Top-level research console for the doriiOS marine knowledge vault. The vault is the local source of truth for species, papers, areas, findings, sources, and monitoring runs. Live APIs such as OBIS, GBIF, WoRMS, Crossref, OpenAlex, Europe PMC, NWIS, ERDDAP, and Marine Regions fill gaps, but the markdown vault is what researchers can audit, sort, and reuse.
Research entrypoints
| Lane | Open | Primary use | Sort keys |
|---|
| Species | Species — Map of Content | Curated aquatic taxa, traits, IUCN, occurrence context | habitat, iucn.category, occurrence.silenceLabel |
| Taxa | Taxa Map of Content | Taxonomic groupings for review and coverage planning | rank, name, tags |
| Papers | paper/ notes | Literature candidates, article signals, DOI/PMID/OpenAlex evidence | year, doi, source, generated |
| Findings | finding/ notes | Saved agent dossiers and user research questions | generated, model, citations |
| Areas | Areas — Map of Content | MPAs, EEZs, sanctuaries, and key research regions | areaType, country, tags |
| Ecoregions | Ecoregions — Map of Content | Marine Ecoregions of the World context | realm, province, tags |
| Datasets | Dataset Map of Content | Data provenance and source coverage | recordCount, obisDatasetID, sources |
| Threats | Threats — Map of Content | Anthropogenic and natural pressure context | scope, tags, related |
| Sources | OBIS — Ocean Biodiversity Information System | Provenance notes for APIs and data providers | type, tags, related |
Agent workflow
- Resolve the question or live signal into taxa, place, habitat, and source IDs.
- Gather occurrence evidence from OBIS/GBIF/WoRMS and environmental context from
NWIS/ERDDAP/Marine Regions where relevant.
- Find recent and foundational papers, then deduplicate by DOI, PMID,
OpenAlex ID, and normalized title.
- Cross-reference freshwater, saltwater, brackish, and anadromous context before
summarizing any ecological claim.
- Save the result as a sortable markdown note:
signal, monitor-run,
finding, or enriched paper.
- Cite only existing vault wikilinks or plain external citations. Do not invent
[[vault/path]] links.
Quality checks
| Check | Why it matters | Vault signal |
|---|
| Existing wikilinks only | Prevents fake internal citations | Dangling links render muted/italic |
| Habitat class present | Keeps marine/freshwater comparisons explicit | habitat or habitats field |
| Source IDs retained | Makes papers and occurrences traceable | doi, pmid, openalexId, aphiaID |
| Severity and confidence | Lets monitoring output be sortable | severity, confidence, evidenceScore |
| Generated date | Supports recency filters and audits | generated ISO timestamp |
Obsidian sorting recipes
- Papers by year:
type = "paper" sorted by year desc, then generated desc. - High-risk species:
type = "species" where iucn.category is CR, EN, or VU. - Recent dossiers:
type = "finding" sorted by generated desc. - Monitoring evidence:
type = "signal" or type = "monitor-run" sorted by
severity desc, confidence desc, and generated desc.
- Freshwater/saltwater comparisons: filter by
habitat, habitats, or tags such
as habitat/marine, habitat/freshwater, habitat/brackish, and habitat/anadromous.
Conventions
- Note paths are vault-relative without
.md. [[species/balaenoptera-musculus]]
resolves to src/data/vault/species/balaenoptera-musculus.md.
- Tags follow a
namespace/value taxonomy defined in Tag taxonomy. - Frontmatter spec is in Frontmatter schema.
- Notes with
manual: true in frontmatter are preserved by the ETL - only the
frontmatter is merged on the next sync, the body stays as written.