feat: add scientific knowledge graph module

[grantf04]

@algora-pbc /claim #17

Closes #17

What this adds

Adds a self-contained scientific-knowledge-graph/ module for scientific entity extraction, linked graph metadata, entity pages, graph navigation/search, filters, AI recommendations, JSON APIs, tests, and a reviewer dashboard.

Requirement mapping

• Entity extraction → implemented by extractEntities, covering concepts, authors, affiliations/institutions, tools/software, cited DOIs, and ontology-backed entities.
• Linked data and schema.org metadata → implemented by buildGraph, which returns typed nodes, relationship edges, and schema.org payloads.
• Entity pages → implemented by buildEntityPage with usage contexts, citation reach, and relationships.
• Knowledge navigation and graph search → implemented by queryGraph, including dataset, CRISPR/protocol, notebook reuse, institution, type, domain, and reproducibility filters.
• Dynamic node types → represented across papers, datasets, notebooks, protocols, authors, concepts, tools, DOIs, ontologies, funders, and institutions.
• AI research recommendations → implemented by recommendResearch using interests, recent project activity, graph proximity, citation count, and reproducibility score.
• Discovery/sidebar/digest style output → rendered in the dashboard and exposed via /api/recommendations.

How to verify in under 5 minutes

cd scientific-knowledge-graph
npm test
npm start

Open http://localhost:4131 and verify the dashboard shows graph node/edge counts, extracted entity nodes, the CRISPR entity page, knowledge-navigation query results, and ranked recommendations.

Optional API smoke checks:

curl -s http://localhost:4131/api/dashboard
curl -s "http://localhost:4131/api/query?q=CRISPR"
curl -s http://localhost:4131/api/entities/concept-crispr

Validation

Commands run:

• npm test - 4 tests passing
• curl -s http://localhost:4131/api/dashboard - returns 26 nodes, 28 edges, and 5 recommendations
• curl -s "http://localhost:4131/api/query?q=CRISPR" - returns 7 nodes and 6 edges
• curl -i -s http://localhost:4131/package.json - returns 404 without crashing the server
• Browser demo verified at http://127.0.0.1:4131/: graph index, entity page, knowledge navigation, and AI recommendations render with 0 console errors
• ffprobe verified the committed demo video is 1280x760 and 8 seconds long

Demo

• Short demo video: scientific-knowledge-graph-demo.mp4
• Screenshot: dashboard.png
• Demo script: scientific-knowledge-graph/docs/demo-script.md

Scope

This PR is intentionally self-contained under scientific-knowledge-graph/ and avoids unrelated root-level changes except adding the module link to the root README.

[grantf04]

@algora-pbc /claim #17

[grantf04]

/claim #17