Informs the Contributor about loaded/updated dataset and provides access for review"]:::MSKCC
informContributor --> contributorReviews["CONTRIBUTOR: Reviews and may corrects data as needed"]:::Contributor -.-> uploadscBioData
informContributor --> updateGFPortal["MSKCC: Updates main GF Data Portal with accession to share with funders/other teams"]:::MSKCC
updateGFPortal --> moveToPhaseIII["CONTRIBUTOR: Confirm move to Phase III release"]:::Contributor
moveToPhaseIII --> copiesDataPublic["MSKCC: Makes data available in public MSKCC"]:::MSKCC

```