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Bioelectric Data Commons

In progress. Version one is the schema and the first slice of the literature.

Bioelectric Data Commons

In progress. Version one is the schema and the first slice of the literature.

A typed claim-graph of the bioelectricity literature: every published result as a claim with its species, its evidence tag and its paper, queryable as data.

What it does, step by step
  1. Turn papers into claimsEach result becomes a typed node: what was done, in which organism, with what evidence, cited to a PubMed id that resolves.
  2. Keep the claim ladder honestThree tags and no upgrades: established (replicated, mechanism anchored), unresolved (real evidence, mechanism open), engineering vision (nobody has done it). The three famous overclaims are tagged as visions, not results.
  3. Make it queryableAsk the graph which primitives write anatomy, in which species, with which tools, and get citations back instead of prose.
How it is built

A LinkML schema over Postgres with vector search for the text, object storage for the sources, and ORCID login for contributors. Funding path: focused research organisation and public science grants.

  • LinkML schema
  • Supabase Postgres with pgvector
  • Cloudflare R2
  • ORCID OAuth
  • NCBI E-utilities for citation verification
  • A citation is verified by machine, not memory: eleven wrong PubMed ids were once found in a sister fact file, six of them near misses on real unrelated papers; every id now resolves before it is written.
  • The tag on a claim can only go down, never up; a document cannot promote a vision to a result by rewording it.
paper ──► claim { what · species · tag EST|UR|EV · PMID } ──► graph
                                                  └─ verified against NCBI before it is stored
query ──► "which primitives write form in vertebrates?" ──► claims + citations

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