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- Taskfile with check, build, serve, publish, and viz tasks - task publish validates, builds, rewrites links for object storage, and uploads to Tigris - Client-side link fix covers sidebar, search, and graph navigation on the bucket copy - Pre-review banner on the bundle's root index Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Architecture, data-structure hierarchy, and repository map rendered to SVG from .excalidraw sources beside each page - Diagram builders and headless renderer under tools/diagrams - Raw source material kept in a gitignored sources/ folder Co-Authored-By: Claude Fable 5.1 <[email protected]>
Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Codex tightening pass over 112 documents, then a five-area review by Opus agents: 12 documents reverted, about 100 repaired where qualifiers, disclaimers, quoted source material, or rules were lost - Live links added to the application profiles; call-to-action vendor generalized; sub-taxonomies named per the project lead - Plans and idea inventories under docs/plans for the restructure around the project's ideas; review reports kept under sources/ Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Assets-only Worker per target (dev, staging, prod); task deploy, deploy:staging, deploy:prod; push to main deploys staging - Diagrams recomposed as vertical compositions readable at column width; shared Excalidraw helpers and renderer under tools/diagrams - Click-to-zoom overlay plugin for the site, width-fitted with pan and zoom - Verification tool and review tasks for marking documents stable - Object-storage publishing path and GitHub Pages workflow removed Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Five named pillars: Foundation Context, Data Structures, SDKs, Use Cases, Sample Applications - CDEs and finding models are one content in two collections, both moving to the CDE schema rewrite - Agreed outline with the current pages that collapse into each part, and a drafts staging area - Source eligibility rule and terminology recorded in the build plan Co-Authored-By: Claude Fable 5.1 <[email protected]>
- One table per pillar section, Finding models and CDEs merged with a cluster column - Every idea has exactly one home; all sources are team artifacts - Remaining boundary flags resolved or marked as staying Co-Authored-By: Claude Fable 5.1 <[email protected]>
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Copilot review overview
🟡 Changes recommended
Critical verification and lightbox failures, along with unresolved deployment and base-URL issues, block approval.
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Review effort: Lite
Findings: 2
Open (5)
What changed in this PR
Bootstraps the OKF knowledgebase with validation tooling, Excalidraw diagrams, Quartz/Cloudflare hosting, documentation revisions, and restructure planning.
Changes:
- Adds task, verification, bundle-check, diagram-rendering, and deployment workflows.
- Configures Cloudflare targets and lightbox support.
- Tightens knowledge content and records review and restructure plans.
| File | Reviewed change |
|---|---|
tools/verify.py |
Adds document verification and status reporting. |
tools/diagrams/render_template.html |
Provides Excalidraw SVG rendering. |
tools/diagrams/README.md |
Documents diagram authoring and rendering. |
tools/diagrams/build_hierarchy.py |
Builds the hierarchy diagram. |
Taskfile.yml |
Adds validation, build, deploy, review, and visualization tasks. |
site/wrangler.jsonc |
Defines Cloudflare deployment targets. |
site/quartz.config.yaml |
Registers the lightbox plugin. |
site/okf-lightbox-plugin/package.json |
Declares the lightbox plugin package. |
site/build.sh |
Adds configurable Quartz builds and base URLs. |
README.md |
Updates usage, validation, and hosting documentation. |
knowledge/semantic-foundation/terminologies/ontologies-used.md |
Tightens terminology documentation. |
knowledge/semantic-foundation/terminologies/med-ontology-lookup.md |
Tightens lookup-tool documentation. |
knowledge/semantic-foundation/terminologies/index.md |
Updates terminology navigation. |
knowledge/semantic-foundation/index.md |
Updates semantic-foundation navigation. |
knowledge/semantic-foundation/finding-models/index.md |
Updates finding-model navigation. |
knowledge/semantic-foundation/finding-models/identifiers.md |
Clarifies identifier rules. |
knowledge/semantic-foundation/finding-models/finding-taxonomies.md |
Clarifies taxonomy content. |
knowledge/semantic-foundation/finding-models/finding-model-format.md |
Clarifies format and metadata behavior. |
knowledge/semantic-foundation/finding-models/enrichment-pipeline.md |
Tightens enrichment documentation. |
knowledge/semantic-foundation/finding-models/content-catalog.md |
Tightens catalog documentation. |
knowledge/semantic-foundation/finding-models/authoring-workflow.md |
Tightens authoring guidance. |
knowledge/semantic-foundation/exam-types/overview.md |
Clarifies exam-type usage. |
knowledge/semantic-foundation/common-data-elements/index.md |
Updates CDE navigation. |
knowledge/semantic-foundation/common-data-elements/cdes-and-radelement.md |
Clarifies CDE schema and usage. |
knowledge/semantic-foundation/anatomic-locations/tooling.md |
Tightens anatomy tooling documentation. |
knowledge/semantic-foundation/anatomic-locations/lineage-and-current-implementation.md |
Clarifies dataset lineage. |
knowledge/semantic-foundation/anatomic-locations/laterality-conventions.md |
Clarifies laterality rules. |
knowledge/semantic-foundation/anatomic-locations/index.md |
Updates anatomy navigation. |
knowledge/semantic-foundation/anatomic-locations/data-model.md |
Clarifies the anatomy data model. |
knowledge/roadmap/roadmap-2026.md |
Tightens the project roadmap. |
knowledge/roadmap/open-questions.md |
Updates open-question scope. |
knowledge/roadmap/ipl-data-model-system.md |
Tightens the IPL roadmap. |
knowledge/roadmap/index.md |
Updates roadmap navigation. |
knowledge/roadmap/finding-model-content-direction.md |
Tightens content-direction planning. |
knowledge/roadmap/exam-types.md |
Tightens exam-type planning. |
knowledge/repositories/index.md |
Updates repository navigation. |
knowledge/references/status-update-2026-01.md |
Tightens status-deck extract framing. |
knowledge/references/oifm-overview-extract.md |
Clarifies extract provenance. |
knowledge/references/oifm-metadata-fields-extract.md |
Clarifies metadata extract provenance. |
knowledge/references/index.md |
Updates reference navigation. |
knowledge/references/finding-model-schema.md |
Tightens schema reference framing. |
knowledge/references/cde-schema-differences.md |
Tightens CDE schema comparison. |
knowledge/log.md |
Records editorial review work. |
knowledge/index.md |
Adds draft-status guidance and navigation. |
knowledge/history/use-cases.md |
Tightens the use-case catalog. |
knowledge/history/timeline.md |
Tightens the project timeline. |
knowledge/history/index.md |
Updates history navigation. |
knowledge/guides/migration-ledger.md |
Tightens migration guidance. |
knowledge/glossary/umls.md |
Tightens the UMLS definition. |
knowledge/glossary/technical-finding.md |
Clarifies technical-finding guidance. |
knowledge/glossary/tag.md |
Tightens the tag definition. |
knowledge/glossary/snomed-ct.md |
Tightens the SNOMED CT definition. |
knowledge/glossary/radlex.md |
Refreshes generated metadata. |
knowledge/glossary/radelement.md |
Clarifies RadElement conflicts. |
knowledge/glossary/provenance.md |
Clarifies provenance requirements. |
knowledge/glossary/presence.md |
Clarifies presence semantics. |
knowledge/glossary/oifm.md |
Tightens the OIFM definition. |
knowledge/glossary/observation.md |
Tightens the Observation definition. |
knowledge/glossary/loinc.md |
Clarifies LOINC usage. |
knowledge/glossary/loinc-rsna-radiology-playbook.md |
Tightens Playbook documentation. |
knowledge/glossary/laterality.md |
Clarifies laterality assignment. |
knowledge/glossary/index.md |
Updates glossary navigation. |
knowledge/glossary/index-code.md |
Clarifies index-code semantics. |
knowledge/glossary/imaging-diagnostic-report.md |
Tightens the IHE IDR definition. |
knowledge/glossary/gamuts.md |
Tightens the Gamuts definition. |
knowledge/glossary/fma.md |
Tightens the FMA definition. |
knowledge/glossary/finding-taxonomy.md |
Clarifies taxonomy structure. |
knowledge/glossary/finding-class.md |
Tightens the FindingClass definition. |
knowledge/glossary/fhir-diagnostic-report.md |
Tightens the FHIR DiagnosticReport definition. |
knowledge/glossary/fhir-condition.md |
Tightens the FHIR Condition definition. |
knowledge/glossary/extraction.md |
Clarifies extraction behavior. |
knowledge/glossary/exam-type.md |
Tightens the exam-type definition. |
knowledge/glossary/exam-finding-list.md |
Clarifies Exam Finding List requirements. |
knowledge/glossary/element-binding.md |
Tightens the element-binding definition. |
knowledge/glossary/data-element.md |
Tightens the DataElement definition. |
knowledge/glossary/contributor.md |
Clarifies contributor handling. |
knowledge/glossary/contained-by-and-part-of.md |
Clarifies anatomy hierarchies. |
knowledge/glossary/coding.md |
Tightens coding workflow. |
knowledge/glossary/change-from-prior.md |
Clarifies temporal attributes. |
knowledge/glossary/cde.md |
Tightens the CDE definition. |
knowledge/glossary/cde-set.md |
Tightens the CDE-set definition. |
knowledge/glossary/cde-labeled-fhir-observation.md |
Clarifies CDE/FHIR representation. |
knowledge/glossary/cde-element.md |
Tightens the CDE-element definition. |
knowledge/glossary/body-region.md |
Clarifies body-region usage. |
knowledge/glossary/attribute.md |
Clarifies attribute semantics. |
knowledge/glossary/attribute-value.md |
Refreshes generated metadata. |
knowledge/glossary/assessment-scheme.md |
Clarifies assessment schemes. |
knowledge/glossary/anatomic-scope.md |
Clarifies anatomic scope. |
knowledge/glossary/anatomic-location.md |
Tightens anatomy terminology. |
knowledge/drafts/index.md |
Adds restructure staging navigation. |
knowledge/data-structures/technical-imaging-findings.md |
Tightens migrated findings documentation. |
knowledge/data-structures/sample-data.md |
Clarifies sample-data documentation. |
knowledge/data-structures/index.md |
Updates data-structure navigation. |
knowledge/data-structures/anatomic-location-assignment-rules.md |
Tightens migrated assignment rules. |
knowledge/applications/index.md |
Updates application navigation. |
knowledge/applications/finding-models-site.md |
Tightens the catalog-site profile. |
docs/plans/repository-review.md |
Records repository review and follow-ups. |
docs/plans/lean-content-pass.md |
Records the first editorial pass. |
docs/plans/lean-content-full-review.md |
Records the full editorial review. |
CHANGELOG.md |
Summarizes reader-facing changes. |
.gitignore |
Ignores generated and private source artifacts. |
.github/workflows/site.yml |
Removes the GitHub Pages deployment. |
.github/workflows/deploy.yml |
Adds Cloudflare staging deployment. |
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| "main": "./dist/index.js", | ||
| "exports": { | ||
| ".": { | ||
| "import": "./dist/index.js" | ||
| }, | ||
| "./components": { | ||
| "import": "./dist/components/index.js" |
| if isinstance(data["verified"], dict): | ||
| fm = re.sub(r"^verified:.*$", f"verified:\n - {{ by: {data['verified']['by']}, at: {data['verified']['at']} }}\n{entry}", fm, count=1, flags=re.M) | ||
| else: | ||
| fm = re.sub(r"^(verified:\n(?: - .*\n?)*)", lambda m: m.group(1).rstrip("\n") + "\n" + entry + "\n", fm, count=1, flags=re.M) |
| path: ~/.npm | ||
| key: ${{ runner.os }}-npm-${{ hashFiles('site/quartz.config.yaml') }} | ||
| - name: Build | ||
| run: bash site/build.sh |
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| serve: | ||
| desc: Serve the site locally with live reload | ||
| cmds: | ||
| - bash site/build.sh serve |
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| uv run python /home/talkasab/oidm-knowledge/tools/diagrams/render_excalidraw.py \ | ||
| /home/talkasab/oidm-knowledge/knowledge/<dir>/<name>.excalidraw \ | ||
| -o /home/talkasab/oidm-knowledge/sources/<name>-vN.png \ | ||
| --svg /home/talkasab/oidm-knowledge/sources/<name>-vN.svg |
- Foundation Context anchor with finding models and CDEs, anatomic locations, exam types, and standards sections - The common graph explained once, then the two collections and the urgent document-to-graph direction - Every claim dated and attributed; differing sources shown side by side; all pages draft status - Staged under knowledge/drafts beside the current pages until cross-review Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Data Structures, Use Cases, and Sample Applications drafted and corrected: application links added, manuscript links removed, demonstrations attributed to their public sources - Introduction, Foundation Context, and SDKs drafts corrected: provenance labels restored, uncommitted CDE decisions no longer cited, absence claims scoped to reviewed sources - Review dispositions recorded for every finding; all pages remain draft Co-Authored-By: Claude Fable 5.1 <[email protected]>
- An overview, then a directory per pillar with a document per key idea; no page budget - Finding models and CDEs as a hub with children for OIFM content, definition formats, and identifiers; the next-generation schema for both collections - Use Cases and Sample Applications as lists with a few fleshed-out pages - The project lead's guidance recorded verbatim; a dashboard of page and figure status Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Health Icons and Lucide icons, recolored per band at build time, with licenses recorded - Image, boxed-label, and inset-arrow helpers and a shared palette in the Excalidraw library - Renderer notes on true-width PNG output and close-up inspection Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Overview: what OIDM is for across the imaging lifecycle, the two contexts, the core pieces, use cases, sample applications, where things stand - Foundation Context index: three axes over existing standards and the relationships among them - Figures as Excalidraw builders with SVG renders: the two planes, the five-pillar stack, the three axes, and the Foundation Context mini-network Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Finding Models and Common Data Elements: one kind of content in two collections, beta and release channels, cross-linked - The next-generation schema: node types, edges, and the relationship table verified against the pinned CDE branch - Relationships among definitions: manifestation and causation, associated findings, edge properties, the derived differential, assessment schemes - Two-planes figure embedded in the Overview; every page cross-reviewed with provenance dispositions Co-Authored-By: Claude Fable 5.1 <[email protected]>
…d figures - Two planes: specific exam, Playbook entry, exam family, modality, anatomy chain, a negative finding, node kinds colored - Three axes: section bands per column with example hierarchies; measurements by kind - Mini-network: solid arrowheads; assessment schemes as ovals everywhere - Pillar stack: castellated seams joining applications, SDKs, structures, and foundation (variants kept for the choice) - Nodule neighborhood drawn from the pinned CDE graph, illustrative of pending updates; shape and color conventions recorded Co-Authored-By: Claude Fable 5.1 <[email protected]>
…6-09-30 - Verbatim guidance for the Overview, Foundation Context, hub, schema, relationships, and figures - Glossary dropped in favor of one grown from the new pages; vendor and contributor names kept generic; deck and CDE figures usable - Dashboard of page and figure status with links for peruse Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Raw sources in a private bucket, references with redrawn figures, the team-facing bundle, and the presentation pages the site builds - Pre-review pages go to staging only, labeled DRAFT / Awaiting Review; production refuses unverified pages - Handoff document with every content ruling, the review process, the model policy, the site mechanics, and the source locations Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Sixteen original logo and mark files (SVG and transparent PNG) with the 2023 style guide - Manifest of source paths and checksums; notes on colors, logo variants, and use in site content and diagrams - No theme, header, favicon, or diagram changes Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Installed skills match upstream scaccogatto/okf-skills byte for byte; custom code is the house checker, verification helper, and publishing integration - Alternative validators run against 29 labeled fixtures; shared impossible-date crash and differing check scope recorded - Research only: no tooling, bundle, or site changes Co-Authored-By: Claude Fable 5.1 <[email protected]>
- One summary per Excalidraw board with its ideas, status, pillar connections, and local capture paths - Captures, checksums, and live links stay in the gitignored sources mirror; no live links or meeting names in the public summaries - Staged under docs/references until the layers plan moves references into the bundle Co-Authored-By: Claude Fable 5.1 <[email protected]>
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Brings the repository from the initial pre-review draft to the current working state.
The base is the initial-draft commit; everything since comes through this PR.
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