re-consolidate portals.qmd

Author: bbest

_quarto.yml

@@ -30,8 +30,6 @@ book:
     - api.qmd
     - db.qmd
     - portals.qmd
-    - portals_a.qmd
-    - portals_b.qmd
     - refs.qmd
 
 bibliography: ["refs/packages.bib"]

portals.qmd

@@ -6,6 +6,92 @@ title: "Portals"
 
 CalCOFI data is available through various portals, each serving different purposes and user needs. This document outlines the main access points and their characteristics.
 
+## Data Flow
+
+While it would be ideal for CalCOFI data to be available through a single portal, each portal has its strengths and limitations. The following diagram illustrates one possible realization of data flow between CalCOFI data and the portals: from raw data to the integrated database to portals and meta-portals.
+
+```{mermaid}
+%%{init: {
+  'theme': 'base',
+  'themeVariables': {
+    'primaryColor': '#E0E7FF',
+    'primaryTextColor': '#312E81',
+    'primaryBorderColor': '#6366F1',
+    'lineColor': '#818CF8',
+    'secondaryColor': '#FEF3C7',
+    'tertiaryColor': '#ECFDF5'
+  }
+}}%%
+
+graph TD
+  %% nodes with styles
+  raw([raw data]):::source
+  db[(database)]:::database
+  
+  subgraph calcofi[CalCOFI.io]
+    web[calcofi.org]:::website
+    api[APIs]:::api
+    lib[library]:::code
+    app[apps]:::code
+    flow[workflows]:::code
+  end
+  
+  subgraph portals[Portals]
+    edi[EDI]:::portal
+    obis[OBIS]:::portal
+    erddap[ERDDAP]:::portal
+    ncei[NCEI]:::portal
+  end
+  
+  subgraph meta[Meta-Portals]
+    odis[ODIS]:::metaportal
+    datagov[data.gov]:::metaportal
+  end
+  
+  %% edges
+  raw --> db
+  db  --> api
+  db  --> web
+  api --> lib
+  api --> app
+  api --> flow
+  flow  --> portals
+  portals -->|sitemap| odis
+  portals --> datagov
+
+  %% Custom styles
+  classDef source fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
+  classDef database fill:#FEF3C7,stroke:#D97706,stroke-width:2px
+  classDef website fill:#F3E8FF,stroke:#9333EA,stroke-width:2px
+  classDef api fill:#E0E7FF,stroke:#6366F1,stroke-width:2px
+  classDef code fill:#DBEAFE,stroke:#3B82F6,stroke-width:2px
+  classDef portal fill:#F0FDF4,stroke:#22C55E,stroke-width:2px
+  classDef metaportal fill:#FEF2F2,stroke:#DC2626,stroke-width:2px
+
+  %% Style subgraphs
+  style calcofi fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
+  style portals fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
+  style meta fill:#F8FAFC,stroke:#CBD5E1,stroke-width:2px
+```
+
+In practice, CalCOFI is a partnership with various contributing members, so the authoritative dataset might flow differently, such as from EDI to the database to the other portals. The other portals, such as OBIS or ERDDAP, serve different audiences or purposes. The meta-portals like ODIS and Data.gov then index these portals to provide broader discovery of CalCOFI datasets.
+
+## Portals
+
+| Portal | Full Archive | Versioning | DOI issued | Query by xyt | Query by taxa | Multiple formats | API Access |
+|----|----|----|----|----|----|----|----|
+| **EDI** | :green_circle: | :green_circle: | :green_circle: | :yellow_circle: | :yellow_circle: | :red_circle: | :yellow_circle: |
+| **NCEI** | :green_circle: | :green_circle: | :green_circle: | :red_circle: | :red_circle: | :red_circle: | :yellow_circle: |
+| **OBIS** | :yellow_circle: | :yellow_circle: | :yellow_circle: | :green_circle: | :green_circle: | :yellow_circle: | :green_circle: |
+| **ERDDAP** | :yellow_circle: | :red_circle: | :red_circle: | :green_circle: | :yellow_circle: | :green_circle: | :green_circle: |
+
+<!-- TODO: get emojis to show in PDF -->
+
+------------------------------------------------------------------------
+
+† Capability: :red_circle: none; :yellow_circle: partial; :green_circle: full
+
+
 ### EDI (Environmental Data Initiative)
 
 -   Complete dataset archives using DataOne software and EML metadata