foraminifera.org Open Science Platform

Plate VDevelopment Plan

A phased path from taxonomic spine to global infrastructure.

The platform follows a Foundation → Core → Validation → Scale → Ecosystem lifecycle. Phases are not strictly sequential — Nomia and Testaria develop in parallel. Current status: Pre-MVP.

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Status Done In progress PlannedNo specific calendar dates committed
  1. 1–2
    Phase 1–2

    Taxonomic spine and data layer

    In progress

    Establish the foundational standards: AphiaID-keyed WoRMS synchronisation, the character vocabulary, and a pilot dataset of known species. Prove the concept end-to-end on a bounded cohort before scaling.

    • WoRMS AphiaID sync — forams_* → foram2_* → OpenSearch (ingested)
    • WoRMS MCP server built and operational
    • Character vocabulary v0 (P0.2) — seeded from Foraminifera.eu schema + Loeblich & Tappan
    • Data model v0.1 (P0.1) — entities, provenance, morphology / interpretation boundary
    • Pilot cohort V1 — shallow-platform benthics, extant material
    • Synonymy resolution via gnparser / gnverifier + ColDP model
  2. 3
    Phase 3

    Morphological search on real data

    In progress

    Take the Testaria identification filter from a mock-data demo to a working system backed by the real character matrix. A minimum viable character set (~5–8 characters) with controlled-state vocabulary is enough to prove reproducible identification.

    • Testaria MVP demo running on mock data (in progress)
    • Minimum character set and controlled state vocabulary (in design)
    • Full Supabase + OpenSearch query layer (in design)
    • Faceted filter UI and ranked candidate output
    • CSV export — species list + references + reliability record
    • Methodological article + pilot dataset DOI (Zenodo)
  3. 4
    Phase 4

    Literature → structured data pipeline

    Planned

    Industrialise the bibliographic ingestion pipeline: acquire publications, convert PDFs to structured records, extract morphological character candidates via NLP, and populate the reference and species-description banks.

    • Bibliographic acquisition — OpenAlex / CORE / Semantic Scholar / Zotero
    • PDF → Markdown conversion (GROBID / Docling / Nougat)
    • Species-name detection (GNfinder) and metadata extraction
    • Character candidate extraction with LLM assist + human review
    • Community contribution protocol and co-curation staging queue
  4. 5
    Phase 5

    Ecology layer and open data exports

    Planned

    Add the ecology and distribution dimension, and open the platform fully to the global biodiversity network. Citable releases make the catalogue a referenceable scientific object.

    • EcologyDistribution entity — occurrence / environmental parameters
    • Darwin Core / ColDP export for GBIF and OBIS
    • BENFEP, ForCenS, and BFR2 dataset integration
    • Public REST / GraphQL / MCP API for human and agent consumption
    • Webhooks for partner ingest and release notification
    • Citable versioned releases with DOI (Zenodo)
  5. 6
    Phase 6

    Education and communication layer

    Planned

    Build the public-facing educational layer that converts the dense scientific catalogue into structured learning materials. Foram World is conditioned on data maturity — it only becomes meaningful once the catalogue has sufficient depth.

    • Species educational cards — visual guides, morphological diagrams
    • Blog and curated publication feed (Sanity-managed content)
    • Highlighted terms and recently indexed taxa
    • Structured learning pathways for new researchers
    • Direct links to species records and identification tool
  6. 7
    Phase 7

    High-quality image layer and 3D visualisation

    Planned

    Expand the media layer with curated photomicrographic archives and optional 3D specimen visualisation. Image-based identification (CNN) may enter as a complementary future layer — not the core approach.

    • Specimen image ingest with per-image licence governance
    • Visual comparison panel alongside the morphological filter output
    • 3D specimen visualisation (open decision)
    • Image-based classification layer (future, not core)

⟢ Scientific Publications

Publications timed to build credibility and attract funding.

Publications are a strategic instrument, not an afterthought. Each phase produces a citable scientific record that registers progress and opens doors to institutional funding.

Phase 1–2

Morphological filter methodology

Methodological article + pilot seed dataset (DOI via Zenodo) + congress abstract

Phase 3–4

Nomia pipeline + ecology integration

Pipeline paper + Darwin Core / FAIR integration description

Validation (Q1/Q2)

Inter-rater concordance study

Explicit reliability methodology and confidence-scoring validation

Continuous

Citable catalogue releases

Versioned DOI releases as the catalogue grows; conference dissemination once minimum species count is reached

5–10+ year horizon · Open Science

The platform does not end — it updates perpetually.

Each phase stabilises the standards that unlock the next. Once the pilot cohort forges the vocabulary, all subsequent taxonomic classes can scale against it. The mission is long; the path is clear.

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