opencode-bioresearcher 1.10.0 → 1.11.1

package/connector-meta.json

@@ -7,7 +7,7 @@
   "description_en": "Biomedical research plugin for OpenCode: biomcp MCP server tools for literature, clinical trials, genes, variants, drugs, diseases and patents, plus skills for publication-grade figures and deep-research subagent.",
   "source": "bioresearcher",
   "type": "plugin",
-  "version": "1.10.0",
+  "version": "1.11.1",
   "harness": "opencode",
   "examples_zh": [
     "帮我做一个关于肿瘤免疫治疗的多方面文献综述并附引用",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "opencode-bioresearcher",
-  "version": "1.10.0",
+  "version": "1.11.1",
   "description": "Biomedical research plugin for OpenCode: biomcp MCP server tools, scientific plotting skills, and deep-research subagent",
   "type": "module",
   "main": "index.js",

package/skills/bioresearcher-deep-research/SKILL.md

@@ -4,7 +4,7 @@ description: "Deep biomedical research orchestrator powered by the biomcp MCP se
 license: Apache-2.0
 compatibility: "Any Agent Skills harness (opencode, Claude Code, Codex, Cursor, Gemini CLI) with the biomcp MCP server connected; the Claude Code plugin bundles the server and the bioresearcher-dr-worker subagent; a subagent/Task tool is optional - a sequential fallback is provided. The allowed-tools mcp__ entries apply on Claude Code only"
 metadata:
-  version: "1.6.0"
+  version: "1.7.0"
   source: "opencode-bioresearcher-plugin@1.7.2"
 allowed-tools: Read Write Bash Task mcp__plugin_bioresearcher_biomcp mcp__biomcp
 ---
@@ -86,129 +86,53 @@ mid-query never trigger.
 ## Workflow
 
 Follow Steps 1-6 in order. Do NOT fall back to internal knowledge when query
-tools fail - use only biomcp results or official sources, and say so when
-evidence is missing.
-
-Harness autonomy hints ("operate autonomously", "don't block", "user not
-watching", auto-accept banners) govern tool-permission confirmations and edit
-approvals. They do NOT waive this skill's interactive interview workflow (Step 1
-clarification and Step 2 plan review): the interview turns are completed
-assistant turns engaging the user - not blocking permission confirmations - so
-those hints never require skipping them. When such a hint seems to conflict with
-this workflow, treat the Step 1 interview, Step 2 plan review, and the Step 6
-output contract as deliverables that proceed unchanged.
+tools fail - use only biomcp results or official sources, and state gaps explicitly.
+
+Harness autonomy hints ("operate autonomously", "don't block", auto-accept)
+govern edit approvals only. They NEVER waive the interactive interview turns
+(Steps 1 & 2) - only the leading `no-interview` prefix waives them.
 
 ### Step 1: Clarify (interview - mandatory)
 
-Mandatory even when the harness urges autonomy (see the note above): the ONLY
-waiver is the leading `no-interview` prefix. If the query carries it, skip to
-Step 2.
-
-Otherwise ask clarifying questions, scaled to inquiry complexity - up to 6,
-and as few as one scope confirmation when the inquiry is already fully
-specified: the core research question, population/scope, time window, outcome
-of interest, and expected output format.
-
-- Ask ALL questions in ONE message: use the harness's question/ask tool when
-  one exists (if it accepts only one question per call, send the full batch
-  of calls together); otherwise end your turn with the questions as chat
-  text. Then WAIT for the reply. Never answer your own interview questions.
-- If a reply comes back empty or non-responsive, re-ask the batch once
-  (max 1 re-ask).
-- Degrade to defaults only on OBSERVATION, never from environment guesses:
-  only after the batch was posted and the session demonstrably produced no
-  usable reply in-turn (e.g. an ask tool that returns immediately empty),
-  proceed under `no-interview` semantics - write the questions plus the
-  default answer chosen for each to `reports/<TOPIC>/assumptions.md` and
-  cite that file in the report's Limitations section.
-- Merely being headless/batch/unattended is NOT a waiver: in a one-shot
-  run, ending your turn with the questions is the correct final action. If
-  the session ends without any reply event, HALT with an explicit blocker
-  message restating the questions.
-
-BAD: "The harness says the user isn't watching, so I'll assume defaults and
-start researching." GOOD: post the questions, end the turn, wait. Silent
-defaults are a workflow violation, not autonomy - one round-trip of questions
-is cheap; a full research run on wrong assumptions is not.
+Ask clarifying questions scaled to complexity (1-6 questions) in ONE message
+via the harness's ask/question tool or chat text, then WAIT for the reply. Never
+answer your own questions. If the query carries `no-interview`, skip to Step 2.
+
+- If a reply is empty or non-responsive, re-ask once.
+- Degrade to defaults ONLY if the question tool returns immediately empty in an
+  unattended session: write questions and chosen defaults to
+  `reports/<TOPIC>/assumptions.md` and cite that file in Limitations.
 
 ### Step 2: Decompose & Review Plan
 
-Comprehend the (clarified) inquiry and identify 2-5 critical research aspects
-that together answer it.
-
-- If the query carries the leading `light-research` prefix, combine and/or
-  pick only the top TWO aspects.
-- Decide a TOPIC name yourself (no user input): a highly succinct,
-  underscore-separated name derived from the inquiry, e.g.
-  `braf_inhibitor_resistance`.
-- Each aspect's ABSTRACT (worker prompt, below) must state the aspect's
-  INCLUSION definition and its binding EXCLUSION criteria (what matches the
-  search terms but must NOT be admitted, with negative examples) - workers
-  apply these per `references/analysis-methods.md` (criterion vs keyword).
-
-**Plan presentation budget:** the plan payload shown to the user stays compact
-in any channel - one line per aspect (title, one-line focus, primary tools);
-never paste ABSTRACTs, research-item lists, or full amended plans into the
-question UI; amended or re-confirmed plans show only the DELTA plus the
-compact list. The full plan (ABSTRACTs with boundaries, research items) is
-written to `reports/<TOPIC>/plan.md` when work starts (Step 3).
-
-**Interview waiver (`no-interview`):**
-If the query carries the leading `no-interview` prefix, skip the plan review
-turn entirely: finalize the 2-5 aspects, track them with the harness's todo
-mechanism if available (TodoWrite or equivalent), and proceed immediately to
-Step 3 and Step 4.
-
-**Plan review (interview mode - default):**
-When running in interview mode (without `no-interview`), present your proposed
-research area plan to the user before launching workers:
-
-1. Formulate and present:
-   - A structured list of the 2-5 research aspects (or top 2 under
-     `light-research`), each with an aspect title, 1-2 sentence focus summary,
-     and primary tools/evidence sources (e.g. PubMed/articles,
-     ClinicalTrials.gov, genes, drugs, patents).
-   - An explicit prompt inviting user feedback and adjustments on these
-     research areas.
-2. End your turn with the plan proposal (using the harness's question/ask tool
-   when available, or chat text) and WAIT for the user's reply. Do not spawn
-   workers or create output directories before receiving user feedback.
+Comprehend the inquiry and identify 2-5 critical research aspects (top 2 under
+`light-research`). Decide a TOPIC name (succinct, underscore-separated, e.g.
+`braf_inhibitor_resistance`). Each aspect's ABSTRACT defines INCLUSION and binding
+EXCLUSION criteria per `references/analysis-methods.md`.
+
+**Plan presentation budget:** keep the plan compact - one line per aspect (title,
+focus, primary tools); never paste raw ABSTRACTs into the question UI.
+
+**Plan review (default mode):**
+1. Present the 2-5 aspects to the user with tools/sources and invite feedback.
+2. End your turn (via ask tool or chat) and WAIT for the reply. Do not spawn
+   workers or create output directories before feedback.
 3. User feedback handling:
-   - **Case A (approval / "looks good" / "proceed"):** Proceed directly to
-     Step 3 and Step 4.
-   - **Case B (default feedback - modifications without re-review request):**
-     Incorporate the user's requested adjustments, additions, drops, or scope
-     changes into the research aspects immediately (strictly adhering to the
-     2-5 aspect ceiling, or top 2 under `light-research`). Then **PROCEED
-     DIRECTLY to Step 3 and Step 4. Do NOT ask for another round of
-     confirmation.**
-   - **Case C (special case - explicit re-confirmation requested):** ONLY if the
-     user explicitly asks to review or confirm the revised plan (e.g. "show me
-     the updated plan before starting" or "revise the plan and ask me again"),
-     present the updated plan in a new turn and wait for confirmation before
-     dispatching subagents (limit plan re-confirmations to at most 2 rounds).
-   - **User inquiries during review:** If the user asks a clarifying question
-     (e.g. "can we include pediatric trials?"), answer succinctly in 1-2
-     sentences, incorporate the suggested scope into the relevant aspect, and
-     proceed directly to Step 3 and Step 4 unless explicit re-confirmation was
-     demanded.
-
-**Degrade to defaults on OBSERVATION:**
-Like Step 1, degrade only after the plan was posted and the session
-demonstrably produced no usable reply in-turn (e.g. an ask tool returning
-immediately empty in unattended/headless runs): proceed under the initial
-proposed plan, record the default plan in `reports/<TOPIC>/assumptions.md`,
-and cite that file in the report's Limitations section.
-
-Track the finalized aspect list with the harness's todo mechanism if available
-(TodoWrite or equivalent); otherwise keep it in working memory.
+   - **Approval / "proceed":** Proceed directly to Step 3 and Step 4.
+   - **Feedback / modifications:** Incorporate adjustments immediately and
+     PROCEED DIRECTLY to Step 3 and Step 4. Do NOT ask for another confirmation.
+   - **Explicit re-confirmation requested:** Only if the user explicitly asks to
+     review the revised plan, present it in a new turn (max 2 rounds).
+4. **Waiver / Degrade:** Skip plan review turn if query has `no-interview`, or
+   degrade per Step 1 rules if unattended (record plan in `assumptions.md`).
+
+Track finalized aspects in the harness's todo tool (TodoWrite or equivalent).
 
 ### Step 3: Create the output directory
 
 Write the durable research plan to `reports/<TOPIC>/plan.md` (aspect list,
-each aspect's ABSTRACT with inclusion/exclusion boundaries, research items) -
-this is the post-feedback snapshot the question UI never needs to carry. The
-write tool auto-creates parent directories - do NOT use bash mkdir for this.
+each aspect's ABSTRACT with boundaries, research items). The Write tool
+auto-creates parent directories - do NOT use bash mkdir for this.
 
 ### Step 4: Research each aspect
 
@@ -219,6 +143,13 @@ run the sequential tier below without fabrication - evidence gathering is
 unavailable until the server is wired (run the `bioresearcher-onboard`
 skill or see Prerequisites).
 
+**Tier dispatch hierarchy:** When a subagent tool (`task` or `Task`) is
+available in the harness, parallel worker dispatch (Tier A or Tier B) is
+MANDATORY to maintain research parallelism and isolated worker contexts.
+Subagents inherit all configured tools (biomcp, shell, filesystem) automatically;
+do NOT dispatch exploratory probe tasks to test tool access.
+Tier C is strictly a degraded fallback when no subagent tool exists.
+
 **Tier A - dedicated worker subagent (preferred when available):** if the
 harness offers the `bioresearcher-dr-worker` subagent type (installed with
 the bioresearcher Claude Code plugin; scoped name
@@ -243,6 +174,7 @@ TOPIC: <TOPIC>
 YOUR RESEARCH FOCUS: <RESEARCH-ASPECT>
 DESCRIPTION: <ABSTRACT>
 SKILL_DIR: <absolute path to this skill's directory>  # Tier B only; a literal path string workers substitute into commands - NOT an env var
+EXECUTION RULE: Do NOT read or inspect evidence-ledger.py or other skill scripts; all schemas and commands are fully specified here.
 ```
 
 ABSTRACT is <200 words describing the exact focus, a list of detailed
@@ -256,38 +188,37 @@ VERBATIM - they are binding, never loosened in translation.
 
 Record finished workers via the todo list. If subagents are stuck without
 progress for too long, prompt the user: "If subagents are stuck without
-progress for too long, interrupt and ask me to resume work." Restart failed
-workers as needed (retry <= 3 per worker); gap top-ups follow the serialized
-ownership-transfer protocol in `references/worker-protocol.md`.
-
-**Tier C - sequential (no subagent tool):**
-
-Process aspects one at a time in the main conversation. For each aspect, apply
-the same worker rules from `references/worker-protocol.md` (tool selection per
-`references/tool-selection.md`, citation discipline and the evidence ledger per
-`references/citations.md` and worker-protocol rule 8, retry <= 3, no
-re-delegation) and write the same per-aspect files (report + ledger). State
-which aspect is being worked on before starting each one.
-
-**All tiers, per aspect:**
-
-- Query biomcp tools per `references/tool-selection.md`; filter at the source
-  (specific terms, `limit`, `sections`) rather than retrieving broadly.
-- Make MCP calls sequentially, not concurrently.
-- Collect identifiers for every source used: PMIDs/PMCIDs/DOIs (articles),
-  NCT IDs (trials), patent IDs, accessions (GEO/SRA), database IDs
-  (genes/drugs/variants).
-- Maintain the evidence ledger `reports/<TOPIC>/evidence/<ASPECT>.jsonl` per
-  `references/worker-protocol.md` rule 8: after EACH biomcp call, append one
-  record per potentially-citable source with fields copied verbatim from the
-  tool result, batching all records from one tool result into a single
-  `evidence-ledger.py add` call (never one call per record, never per-record
-  scratch files); title-less records (LitSense hints) are enriched via
-  `article_get(pmid)` before citing.
-- Write findings to `reports/<TOPIC>/<ASPECT>.md` (underscore-separated
-  ASPECT name) citing sources with semantic cite-key markers
-  (`[@pmid:21639808]`) - NO bibliography section; numbering and the
-  bibliography are generated later from the ledger by `render` (Step 5b).
+progress for too long, interrupt and ask me to resume work."
+
+**Tier C - sequential (strictly when no subagent tool exists):**
+If the harness has no subagent tool (`task` / `Task`), process aspects one at a
+time in the main conversation per `references/worker-protocol.md`.
+
+**Worker completion gate (all tiers):**
+When each worker finishes, before marking the aspect complete in the todo list, run:
+```bash
+python3 <skill_dir>/scripts/evidence-ledger.py check \
+  reports/<TOPIC>/evidence/<ASPECT>.jsonl \
+  --markers reports/<TOPIC>/<ASPECT>.md
+```
+- Exit 0: mark aspect complete in todo list.
+- Exit 1:
+  - Trivial syntax/quarantine error in ledger: fix directly using Edit/Write.
+  - Missing records or unresolved markers: dispatch a top-up remediation worker
+    with the check diagnostic output per `references/worker-protocol.md` (max 2
+    remediation retries). Never guess or re-point IDs.
+  - If retries fail: strip the unresolved marker, qualify the claim in the
+    report with a caution note, log the failed ID in `## Evidence Gaps` and
+    `reports/<TOPIC>/assumptions.md`, and proceed.
+- Without Bash/Python access: re-read the aspect ledger and confirm every marker
+  in `<ASPECT>.md` resolves to a ledger record before marking complete.
+
+**Worker execution rules (summary):**
+Query biomcp sequentially per `references/tool-selection.md`, append records to
+`reports/<TOPIC>/evidence/<ASPECT>.jsonl` after each search using `evidence-ledger.py add`
+(never invent values), and write findings with `[@key]` markers to `reports/<TOPIC>/<ASPECT>.md`
+(no bibliography; PDB entries follow the dual-entity rule in `references/worker-protocol.md`).
+See `references/worker-protocol.md` for full schemas.
 
 ### Step 5: Synthesize (cite-key draft)
 
@@ -324,12 +255,11 @@ python3 <skill_dir>/scripts/evidence-ledger.py verify \
   reports/<TOPIC>/evidence/sources.jsonl --apply
 ```
 
-- `merge` unions the per-aspect JSONLs (its own output and `_`-prefixed
-  quarantine files are excluded automatically; malformed lines are
-  quarantined to `evidence/_invalid.jsonl`).
+- `merge` unions the per-aspect JSONLs (malformed lines quarantined to `_invalid.jsonl`).
 - `verify` cross-checks article records against NCBI esummary and backfills
-  ONLY missing fields (epub-ahead-of-print records legitimately stay
-  locator-less). It also sets titles on title-less records.
+  missing fields (including authors, title, journal, locators). Records with
+  conflicting titles or DOIs are flagged with warnings and left unverified.
+  `--apply` mutates the ledger file in place; review changes via script output.
 
 ### Step 5b: Render the final report (numbering authority)
 
@@ -368,52 +298,38 @@ python3 <skill_dir>/scripts/vet-references.py reports/<TOPIC>/final_report.md --
 - Layer 2 (fail-safe): on API timeout, rate-limiting, or network failure the
   script exits 0 and keeps pre-vetting citations unchanged. Non-PMID
   citations (clinical trials, patents, genes, web URLs) are preserved.
-- Exit 1 means STOP: repair the draft or ledger, re-render, and re-vet - never
-  proceed to Step 6 with a failing audit. Review printed warnings even on
-  exit 0 (e.g. PMID/title mismatches).
+- Exit 1 means STOP: repair the draft or ledger, re-render, and re-vet.
+- Warning disposition: every warning emitted during `verify` or `vet-references`
+  must be resolved (fixed in draft/ledger and re-rendered) or explicitly
+  justified in Limitations before Step 6.
+- `--apply` mutates `final_report.md` in place; review printed `- OLD:` / `+ NEW:`
+  updates (or use `--diff` for unified diffs).
 - If the script is unreachable, proceed to Step 6 with the rendered report and
   state the gap in the final summary.
 
 ### Step 6: Write final report + HTML
 
 - Ensure `reports/<TOPIC>/final_report.md` is finalized and vetted.
-- Then render `reports/<TOPIC>/final_report.html` - ALWAYS by default,
-  unless the query carries the leading `no-html` prefix or the user
-  explicitly declined HTML. The markdown report is the complete deliverable;
-  HTML is only a rendering, so never block finishing the session on it.
-
-  Replace `<skill_dir>` with the full path to this skill's directory
-  (`${CLAUDE_PLUGIN_ROOT}/skills/bioresearcher-deep-research` on Claude Code
-  plugin installs; in harnesses that inject SKILL.md without filesystem
-  access the script is unreachable - go straight to the gap step below).
-  Run from the working directory containing `reports/<TOPIC>/` and anchor
-  the output path to the `final_report.md` location:
+- Then render `reports/<TOPIC>/final_report.html` (always by default, unless
+  `no-html` prefix was passed or user explicitly declined HTML).
+  The markdown report is the deliverable; HTML is only a rendering.
+
+  Anchor the output path to the `final_report.md` location:
 
   ```bash
   uv run --with markdown python <skill_dir>/scripts/markdown-to-html.py \
     reports/<TOPIC>/final_report.md -o reports/<TOPIC>/final_report.html
   ```
 
-  Conversion ladder - attempt in order; a rung fails if its tool is missing,
-  its command exits non-zero, or execution is denied; one attempt per rung,
-  then fall through:
-
+  Conversion ladder (attempt in order; fall through on failure):
   1. `uv` on PATH: the command above.
-  2. `python3 -c "import markdown"` succeeds: run
-     `python3 <skill_dir>/scripts/markdown-to-html.py` with the same args.
-  3. `pandoc` on PATH: `pandoc reports/<TOPIC>/final_report.md -o
-     reports/<TOPIC>/final_report.html --standalone` (its styling differs
-     from the script's GitHub-like CSS - that is not a failure).
-  4. No rung succeeded: keep markdown-only and state the gap explicitly in
-     the final summary (the reason + the `bioresearcher-python-setup-uv`
-     skill as remediation).
-
-  Never install converters into the environment (no apt/pip/npm installs);
-  `uv run --with` ephemeral overlays are the sanctioned exception. After a
-  successful rung, verify `final_report.html` exists and is non-empty before
-  declaring success. Do NOT read the full markdown into memory for the
-  conversion - pass the file path. The final summary must name which
-  artifacts exist and, when HTML is absent, why.
+  2. `python3 -c "import markdown"` succeeds: run `python3 <skill_dir>/scripts/markdown-to-html.py reports/<TOPIC>/final_report.md -o reports/<TOPIC>/final_report.html`.
+  3. `pandoc` on PATH: `pandoc reports/<TOPIC>/final_report.md -o reports/<TOPIC>/final_report.html --standalone`.
+  4. None succeeded: keep markdown-only; state reason in summary and Limitations.
+
+  Never run apt/pip/npm installs; `uv run --with` ephemeral overlays are the
+  sanctioned exception. Verify `final_report.html` exists and is non-empty before
+  declaring success.
 
 ## Output layout
 

package/skills/bioresearcher-deep-research/references/citations.md

@@ -23,8 +23,8 @@ Multiple:  Several studies confirm the association [@pmid:21639808; @nct:NCT0428
 - Keys are the ledger's derived canonical keys (the `add` banner echoes
   them): `pmid:` > `doi:` > `pmcid:` for articles, `nct:` for trials,
   `patent:`, `gene:`, `clinvar:`, `chembl:`/`chebi:`/`unii:` for drugs,
-  ontology ids for diseases, accessions for datasets, `url:`/`title:` for
-  web/other. A `doi:`/`pmcid:` marker whose record was promoted to a `pmid:`
+  ontology ids for diseases, accessions/PDB for datasets (`geo:`, `sra:`, `gb:`, `pdb:`),
+  `url:`/`title:` for web/other. A `doi:`/`pmcid:` marker whose record was promoted to a `pmid:`
   key by merge still resolves.
 - A bracket whose tokens are not namespace+shape-valid cite-keys (prose like
   `[@home]`, pandoc-style `[@Chapman2011]`) is left verbatim.
@@ -136,9 +136,10 @@ Example:
 [7] Cutaneous melanoma. MONDO:0002025. https://monarchinitiative.org/MONDO:0002025
 ```
 
-### Datasets / sequences (geo_get / sra_get / genbank_get)
+### Datasets / structures / sequences (pdb / geo_get / sra_get / genbank_get)
 
 ```
+[N] PDB structure [PDB_ID]: [title]. [[method]] Resolution: [res]. https://www.rcsb.org/structure/[PDB_ID]
 [N] GEO series GSEXXXXXX: [title]. [organism]. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSEXXXXXX
 [N] SRA run SRRXXXXXXX: [experiment description]. https://trace.ncbi.nlm.nih.gov/Traces/?run=SRRXXXXXXX
 [N] GenBank accession XXXXXXXX.X: [definition]. https://www.ncbi.nlm.nih.gov/nuccore/XXXXXXXX.X

package/skills/bioresearcher-deep-research/references/ensembl-pdb.md

@@ -132,3 +132,5 @@ Structure workflow:
   the workspace matters.
 - Chain ensembl_lookup -> gene_get for human annotation; ensembl_region ->
   variant_get for variant detail; pdb citation sections -> article_get.
+  Never copy `summary.title` (structure title) or `summary.authors` (depositors)
+  into `article` records; deposition titles and authors belong to the coordinate entry.

package/skills/bioresearcher-deep-research/references/tool-selection.md

@@ -68,6 +68,8 @@ QUESTION TYPE
 ├─ Orthologues / consequences / regions / structures
 │   → ensembl_lookup / ensembl_homology / ensembl_consequence / ensembl_region
 │   → pdb (query | pdb_id | pdb_id+download)
+│      - Cite structure: dataset [@pdb:XXXX]
+│      - Cite paper: chain summary.pmid -> article_get(pmid) -> article [@pmid:XXXX]
 │   → details: references/ensembl-pdb.md
 │
 ├─ Ambiguous / multi-entity free text ("BRAF V600E melanoma")

package/skills/bioresearcher-deep-research/references/worker-protocol.md

@@ -18,6 +18,7 @@ TOPIC: <TOPIC>
 YOUR RESEARCH FOCUS: <RESEARCH-ASPECT>
 DESCRIPTION: <ABSTRACT>
 SKILL_DIR: <absolute skill dir>   # Tier B only; resolve before dispatch
+EXECUTION RULE: Do NOT read or inspect evidence-ledger.py or other skill scripts; all schemas and commands are fully specified here.
 ```
 
 - ABSTRACT: <200 words describing the exact focus, a list of detailed
@@ -101,9 +102,10 @@ SKILL_DIR: <absolute skill dir>   # Tier B only; resolve before dispatch
       {"schema":"bioresearcher-evidence/1","type":"gene","ids":{"ncbi_gene":"673","hgnc":"HGNC:1097"},"title":"B-Raf proto-oncogene, serine/threonine kinase","meta":{"symbol":"BRAF"},"url":"https://www.ncbi.nlm.nih.gov/gene/673","provenance":[...]}
       {"schema":"bioresearcher-evidence/1","type":"variant","ids":{"clinvar":"13961","rs":"rs113488022"},"title":"NM_004333.6(BRAF):c.1799T>A","meta":{"gene":"BRAF","protein_change":"V600E","significance":"Pathogenic"},"provenance":[...]}
       {"schema":"bioresearcher-evidence/1","type":"drug","ids":{"chembl":"CHEMBL1229517"},"title":"vemurafenib","meta":{"indication":"BRAF V600E-mutant melanoma","source_section":"FDA label (drug_get safety section)"},"provenance":[...]}
-      {"schema":"bioresearcher-evidence/1","type":"disease","ids":{"mondo":"MONDO:0002025"},"title":"Cutaneous melanoma","url":"https://monarchinitiative.org/MONDO:0002025","provenance":[...]}
-      {"schema":"bioresearcher-evidence/1","type":"dataset","ids":{"geo":"GSE12345"},"title":"Series title","provenance":[...]}
-      {"schema":"bioresearcher-evidence/1","type":"web","ids":{"url":"https://..."},"title":"Page Title","meta":{"organization":"FDA","accessed":"2026-09-10"},"provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"disease","ids":{"mondo":"MONDO:0002025"},"title":"Cutaneous melanoma","url":"https://monarchinitiative.org/MONDO:0002025","provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"dataset","ids":{"geo":"GSE12345"},"title":"Series title","provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"dataset","ids":{"pdb":"6N65"},"title":"KRAS G-quadruplex G16T mutant","meta":{"method":"X-RAY DIFFRACTION","resolution":"1.6 Å"},"url":"https://www.rcsb.org/structure/6N65","provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"web","ids":{"url":"https://..."},"title":"Page Title","meta":{"organization":"FDA","accessed":"2026-09-10"},"provenance":[...]}
       {"schema":"bioresearcher-evidence/1","type":"other","ids":{"url":"https://..."},"title":"Any other citable source (FDA page, guideline, ...)","provenance":[...]}
       ```
 
@@ -115,15 +117,32 @@ SKILL_DIR: <absolute skill dir>   # Tier B only; resolve before dispatch
       take the standard retry ladder (rule 6), then leave the record in the
       ledger with a gap note in the aspect file - the orchestrator's verify
       step backfills what it can.
+    - PDB dual-entity discipline: when querying `pdb`, distinguish between
+      citing the macromolecular structure and citing the associated publication:
+      - To cite the published paper: set `type: "article"` with `ids.pmid` (or
+        `ids.doi`). NEVER copy `summary.title` (structure title) or
+        `summary.authors` (deposition list) from the PDB result into the
+        article record. Enrich via `article_get(pmid)` for canonical article
+        metadata, or leave title/authors null for orchestrator verification.
+      - To cite the 3D structure itself: set `type: "dataset"` with `ids.pdb:
+        "<PDB_ID>"` and `title: summary.title`. Canonical key derived:
+        `pdb:<PDB_ID>`. Marker: `[@pdb:<PDB_ID>]`.
     - With Bash available (the orchestrator provides `SKILL_DIR` in the
       prompt): append with
       `python3 <SKILL_DIR>/scripts/evidence-ledger.py add <file> --stdin`,
       substituting the SKILL_DIR value from your prompt LITERALLY - it is a
       path string, NOT an environment variable (`$SKILL_DIR` in a shell
-      resolves to nothing and breaks the call). Pass a JSON ARRAY of the
-      batch's records (a heredoc works well), or equivalently
-      `add <file> @<batch.json>` with an array file. Both validate,
-      normalize, and accept every record in one call, and the banner echoes
+      resolves to nothing and breaks the call). Pass records via a shell heredoc
+      or with an array/JSONL file (`add <file> @<batch.json>`):
+      ```bash
+      python3 <SKILL_DIR>/scripts/evidence-ledger.py add reports/<TOPIC>/evidence/<YOUR-FOCUS>.jsonl --stdin << 'EOF'
+      [
+        {"schema":"bioresearcher-evidence/1","type":"article","ids":{"pmid":"..."},"title":"...","provenance":[{"aspect":"<YOUR-FOCUS>","tool":"article_search","args":{},"retrieved_at":"<ISO>"}]}
+      ]
+      EOF
+      ```
+      (A JSON array `[...]`, a single JSON object `{...}`, or newline-delimited JSONL lines are all accepted by `--stdin` or `@<file>`).
+      Both validate, normalize, and accept every record in one call, and the banner echoes
       the derived canonical keys - cite those keys. Re-adding the same key
       MERGES fill-only (never overwrites a non-null value): later adds for
       the same source are safe and expected (e.g. enriching a record after a
@@ -136,9 +155,13 @@ SKILL_DIR: <absolute skill dir>   # Tier B only; resolve before dispatch
       timestamp. Fields the tool did not return stay null; values inferred
       from your own query parameters (e.g. a phase filter) may enter `meta`
       ONLY with the filter captured in `provenance.args` and the inference
-      disclosed in the report. Without Bash ONLY (e.g. the Claude plugin
-      worker): write raw JSONL lines with the Write tool; the orchestrator's
-      merge validates them.
+      disclosed in the report. When querying ClinicalTrials.gov
+      (`trial_search` / `biomcp_trial_search`), use exact uppercase underscore
+      enum values for `status`: `RECRUITING`, `ACTIVE_NOT_RECRUITING`,
+      `COMPLETED`, `TERMINATED` (commas or spaces in status trigger HTTP 400
+      Bad Request from ClinicalTrials.gov). Without Bash ONLY (e.g. the Claude
+      plugin worker): write raw JSONL lines with the Write tool and re-read the
+      ledger to match markers; the orchestrator validates via `check` upon return.
     - BEFORE reporting completion, run
       `python3 <SKILL_DIR>/scripts/evidence-ledger.py check <file> --markers <YOUR-FOCUS>.md` -
       it must exit 0: no quarantined lines, and every `[@key]` marker in
@@ -155,14 +178,29 @@ SKILL_DIR: <absolute skill dir>   # Tier B only; resolve before dispatch
 
 Aspect-file ownership is SERIALIZED, never concurrent: a top-up worker
 adopts the original worker's contract only after that worker has terminated.
-The orchestrator dispatches it with the prior worker's evidence-gaps list:
+The orchestrator dispatches it when `evidence-ledger.py check` fails or for evidence gaps:
 
-- Append to the SAME per-aspect ledger via `add` (upsert merge is safe).
-- Update the SAME aspect .md via read-then-targeted edits confined to the
-  gap sections - never rewrite unrelated content, other aspects, or the
-  orchestrator's draft.
+- Target scope: touch ONLY `reports/<TOPIC>/<ASPECT>.md` and
+  `reports/<TOPIC>/evidence/<ASPECT>.jsonl`. Never edit other aspects or the
+  synthesis draft.
+- For unresolved markers: fetch canonical metadata via biomcp (`article_get`,
+  `trial_get`) and append via `add`. If no valid source exists, remove or
+  qualify the claim in `<ASPECT>.md` and document the gap under `## Evidence Gaps`.
+  Never invent or guess cite-keys.
+- For quarantined lines: fix the JSON formatting in the ledger.
 - End with `check <file> --markers <aspect>.md` (exit 0) before reporting.
 
+### Remediation worker prompt template
+
+```md
+TOPIC: <TOPIC>
+YOUR RESEARCH FOCUS: <RESEARCH-ASPECT> (REMEDIATION)
+DIAGNOSTIC OUTPUT:
+<stdout and stderr from: evidence-ledger.py check reports/<TOPIC>/evidence/<ASPECT>.jsonl --markers reports/<TOPIC>/<ASPECT>.md>
+TASK: Resolve quarantined lines in reports/<TOPIC>/evidence/<ASPECT>.jsonl and fetch canonical metadata for unresolved markers via biomcp. Touch no other aspects or synthesis files. End with `evidence-ledger.py check` (must exit 0).
+SKILL_DIR: <absolute path to this skill's directory>
+```
+
 ## Retry ladder (per query)
 
 ```