Scholar - Research Paper Sidecar Companion

Scheduling

Goal

Search, fetch, generate, validate, analyze, review, and compare scholarly paper sidecars using the Knows .knows.yaml spec for token-efficient research workflows.

Intent signature

• User asks for academic literature search, sidecar generation, sidecar validation, paper claims/evidence summary, structural paper comparison, or peer review as sidecar.
• User references Knows, .knows.yaml, knows.academy, OpenAlex, claims, evidence, relations, or paper sidecars.

When to use

• Reading research papers token-efficiently via Knows sidecars (~700 tokens for claims-only vs ~10K for full PDF)
• Generating .knows.yaml sidecars from your own paper drafts, LaTeX, or research notes
• Validating sidecar structure (rule-based) before sharing
• Producing peer reviews as sidecars
• Querying or summarizing existing sidecars
• Structurally comparing two papers (claims, methods, evidence)
• Searching/fetching sidecars from knows.academy (2026 papers only; current counts via /api/proxy/jobs/stats)

When NOT to use

• General web search or non-academic content -> use oma-search
• Translating papers -> use oma-translation
• PDF parsing only (no sidecar) -> use oma-pdf
• Submitting sidecars back to knows.academy -> out of scope (host LLM only consumes/produces locally)
• Full peer-review workflow with editor system -> out of scope

Expected inputs

• Paper, abstract, draft, LaTeX, research notes, sidecar file, DOI, OpenAlex ID, Knows record ID, or search query
• Desired mode: generate, validate, review, analyze, compare, or remote fetch
• Optional strictness, section filter, or CI behavior

Expected outputs

• .knows.yaml sidecar, review sidecar, lint report, search/fetch result, natural-language analysis, or structural comparison
• Sidecars conforming to v0.9.0 / paper@1 profile
• Validation status and warnings before sharing generated sidecars

Dependencies

• oma scholar CLI subcommands
• knows.academy public API; OpenAlex and Semantic Scholar fallbacks
• resources/sidecar-spec.md, API endpoints, OpenAlex setup, upstream cache, checklist, and execution protocol

Control-flow features

• Branches by mode, source availability, Knows/OpenAlex coverage, strict vs lenient validation, and fetched section
• Reads/writes YAML sidecars and may call public APIs
• Avoids fabrication when source evidence is missing

Structural Flow

Entry

1. Identify mode and source artifact/query.
2. Resolve paper identity through Knows or OpenAlex when needed.
3. Load sidecar spec and mode-specific protocol.

Scenes

1. PREPARE: Select mode and gather source or remote identifiers.
2. ACQUIRE: Fetch paper metadata, sidecar sections, or local source text.
3. REASON: Extract claims, evidence, relations, provenance, or comparison structure.
4. ACT: Generate, lint, review, analyze, compare, or fetch sidecar data.
5. VERIFY: Validate schema, enums, IDs, relations, and provenance.
6. FINALIZE: Return sidecar, report, summary, or comparison with caveats.

Transitions

• If knows.academy lacks the paper, fall back to OpenAlex metadata/abstract.
• If generating a sidecar, run lint before sharing.
• If consuming third-party sidecars with dangling references, use lenient mode when appropriate.
• If source evidence is absent, omit fields instead of guessing.

Failure and recovery

• If remote API times out, retry or use OpenAlex fallback.
• If YAML fails parsing, fix indentation and scalar types.
• If relation density or orphan statements warn, add supported-by relations when source evidence supports them.

Exit

• Success: requested sidecar operation completes with validation status.
• Partial success: missing metadata, fallback source, or validation warnings are explicit.

Logical Operations

Actions

Action	SSL primitive	Evidence
Select mode	SELECT	Generate/Validate/Review/Analyze/Compare/Remote
Read paper or sidecar	READ	Source files or YAML
Request remote data	REQUEST	Knows/OpenAlex APIs
Infer claims/evidence/relations	INFER	Sidecar generation/analysis
Write sidecar	WRITE	.knows.yaml outputs
Validate sidecar	VALIDATE	oma scholar lint
Report result	NOTIFY	Summary or lint report

Tools and instruments

• oma scholar search|resolve|get|lint
• Knows public API, OpenAlex fallback, sidecar spec, checklist

Canonical command path

oma scholar search "<query>"
oma scholar resolve "<title-or-doi>"
oma scholar get "<record-id-or-doi>"
oma scholar lint "<paper.knows.yaml>"

Resource scope

Scope	Resource target
LOCAL_FS	Paper drafts, sidecar YAML, review sidecars
NETWORK	knows.academy and OpenAlex APIs
PROCESS	oma scholar CLI and lint
USER_DATA	User-provided paper content and research notes

Preconditions

• Mode and source are identifiable.
• Spec rules are available for generation or validation.

Effects and side effects

• May create local sidecar or review sidecar files.
• May query public scholarly APIs.
• Does not submit sidecars back to knows.academy.

Guardrails

1. Target spec is v0.9.0 / paper@1 profile (review sidecars use review@1): verified against production sidecars from knows.academy; see resources/sidecar-spec.md
2. Host LLM generates sidecars: never shell out to anthropic SDK or external LLM CLI; this skill runs inside an agent
3. Anti-fabrication: if DOI/venue/year is not visible in source, omit the key entirely; never write doi: TODO or guess
4. Top-level metadata: title, authors, venue, year live at the top level (no metadata wrapper)
5. Field names are exact: statement_type, evidence_type, predicate, artifact_type (not type/claim)
6. Provenance has SINGLE actor: provenance.actor is one object, NOT a provenance.actors array
7. Confidence is an object: {claim_strength: ..., extraction_fidelity: ...}, both from high|medium|low
8. Coverage is an object: coverage.statements (4-value enum) + coverage.evidence (3-value enum)
9. Closed enums: actor tool|person|org (never ai/llm/model); artifact role subject|supporting|cited; predicates in present tense
10. Numbers unquoted: value: 22, never value: '22'
11. Relation density: average ≥1.5 relations per statement; every claim needs supported_by evidence (checklist rule — lint enforces only the average-ratio warning and a per-id warning for statements with zero relations)
12. ID format: descriptive kebab-case with prefix: stmt:privacy-budget-tradeoff, ev:cifar10-accuracy-table, art:paper
13. Validate before sharing: run oma scholar lint after Generate and Review; cross-record refs (record_id#local_id) in review sidecars are recognized and not flagged as dangling
14. Remote API has no auth: https://knows.academy/api/proxy/* is public; do not invent auth headers
15. Partial fetch param is section (singular): fixed enum statements|evidence|relations|artifacts|citation
16. Fallback API keys are optional: OPENALEX_API_KEY (metadata enrichment) and S2_API_KEY (Semantic Scholar dedicated rate limit) both improve throughput but the cascade degrades gracefully without them
17. Sidecar content stays English: schema fields, IDs, statement text follow upstream convention; user-facing responses follow oma-config.yaml language
18. Spec drift awareness: our local rules track v0.9.0 production behavior, which differs from the upstream knows.md natural-language description; refresh resources/upstream-spec-cache.md periodically

Modes

Mode	Trigger	Output
Generate	"create sidecar from this paper / abstract / draft", "generate .knows.yaml"	{paper}.knows.yaml (host LLM emits, then oma scholar lint validates)
Validate	"lint this sidecar", "validate .knows.yaml"	Pass/fail report with file:line issues
Review	"peer review this paper as sidecar"	{paper}.review.knows.yaml
Analyze	"summarize this sidecar", "what claims does it make?"	Natural-language answer
Compare	"compare paper A and paper B structurally"	Diff table (claims/methods/evidence)
Remote	"find papers on X", "fetch sidecar :id", "get claims only for :id"	Search results / sidecar payload

Provider Fallback (knows.academy → OpenAlex → Semantic Scholar)

knows.academy currently indexes only 2026 papers (mostly arXiv). For older or non-2026 papers (Transformer 2017, BERT 2018, classics, journals), the skill automatically falls back to OpenAlex for metadata and abstract, then to Semantic Scholar (AI TL;DR, citation + influential-citation counts) when OpenAlex also has nothing. See resources/fallback-providers.md.

Use the oma scholar CLI subcommands:

# Hybrid search: knows first, OpenAlex fallback
oma scholar search "vision language action"

# Cross-source resolve: figures out which source has the right paper
oma scholar resolve "Attention Is All You Need"

# Get by id (knows record_id, OpenAlex W-id, DOI, arXiv:<id>, CorpusId:<n>)
oma scholar get "10.48550/arXiv.1706.03762"

When OpenAlex returns the answer (knows.academy lacks the paper), use the returned abstract as input to Mode 1 Generate to produce a local sidecar.

How to Execute

Follow resources/execution-protocol.md step by step for the selected mode.

Quick Reference

Search (knows + auto OpenAlex fallback)

oma scholar search "diffusion super resolution"
oma scholar search --year-min 2024 "vision language action"

Find one specific paper

oma scholar resolve "Attention Is All You Need"
# returns top hit from each source + recommendation

Fetch a sidecar or work

# knows.academy full sidecar
oma scholar get "knows:generated/reconvla/1.0.0"

# Partial fetch (claims only, ~700 tokens, 93% reduction vs PDF)
oma scholar get --section statements "knows:generated/reconvla/1.0.0"

# By DOI or OpenAlex W-id (works regardless of knows.academy availability)
oma scholar get "10.48550/arXiv.1706.03762"

# Semantic Scholar: AI TL;DR + citation/influential-citation counts
oma scholar get "arXiv:1706.03762"

When knows.academy is unreachable, get knows:... automatically falls back to OpenAlex by extracting the slug from the record_id. The result is marked with fallback: "openalex" and contains metadata + abstract, useful for running Mode 1 Generate locally.

Validate

# Strict mode for own Generate output (default)
oma scholar lint paper.knows.yaml

# Lenient mode for third-party / fetched sidecars
oma scholar lint --lenient remote.knows.yaml

# Treat warnings as failures (CI mode)
oma scholar lint --fail-on-warning paper.knows.yaml

About 47% of knows.academy-served sidecars contain at least one dangling cross-reference (typo in subject_ref/object_ref, measured across 15 production samples). Use --lenient when consuming third-party records so these surface as warnings rather than blocking errors.

Raw API (when CLI is unavailable)

curl -s "https://knows.academy/api/proxy/search?q=..."
curl -s "https://knows.academy/api/proxy/sidecars/<encoded-id>"
curl -s "https://knows.academy/api/proxy/partial?record_id=<id>&section=statements"
curl -s "https://knows.academy/api/proxy/jobs/stats"   # platform health

Configuration

Project-specific settings: config/scholar-config.yaml. One key is user-tunable and lives elsewhere — read scholar.base_url from .agents/oma-config.yaml first and fall back to api.base_url in the skill config. Everything else there (endpoint paths, timeouts, id prefixes, lint rules) is protocol shape, not preference.

Troubleshooting

Issue	Solution
[ERROR] *.value: numeric value '22' is quoted	Remove quotes: value: '22' -> value: 22
[ERROR] provenance.actor.type: 'ai' is not allowed	Change to tool, person, or org
[ERROR] *.type: use \statement_type` instead of `type``	Rename type -> statement_type (or evidence_type/predicate/artifact_type)
[ERROR] provenance.actors: v0.9 spec uses singular \actor``	Replace actors: [{...}] array with actor: {...} object
[ERROR] *.object_ref: reference 'X' does not match any defined id	Fix the subject_ref/object_ref to point to a real id, OR use --lenient if consuming third-party data (cross-record record_id#local_id refs are recognized and never flagged)
[WARN] relations: avg relations/statement is N.NN (target ≥ 1.5)	Add more supported_by/depends_on relations
[WARN] statements: only N statements; most papers warrant ≥ 8	Expected when generating from abstract only; full-paper Generate should hit 15+
[WARN] *.predicate: past-tense '...' is suspicious	Switch to present tense (evaluated_on -> evaluates_on)
Remote API returns empty results	Try broader query; check /api/proxy/jobs/stats; CLI auto-falls-back to OpenAlex
knows.academy search failed: fetch failed (stderr)	Platform timeout; fallback to OpenAlex is automatic; retry later for sidecars
OpenAlex 403/429	Set OPENALEX_API_KEY (see resources/setup-openalex.md)
semanticscholar error: HTTP 429 (stderr)	Anonymous pool throttled; CLI retries once then skips the source. Set S2_API_KEY (free form at semanticscholar.org/product/api) for a dedicated limit
YAML won't parse	Check indentation; numbers/booleans must be unquoted; strings with : need quotes

References

• Execution steps: resources/execution-protocol.md
• Sidecar spec rules: resources/sidecar-spec.md
• API endpoints: resources/api-endpoints.md
• OpenAlex setup: resources/setup-openalex.md
• Upstream spec snapshot: resources/upstream-spec-cache.md
• Post-generation checklist: resources/checklist.md
• CLI subcommands: oma scholar search|resolve|get|lint (implementation under cli/commands/scholar/)
• Context loading: ../_shared/core/context-loading.md
• Quality principles: ../_shared/core/quality-principles.md
• i18n rules: ../../rules/i18n-guide.md