SPOKEtest public type documentation

Public, human- and machine-readable documentation for the node and edge types in the public SPOKE biomedical knowledge graph.

This repo is the canonical fetch source for the "?" type-documentation popups in the SPOKEtest Explorer, and is designed to double as compact, structured schema/meaning documentation for any external tool or LLM integrating with the public SPOKE graph.

Layout

type_jsons/
  _manifest.json      # how to render a record (field → display primitive); the schema lives here
  <Type>.json         # one record per node/edge type; filename == the exact type name

Looking up documentation for a type is a plain file fetch: type_jsons/<Type>.json (e.g. type_jsons/Gene.json, type_jsons/INTERACTS_PiP.json). No parsing, no fuzzy matching.

Consuming these files

Fetch raw over HTTPS:

https://raw.githubusercontent.com/<owner>/<repo>/main/type_jsons/<Type>.json
https://raw.githubusercontent.com/<owner>/<repo>/main/type_jsons/_manifest.json

A consumer renders a record by walking _manifest.json's layout and applying the named generic primitive to each field. Field names, order, and labels live in the manifest — not in consumer code — so the record schema can change without any consumer code change.

Record shape (per-source sections)

A type is explicitly multi-source in SPOKE (every edge/node carries a sources list). A record therefore keeps each contributing source's documentation in its own section rather than flattening everything together:

Field	Meaning
type	Exact type name (== filename).
kind	node or edge.
reviewed	Only true records are shown to users. Mirrors the modeling doc's Human Approved flag.
endpoints	(edges) {from, to, direction}.
description	Plain-English, type-level summary. Paraphrased from the modeling docs; confidence-gated (never asserts unstated domain knowledge).
sources	The sources that co-own this type.
common_properties	Properties present regardless of source (e.g. sources, last_updated).
source_contributions[]	One block per source: source, scope, description, properties[].
curator_notes	Human-added context, woven into the natural description. null when none.

Each property carries exact programmatic facts copied verbatim from the modeling docs (type, cardinality via the type string, structural notes) kept distinct from the paraphrased description, plus a provenance tag (extracted from a modeling doc, or curator for human-added content) so regeneration never overwrites human edits.

Status: skeleton / work in progress. INTERACTS_PiP.json is a first hand-authored record used to build and review the rendering pipeline. Content will be reviewed and refined; the eventual generation workflow will emit records in this same shape.