oma-scholar

# 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` (~50K papers indexed)

### When NOT to use

- General web search or non-academic content -> use `oma-search`
- Translating papers -> use `oma-translator`
- 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 and OpenAlex fallback
- `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
```bash
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** — 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: .