diff --git a/bican_flow_diagram/bican_flow_diagram.md b/bican_flow_diagram/bican_flow_diagram.md new file mode 100644 index 0000000..3f35e1f --- /dev/null +++ b/bican_flow_diagram/bican_flow_diagram.md @@ -0,0 +1,66 @@ +# Purpose +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](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 | 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 | 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 +sequenceDiagram + participant NBB + participant IMS + participant BICAN Investigator + participant Specimen Portal + participant SeqLib 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 ->> SeqLib Portal: 4.Library & Pool Generation + + BICAN Investigator ->> SeqCores: 5. Library Shipment + SeqLib Portal ->> SeqCores: 5. SeqCore Dashboard Update & Notification + SeqLib Portal ->> NeMO: 5. NeMO Dashboard Update & Notification + + SeqCores ->> NeMO: 6. Fastq File Deposition + SeqCores ->> SeqLib Portal: 6. Run QC Metric + + NeMO ->> SeqLib Portal: 7. QC Metric Update + + Terra Alignment ->> NeMO: 8. Investigator validation + + + Specimen Portal -->> SeqLib Portal: Information Flow + Specimen Portal -->> DataCatalog: Information Flow + Specimen Portal -->> KnowledgeBase: 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 + DataCatalog -->> NeMO: Information Flow +``` \ No newline at end of file