diff --git a/docs/onboarding/data-analysis.md b/docs/onboarding/data-analysis.md index f4fe6fc..ea0f2e8 100644 --- a/docs/onboarding/data-analysis.md +++ b/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.) diff --git a/docs/workflows/_category_.json b/docs/workflows/_category_.json new file mode 100644 index 0000000..c4b5d6c --- /dev/null +++ b/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" + } + +} diff --git a/docs/workflows/cBioPortal.md b/docs/workflows/cBioPortal.md new file mode 100644 index 0000000..00cdb25 --- /dev/null +++ b/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
and correctness with Gray Foundation data model"]:::Sage + reviewData --> reviewResult["CONTRIBUTOR: Receives confirmation of data completeness
or receives requests for additional data or corrections"]:::Contributor + reviewResult --> decidePrep1 + decidePrep1{{"Does the contributor have the expertise and resources
to independently manage and prepare data submissions for cBioPortal
or is intervention from Sage required to facilitate this process?"}}:::Decision + reviewResult -.-> uploadsData + reviewResult -.-> annotatesDCA + decidePrep1 -->|no| fallbackToSage["SAGE: Handles preparation of
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
phase 3 (data can be viewed by public)"]:::Contributor + moveToPhaseIII --> copiesDataPublic["MSKCC: Makes data available in public cBioPortal"]:::MSKCC + + +```