# Daniel Ari Friedman / docxology

> Canonical site: https://danielarifriedman.com/
> Source repository: https://github.com/docxology/docxology
> Primary public identity: Daniel Ari Friedman, PhD
> ORCID: https://orcid.org/0000-0001-6232-9096
> Wikidata: https://www.wikidata.org/wiki/Q138781444
> This repository is the public research and software index for Daniel Ari Friedman. It collects a curated bibliography, paper folders with README/AGENTS/SKILL documentation, software catalogs, collaborator maps, media references, public identifiers, and website metadata.

Each paper folder under `papers/` may contain `full_text.md` (full page-level text extraction from the PDF or ODT/DOCX/PPTX source) and an `images/` subdirectory (extracted figures and images). Current totals are generated in `data/current-counts.json`; the latest snapshot records 203 paper folders, 199 full-text extractions, 145 image galleries, and 8,959 extracted images. Use `full_text.md` for full-text search, reading, and citation within agent workflows.

## Use These Pages First

- Human homepage: https://danielarifriedman.com/
- Start Here: https://danielarifriedman.com/start-here.html
- Media & Talks: https://danielarifriedman.com/media.html
- Agentic discovery map: https://danielarifriedman.com/discovery.html
- Stable agent route manifest: https://danielarifriedman.com/data/agent-index.json
- Manifest schema registry: `data/agent-index.json` → `schemas` (manifest 1.5, registry 1.5); it documents Work, SoftwareRepository, Repository, ArtworkIndex, VisualArtwork, VideoIndex, VideoObject, Person, Organization, ResumeData, WorkEnrichment, DataCatalog, ClaimWithEvidence, SearchResult, ScholarVerificationReceipt, CoverageException, RepositoryClassification, ReconciliationReport, GeneratedManifest, ReproducibilityLedger, GeneratedReport, PagesArtifactManifest, and ReleaseIntegrity fields. Every `datasets` entry now resolves to a documented schema, and the machine manifest is a superset of the human export hub at `/exports.html`.
- Human search page: https://danielarifriedman.com/search.html
- OpenSearch descriptor: https://danielarifriedman.com/opensearch.xml
- Agent start guide: https://github.com/docxology/docxology/blob/main/AGENT_START.md
- Repository documentation index: https://github.com/docxology/docxology/blob/main/docs/README.md
- Publication sync runbook: https://github.com/docxology/docxology/blob/main/docs/operations/publication-sync.md
- GitHub Pages artifact policy: https://github.com/docxology/docxology/blob/main/docs/operations/github-pages-artifact.md
- Google Search Console follow-up (manual): https://github.com/docxology/docxology/blob/main/docs/seo/gsc-followup.md
- GSC preflight checklist JSON: https://danielarifriedman.com/data/gsc-followup-checklist.json
- Markdown discovery map: https://github.com/docxology/docxology/blob/main/pages/DISCOVERY.md
- Research domains: https://danielarifriedman.com/domains.html
- Domain source map: https://github.com/docxology/docxology/blob/main/pages/DOMAINS.md
- Curated bibliography: https://danielarifriedman.com/publications.html
- Pillar Explainer — Cognitive Security: https://danielarifriedman.com/cognitive-security.html
- Pillar Explainer — Computational Entomology: https://danielarifriedman.com/computational-entomology.html
- Pillar Explainer — Insect Cognition & Collective Intelligence: https://danielarifriedman.com/insect-cognition.html
- Pillar Tutorial — Active Inference & Free Energy Principle: https://danielarifriedman.com/active-inference.html
- Pillar Explainer — Neurosymbolic AI & Active Inference: https://danielarifriedman.com/neurosymbolic-ai.html
- Art gallery (interactive): https://danielarifriedman.com/art.html
- Artwork index (one static page per drawing, VisualArtwork JSON-LD, Flickr backlinks; CC BY-NC): https://danielarifriedman.com/artworks/
- Art collections (themed hubs — Neuroscience & Molecular Biology, Collective Behavior & Ants, Sacred Geometry & Kabbalistic Triangles, Active Inference, Americana & Seals): https://danielarifriedman.com/art-collections/collective-behavior-ants.html
- Art collection — Neuroscience & Molecular Biology: https://danielarifriedman.com/art-collections/neuroscience-molecular-biology.html
- Art collection — Sacred Geometry & Kabbalistic Triangles: https://danielarifriedman.com/art-collections/sacred-geometry-kabbalistic-triangles.html
- Art collection — Active Inference: https://danielarifriedman.com/art-collections/active-inference.html
- Art collection — Americana & Seals: https://danielarifriedman.com/art-collections/americana-seals.html
- Per-work pages index: https://danielarifriedman.com/works/
- Bibliography source table: https://github.com/docxology/docxology/blob/main/pages/BIBLIOGRAPHY.md
- Software catalog: https://danielarifriedman.com/software.html
- Full repository inventory: https://danielarifriedman.com/repositories.html
- Software source table: https://github.com/docxology/docxology/blob/main/pages/SOFTWARE.md
- Resume/CV PDF: https://danielarifriedman.com/resume/resume.pdf
- Resume/CV structured JSON: https://danielarifriedman.com/data/resume.json
- Resume/CV plaintext variants: https://danielarifriedman.com/resume/full.txt
- Cite and verify: https://danielarifriedman.com/cite-verify.html
- Cite and verify source: https://github.com/docxology/docxology/blob/main/pages/CITE_VERIFY.md
- Evidence ledger: https://danielarifriedman.com/evidence.html
- Evidence ledger source: https://github.com/docxology/docxology/blob/main/pages/EVIDENCE.md
- Data catalog: https://danielarifriedman.com/catalog.html
- Public exports index: https://danielarifriedman.com/exports.html
- DataCatalog JSON: https://danielarifriedman.com/data/catalog.json
- Updates page: https://danielarifriedman.com/updates.html
- Changelog source: https://github.com/docxology/docxology/blob/main/CHANGELOG.md
- Profile: https://github.com/docxology/docxology/blob/main/pages/PROFILE.md
- Projections: https://danielarifriedman.com/projections.html — "One surface, many projections" — the longitudinal-record statement page.
- Links: https://github.com/docxology/docxology/blob/main/pages/LINKS.md
- Papers directory: https://github.com/docxology/docxology/tree/main/papers
- Full-text extraction pipeline: https://github.com/docxology/docxology/blob/main/code/orchestrators/extract_paper_texts.py
- Citation metadata: https://github.com/docxology/docxology/blob/main/CITATION.cff
- CodeMeta metadata: https://danielarifriedman.com/codemeta.json
- BibTeX export: https://danielarifriedman.com/bibliography.bib
- CSL JSON export: https://danielarifriedman.com/bibliography.csl.json
- RIS export: https://danielarifriedman.com/bibliography.ris
- Works JSON (canonical machine-readable registry of every work — num, citation_key, url, doi, paper-folder): https://danielarifriedman.com/data/works.json
- Publications JSON-LD (CollectionPage mainEntity): https://danielarifriedman.com/data/publications-ld.json
- Artwork JSON: https://danielarifriedman.com/data/artworks.json
- Artwork compact index: https://danielarifriedman.com/data/artworks-index.json
- Video compact timeline index: https://danielarifriedman.com/data/videos-index.json
- Complete video metadata JSON: https://danielarifriedman.com/data/videos.json
- Software JSON: https://danielarifriedman.com/data/software.json
- Software JSON-LD: https://danielarifriedman.com/data/software-ld.json
- Paired-publication decisions JSON: https://danielarifriedman.com/data/paired-publication-decisions.json
- Current volatile counts JSON: https://danielarifriedman.com/data/current-counts.json
- GitHub repositories JSON: https://danielarifriedman.com/data/github-repositories.json
- People JSON: https://danielarifriedman.com/data/people.json
- Organizations JSON: https://danielarifriedman.com/data/organizations.json
- Claims JSON: https://danielarifriedman.com/data/claims.json
- Resume JSON: https://danielarifriedman.com/data/resume.json
- Reconciliation JSON: https://danielarifriedman.com/data/reconciliation.json
- Work enrichment JSON: https://danielarifriedman.com/data/work-enrichment.json
- Generated-file manifest: https://danielarifriedman.com/GENERATED.md
- Generated-file manifest JSON: https://danielarifriedman.com/data/generated-manifest.json
- Humans/contact file: https://danielarifriedman.com/humans.txt
- Security contact: https://danielarifriedman.com/.well-known/security.txt
- Search index: https://danielarifriedman.com/search-index.json
- RSS feed: https://danielarifriedman.com/feed.xml
- Per-domain RSS feeds: https://danielarifriedman.com/feeds/domain-<slug>.xml — 8 per-domain RSS 2.0 feeds (one per research domain, generated by code/orchestrators/build_domain_feeds.py; slugs: entomology, active-inference, cognitive-security, aii-ecosystem, art-synergetics, biomedicine, computational, presentations-media)
- Public-source snapshot: https://github.com/docxology/docxology/blob/main/reports/public_source_snapshot_2026-10-07.json
- Public-source inventory: https://github.com/docxology/docxology/blob/main/reports/public_source_inventory_2026-10-06.json
- Reconciliation report: https://github.com/docxology/docxology/blob/main/reports/reconciliation_2026-10-07.md
- External-link report: https://github.com/docxology/docxology/blob/main/reports/external_links_2026-10-07.json
- External-link triage: https://github.com/docxology/docxology/blob/main/reports/external_links_triage_2026-10-07.md
- Asset-size report: https://github.com/docxology/docxology/blob/main/reports/asset_size_2026-10-07.json
- Static accessibility report: https://github.com/docxology/docxology/blob/main/reports/accessibility_static_2026-10-07.json
- Visual QA manifest: https://github.com/docxology/docxology/blob/main/reports/visual-qa/2026-10-05/manifest.json

## Public Crawl Policy

- The entire site is public and crawlable (`robots.txt`: `Allow: /`).
- `sitemap.xml` lists **index-priority** URLs (HTML hubs, works pages, citation exports) — not a crawl gate.
- Ops paths (`reports/`, `docs/`, bulk `data/*.json`, ops `.md`) remain public and linked from `discovery.html`, `catalog.html`, and `exports.html`.
- Primary publication index target: `works/{citation_key}.html`. Paper-folder HTML (`papers/{folder}/`) canonicalizes to the work page.

## Source Of Truth Rules

- Treat pages/BIBLIOGRAPHY.md as the curated bibliography source of truth.
- Use docs/operations/publication-sync.md for GitHub + Zenodo publication intake, Zenodo-only backfill, GitHub-only software triage, DOI version refreshes, dry-run review, and apply/validation commands.
- Treat publications.html as the canonical HTML rendering of that bibliography.
- Treat pages/SOFTWARE.md as the curated software source of truth.
- Treat discovery.html and pages/DISCOVERY.md as the place for API endpoints, source queries, and caveats about public index count mismatches.
- Treat pages/EVIDENCE.md and data/claims.json as the claim-level source ledger.
- Treat resume/source.json as the curated source for resume-specific records; bibliography and software content in data/resume.json is merged from data/works.json and data/software.json.
- Treat data/reconciliation.json as the explanation layer for why curated local counts differ from public indexes.
- Treat search.html, search-index.json, opensearch.xml, catalog.html, data/catalog.json, updates.html, GENERATED.md, and feed.xml as generated or index-facing discovery artifacts, not independent sources of truth.
- Public APIs are freshness checks. Counts can include forks, duplicates, versioned software archives, preprints, or over-merged name variants.

## Current Snapshot

Current volatile totals are generated in reports/current_counts.md and data/current-counts.json, with source paths, generation metadata, and rebuild commands. Scholar metrics are sourced from data/scholar-snapshot.json and should not be copied into this file as current prose.

## Optional

Use CITATION.cff for machine-readable citation metadata. Preferred title: "docxology: Daniel Ari Friedman public research and software index".