From 3f4fb6e049f385913fe4dc2b2b2288418807db47 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Tue, 19 Mar 2024 09:28:02 -0600 Subject: [PATCH 1/6] Add page for #82, update refs accordingly --- docs/onboarding/data-analysis.md | 4 ++-- docs/workflows/_category_.json | 14 +++++++++++ docs/workflows/cBioPortal.md | 41 ++++++++++++++++++++++++++++++++ 3 files changed, 57 insertions(+), 2 deletions(-) create mode 100644 docs/workflows/_category_.json create mode 100644 docs/workflows/cBioPortal.md 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..ed19c83 --- /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" + } + +} \ No newline at end of file diff --git a/docs/workflows/cBioPortal.md b/docs/workflows/cBioPortal.md new file mode 100644 index 0000000..8d2b5cb --- /dev/null +++ b/docs/workflows/cBioPortal.md @@ -0,0 +1,41 @@ +--- +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
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
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 + +``` From 12c70f324e1db91ee0f209d2545df730ee2f8020 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Tue, 19 Mar 2024 09:28:56 -0600 Subject: [PATCH 2/6] Lint --- docs/workflows/_category_.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows/_category_.json b/docs/workflows/_category_.json index ed19c83..c4b5d6c 100644 --- a/docs/workflows/_category_.json +++ b/docs/workflows/_category_.json @@ -11,4 +11,4 @@ "description": "This description can be used in the swizzled DocCard" } -} \ No newline at end of file +} From 11732f925af04ad81b995eac01b31340b0cd2f97 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Wed, 20 Mar 2024 14:18:49 +0000 Subject: [PATCH 3/6] change color and small text edits --- docs/workflows/cBioPortal.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/workflows/cBioPortal.md b/docs/workflows/cBioPortal.md index 8d2b5cb..4e8cb9a 100644 --- a/docs/workflows/cBioPortal.md +++ b/docs/workflows/cBioPortal.md @@ -11,31 +11,31 @@ The steps for contribution are [detailed here](https://github.com/cBioPortal/dat flowchart TB - classDef Sage fill:blue,color:white,stroke:#333,stroke-width:2px; + classDef Sage fill:#1A7DBB,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 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 using DCA"]:::Contributor - annotatesDCA --> reviewData["SAGE: Review data/metadata for completeness
and correctness with Gray Foundation data model"]:::Sage - reviewData --> reviewResult["CONTRIBUTOR: Receives OK or requests for additional data or corrections"]:::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{{"Is Contributor able and willing
to do direct contribution?"}}:::Decision + decidePrep1{{"Is direct data contribution to cBioPortal feasible by the contributor?"}}:::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 + decidePrep1 -->|yes| directSubmissionProcess["CONTRIBUTOR: Works directly with MSKCC on
submission process of data to cBioPortal"]:::Contributor + decidePrep1 -->|no| fallbackToSage["SAGE: Handles preparation of
data to be submitted to cBioPortal"]:::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 + 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 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 + 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 ``` From 3a55d41b7c30c5a7da575fc1f79471b9013392ff Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Thu, 4 Apr 2024 12:11:26 -0400 Subject: [PATCH 4/6] Update cBioPortal.md --- docs/workflows/cBioPortal.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows/cBioPortal.md b/docs/workflows/cBioPortal.md index 4e8cb9a..4594248 100644 --- a/docs/workflows/cBioPortal.md +++ b/docs/workflows/cBioPortal.md @@ -23,7 +23,7 @@ flowchart TB 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{{"Is direct data contribution to cBioPortal feasible by the contributor?"}}:::Decision + 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 -->|yes| directSubmissionProcess["CONTRIBUTOR: Works directly with MSKCC on
submission process of data to cBioPortal"]:::Contributor From 5c39771b59a847c2b704ed7ac7ca304d65e6f33c Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Thu, 4 Apr 2024 13:06:21 -0400 Subject: [PATCH 5/6] Update cBioPortal.md --- docs/workflows/cBioPortal.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows/cBioPortal.md b/docs/workflows/cBioPortal.md index 4594248..31e6b63 100644 --- a/docs/workflows/cBioPortal.md +++ b/docs/workflows/cBioPortal.md @@ -23,7 +23,7 @@ flowchart TB 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 + 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 -->|yes| directSubmissionProcess["CONTRIBUTOR: Works directly with MSKCC on
submission process of data to cBioPortal"]:::Contributor From 3e8ce27ffc7a5da3eed657f6f61a1834187b6cd8 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com> Date: Thu, 2 May 2024 13:52:32 -0600 Subject: [PATCH 6/6] Remove directSubmission path --- docs/workflows/cBioPortal.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/workflows/cBioPortal.md b/docs/workflows/cBioPortal.md index 31e6b63..00cdb25 100644 --- a/docs/workflows/cBioPortal.md +++ b/docs/workflows/cBioPortal.md @@ -9,6 +9,8 @@ The steps for contribution are [detailed here](https://github.com/cBioPortal/dat ```mermaid + + flowchart TB classDef Sage fill:#1A7DBB,color:white,stroke:#333,stroke-width:2px; @@ -26,9 +28,7 @@ flowchart TB 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 -->|yes| directSubmissionProcess["CONTRIBUTOR: Works directly with MSKCC on
submission process of data to cBioPortal"]:::Contributor decidePrep1 -->|no| fallbackToSage["SAGE: Handles preparation of
data to be submitted to cBioPortal"]:::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 cBioPortal private instance to be accessible in phase 2 (data can be viewed by consortium)"]:::MSKCC @@ -38,4 +38,5 @@ flowchart TB 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 + ```