From 01365fe9aa443970ba64f8fd9a4fede82287bcb4 Mon Sep 17 00:00:00 2001 From: Puja Trivedi Date: Tue, 12 Mar 2024 10:36:18 -0700 Subject: [PATCH 1/3] added bican flow diagram --- bican_flow_diagram/bican_flow_diagram.md | 52 ++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 bican_flow_diagram/bican_flow_diagram.md diff --git a/bican_flow_diagram/bican_flow_diagram.md b/bican_flow_diagram/bican_flow_diagram.md new file mode 100644 index 0000000..1dad26c --- /dev/null +++ b/bican_flow_diagram/bican_flow_diagram.md @@ -0,0 +1,52 @@ +# Purpose +- The purpose of this diagram is to show how data and materials flow across the BICAN ecosystem. + +# Sequence Diagram +```mermaid +sequenceDiagram + participant NBB + participant IMS + participant BICAN Investigator + participant Specimen Portal + participant Seq Library Portal + participant SeqCores + participant NeMO + participant Terra Alignment + participant DataCatalog as Data Catalog, BICAN Dashboard + participant KnowledgeBase as Knowledge Base, BICAN Cell Atlas + + BICAN Investigator ->> Specimen Portal: 1. Tissue Request + + Specimen Portal ->> IMS: 2. Request Forward + IMS ->> NBB: 2. Request Forward + + IMS ->> Specimen Portal: 3. Status Update + NBB ->> IMS: 3. Status Update + NBB ->> Specimen Portal: 3. Update ROI Drawing + NBB ->> BICAN Investigator: 3. Tissue Shipment + + BICAN Investigator ->> Specimen Portal: 4. Tissue QC Free text & Structured + BICAN Investigator ->> Seq Library Portal: 4.Library & Pool Generation + + BICAN Investigator ->> SeqCores: 5. Library Shipment + Seq Library Portal ->> SeqCores: 5. SeqCore Dashboard Update & Notification + Seq Library Portal ->> NeMO: 5. NeMO Dashboard Update & Notification + + SeqCores ->> NeMO: 6. Fastq File Deposition + SeqCores ->> Seq Library Portal: 6. Run QC Metric + + NeMO ->> Seq Library Portal: 7. QC Metric Update + + Terra Alignment ->> NeMO: 8. Investigator validation + + + Specimen Portal -->> Seq Library Portal: Information Flow + Specimen Portal -->> DataCatalog: Information Flow + Specimen Portal -->> KnowledgeBase: Information Flow + Seq Library Portal -->> KnowledgeBase: Information Flow + Seq Library Portal -->> NeMO: Information Flow + NeMO -->> KnowledgeBase: Information Flow + NeMO -->> DataCatalog: Information Flow + BICAN Investigator -->> DataCatalog: Information Flow + DataCatalog -->> NeMO: Information Flow +``` \ No newline at end of file From 7d5d3eab810fa1d95f359c03330c121cbf0f8807 Mon Sep 17 00:00:00 2001 From: Puja Trivedi Date: Tue, 12 Mar 2024 22:32:01 -0700 Subject: [PATCH 2/3] added table for definitions --- bican_flow_diagram/bican_flow_diagram.md | 34 +++++++++++++++++------- 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/bican_flow_diagram/bican_flow_diagram.md b/bican_flow_diagram/bican_flow_diagram.md index 1dad26c..2032014 100644 --- a/bican_flow_diagram/bican_flow_diagram.md +++ b/bican_flow_diagram/bican_flow_diagram.md @@ -1,5 +1,19 @@ # Purpose -- The purpose of this diagram is to show how data and materials flow across the BICAN ecosystem. +The purpose of this diagram is to show how data and materials flow across the BICAN ecosystem. + +# Definitions +| Node Name | Definition | +|----------------|------------------------------------------------------| +| NBB | Neuro Bio Bank | +| IMS | Information Management Services (https://www.imsweb.com/) | +| BICAN Investigator | TODO | +| Specimen Portal | The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples.| +| SeqLib Portal | The Sequence Library (SeqLib) Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent data-modality-specific archives.| +| SeqCores | TODO | +| NeMO | TODO | +| Terra Alignment | TODO | +| Data Catalog, BICAN Dashboard | TODO | +| Knowledge Base, BICAN Cell Atlas | TODO | # Sequence Diagram ```mermaid @@ -8,7 +22,7 @@ sequenceDiagram participant IMS participant BICAN Investigator participant Specimen Portal - participant Seq Library Portal + participant SeqLib Portal participant SeqCores participant NeMO participant Terra Alignment @@ -26,25 +40,25 @@ sequenceDiagram NBB ->> BICAN Investigator: 3. Tissue Shipment BICAN Investigator ->> Specimen Portal: 4. Tissue QC Free text & Structured - BICAN Investigator ->> Seq Library Portal: 4.Library & Pool Generation + BICAN Investigator ->> SeqLib Portal: 4.Library & Pool Generation BICAN Investigator ->> SeqCores: 5. Library Shipment - Seq Library Portal ->> SeqCores: 5. SeqCore Dashboard Update & Notification - Seq Library Portal ->> NeMO: 5. NeMO Dashboard Update & Notification + SeqLib Portal ->> SeqCores: 5. SeqCore Dashboard Update & Notification + SeqLib Portal ->> NeMO: 5. NeMO Dashboard Update & Notification SeqCores ->> NeMO: 6. Fastq File Deposition - SeqCores ->> Seq Library Portal: 6. Run QC Metric + SeqCores ->> SeqLib Portal: 6. Run QC Metric - NeMO ->> Seq Library Portal: 7. QC Metric Update + NeMO ->> SeqLib Portal: 7. QC Metric Update Terra Alignment ->> NeMO: 8. Investigator validation - Specimen Portal -->> Seq Library Portal: Information Flow + Specimen Portal -->> SeqLib Portal: Information Flow Specimen Portal -->> DataCatalog: Information Flow Specimen Portal -->> KnowledgeBase: Information Flow - Seq Library Portal -->> KnowledgeBase: Information Flow - Seq Library Portal -->> NeMO: Information Flow + SeqLib Portal -->> KnowledgeBase: Information Flow + SeqLib Portal -->> NeMO: Information Flow NeMO -->> KnowledgeBase: Information Flow NeMO -->> DataCatalog: Information Flow BICAN Investigator -->> DataCatalog: Information Flow From ad9815ded5f381ada5867b759e96617e101fa16f Mon Sep 17 00:00:00 2001 From: Puja Trivedi Date: Tue, 12 Mar 2024 22:57:32 -0700 Subject: [PATCH 3/3] added more definitions --- bican_flow_diagram/bican_flow_diagram.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/bican_flow_diagram/bican_flow_diagram.md b/bican_flow_diagram/bican_flow_diagram.md index 2032014..3f35e1f 100644 --- a/bican_flow_diagram/bican_flow_diagram.md +++ b/bican_flow_diagram/bican_flow_diagram.md @@ -5,15 +5,15 @@ The purpose of this diagram is to show how data and materials flow across the BI | Node Name | Definition | |----------------|------------------------------------------------------| | NBB | Neuro Bio Bank | -| IMS | Information Management Services (https://www.imsweb.com/) | +| IMS | [Information Management Services](https://www.imsweb.com) | | BICAN Investigator | TODO | -| Specimen Portal | The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples.| -| SeqLib Portal | The Sequence Library (SeqLib) Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent data-modality-specific archives.| +| Specimen Portal | The [Specimen Portal](https://brain-specimenportal.org) focuses on tissue management from donors to brain slabs and annotated brain samples.| +| SeqLib Portal | The [Sequence Library (SeqLib) Portal](https://brain-specimenportal.org) manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent data-modality-specific archives.| | SeqCores | TODO | -| NeMO | TODO | +| NeMO | The [Neuroscience Multi-omic Archive (NeMO Archive)](https://nemoarchive.org) is a data repository specifically focused on the storage and dissemination of omic data generated from the BRAIN Initiative, SCORCH consortium and other brain research projects.| | Terra Alignment | TODO | -| Data Catalog, BICAN Dashboard | TODO | -| Knowledge Base, BICAN Cell Atlas | TODO | +| Data Catalog, BICAN Dashboard | A searchable [data catalog](https://knowledge.brain-map.org/data) listing all public BICCN and BICAN generated data about cell types.| +| Knowledge Base, BICAN Cell Atlas | The Brain Cell Knowledge Base ingests and standardizes comprehensive cell type information from BICAN's development of a multimodal, multi-species brain cell atlas and disseminate that atlas as an open and interactive community resource for advancing knowledge of the brain.| # Sequence Diagram ```mermaid