docs: salvage scientific research skills

2026-05-12 07:37:24 +08:00 · 2026-05-11 08:07:35 -04:00
parent 0e12267ff2
commit df32d6bea8
13 changed files with 552 additions and 14 deletions
--- a/.claude-plugin/marketplace.json
+++ b/.claude-plugin/marketplace.json
@@ -11,7 +11,7 @@
    {
      "name": "ecc",
      "source": "./",
-      "description": "The most comprehensive Claude Code plugin — 53 agents, 192 skills, 69 legacy command shims, selective install profiles, and production-ready hooks for TDD, security scanning, code review, and continuous learning",
+      "description": "The most comprehensive Claude Code plugin — 53 agents, 195 skills, 69 legacy command shims, selective install profiles, and production-ready hooks for TDD, security scanning, code review, and continuous learning",
      "version": "2.0.0-rc.1",
      "author": {
        "name": "Affaan Mustafa",
--- a/.claude-plugin/plugin.json
+++ b/.claude-plugin/plugin.json
@@ -1,7 +1,7 @@
 {
  "name": "ecc",
  "version": "2.0.0-rc.1",
-  "description": "Battle-tested Claude Code plugin for engineering teams — 53 agents, 192 skills, 69 legacy command shims, production-ready hooks, and selective install workflows evolved through continuous real-world use",
+  "description": "Battle-tested Claude Code plugin for engineering teams — 53 agents, 195 skills, 69 legacy command shims, production-ready hooks, and selective install workflows evolved through continuous real-world use",
  "author": {
    "name": "Affaan Mustafa",
    "url": "https://x.com/affaanmustafa"
--- a/.opencode/opencode.json
+++ b/.opencode/opencode.json
@@ -22,6 +22,11 @@
  "plugin": [
    "./plugins"
  ],
+  "skills": {
+    "paths": [
+      "../skills"
+    ]
+  },
  "agent": {
    "build": {
      "description": "Primary coding agent for development work",
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -1,6 +1,6 @@
 # Everything Claude Code (ECC) — Agent Instructions

-This is a **production-ready AI coding plugin** providing 53 specialized agents, 192 skills, 69 commands, and automated hook workflows for software development.
+This is a **production-ready AI coding plugin** providing 53 specialized agents, 195 skills, 69 commands, and automated hook workflows for software development.

 **Version:** 2.0.0-rc.1

@@ -146,7 +146,7 @@ Troubleshoot failures: check test isolation → verify mocks → fix implementat

 ```
 agents/          — 53 specialized subagents
-skills/          — 192 workflow skills and domain knowledge
+skills/          — 195 workflow skills and domain knowledge
 commands/        — 69 slash commands
 hooks/           — Trigger-based automations
 rules/           — Always-follow guidelines (common + per-language)
--- a/README.md
+++ b/README.md
@@ -350,7 +350,7 @@ If you stacked methods, clean up in this order:
 /plugin list ecc@ecc
 ```

-**That's it!** You now have access to 53 agents, 192 skills, and 69 legacy command shims.
+**That's it!** You now have access to 53 agents, 195 skills, and 69 legacy command shims.

 ### Dashboard GUI

@@ -1338,7 +1338,7 @@ The configuration is automatically detected from `.opencode/opencode.json`.
 |---------|-------------|----------|--------|
 | Agents | PASS: 53 agents | PASS: 12 agents | **Claude Code leads** |
 | Commands | PASS: 69 commands | PASS: 31 commands | **Claude Code leads** |
-| Skills | PASS: 192 skills | PASS: 37 skills | **Claude Code leads** |
+| Skills | PASS: 195 skills | PASS: 37 skills | **Claude Code leads** |
 | Hooks | PASS: 8 event types | PASS: 11 events | **OpenCode has more!** |
 | Rules | PASS: 29 rules | PASS: 13 instructions | **Claude Code leads** |
 | MCP Servers | PASS: 14 servers | PASS: Full | **Full parity** |
@@ -1443,7 +1443,7 @@ ECC is the **first plugin to maximize every major AI coding tool**. Here's how e
 |---------|------------|------------|-----------|----------|
 | **Agents** | 53 | Shared (AGENTS.md) | Shared (AGENTS.md) | 12 |
 | **Commands** | 69 | Shared | Instruction-based | 31 |
-| **Skills** | 192 | Shared | 10 (native format) | 37 |
+| **Skills** | 195 | Shared | 10 (native format) | 37 |
 | **Hook Events** | 8 types | 15 types | None yet | 11 types |
 | **Hook Scripts** | 20+ scripts | 16 scripts (DRY adapter) | N/A | Plugin hooks |
 | **Rules** | 34 (common + lang) | 34 (YAML frontmatter) | Instruction-based | 13 instructions |
--- a/README.zh-CN.md
+++ b/README.zh-CN.md
@@ -160,7 +160,7 @@ Copy-Item -Recurse rules/typescript "$HOME/.claude/rules/"
 /plugin list ecc@ecc
 ```

-**完成！** 你现在可以使用 53 个代理、192 个技能和 69 个命令。
+**完成！** 你现在可以使用 53 个代理、195 个技能和 69 个命令。

 ### multi-* 命令需要额外配置

--- a/docs/zh-CN/AGENTS.md
+++ b/docs/zh-CN/AGENTS.md
@@ -1,6 +1,6 @@
 # Everything Claude Code (ECC) — 智能体指令

-这是一个**生产就绪的 AI 编码插件**，提供 53 个专业代理、192 项技能、69 条命令以及自动化钩子工作流，用于软件开发。
+这是一个**生产就绪的 AI 编码插件**，提供 53 个专业代理、195 项技能、69 条命令以及自动化钩子工作流，用于软件开发。

 **版本:** 2.0.0-rc.1

@@ -147,7 +147,7 @@

 ```
 agents/          — 53 个专业子代理
-skills/          — 192 个工作流技能和领域知识
+skills/          — 195 个工作流技能和领域知识
 commands/        — 69 个斜杠命令
 hooks/           — 基于触发的自动化
 rules/           — 始终遵循的指导方针（通用 + 每种语言）
--- a/docs/zh-CN/README.md
+++ b/docs/zh-CN/README.md
@@ -224,7 +224,7 @@ Copy-Item -Recurse rules/typescript "$HOME/.claude/rules/"
 /plugin list ecc@ecc
 ```

-**搞定！** 你现在可以使用 53 个智能体、192 项技能和 69 个命令了。
+**搞定！** 你现在可以使用 53 个智能体、195 项技能和 69 个命令了。

 ***

@@ -1134,7 +1134,7 @@ opencode
 |---------|-------------|----------|--------|
 | 智能体 | PASS: 53 个 | PASS: 12 个 | **Claude Code 领先** |
 | 命令 | PASS: 69 个 | PASS: 31 个 | **Claude Code 领先** |
-| 技能 | PASS: 192 项 | PASS: 37 项 | **Claude Code 领先** |
+| 技能 | PASS: 195 项 | PASS: 37 项 | **Claude Code 领先** |
 | 钩子 | PASS: 8 种事件类型 | PASS: 11 种事件 | **OpenCode 更多！** |
 | 规则 | PASS: 29 条 | PASS: 13 条指令 | **Claude Code 领先** |
 | MCP 服务器 | PASS: 14 个 | PASS: 完整 | **完全对等** |
@@ -1242,7 +1242,7 @@ ECC 是**第一个最大化利用每个主要 AI 编码工具的插件**。以
 |---------|------------|------------|-----------|----------|
 | **智能体** | 53 | 共享 (AGENTS.md) | 共享 (AGENTS.md) | 12 |
 | **命令** | 69 | 共享 | 基于指令 | 31 |
-| **技能** | 192 | 共享 | 10 (原生格式) | 37 |
+| **技能** | 195 | 共享 | 10 (原生格式) | 37 |
 | **钩子事件** | 8 种类型 | 15 种类型 | 暂无 | 11 种类型 |
 | **钩子脚本** | 20+ 个脚本 | 16 个脚本 (DRY 适配器) | N/A | 插件钩子 |
 | **规则** | 34 (通用 + 语言) | 34 (YAML 前页) | 基于指令 | 13 条指令 |
--- a/manifests/install-modules.json
+++ b/manifests/install-modules.json
@@ -276,7 +276,10 @@
      "paths": [
        "skills/deep-research",
        "skills/exa-search",
-        "skills/research-ops"
+        "skills/research-ops",
+        "skills/scientific-db-pubmed-database",
+        "skills/scientific-thinking-literature-review",
+        "skills/scientific-thinking-scholar-evaluation"
      ],
      "targets": [
        "claude",
--- a/package.json
+++ b/package.json
@@ -207,6 +207,9 @@
    "skills/regex-vs-llm-structured-text/",
    "skills/remotion-video-creation/",
    "skills/research-ops/",
+    "skills/scientific-db-pubmed-database/",
+    "skills/scientific-thinking-literature-review/",
+    "skills/scientific-thinking-scholar-evaluation/",
    "skills/returns-reverse-logistics/",
    "skills/rust-patterns/",
    "skills/rust-testing/",
--- a/skills/scientific-db-pubmed-database/SKILL.md
+++ b/skills/scientific-db-pubmed-database/SKILL.md
@@ -0,0 +1,175 @@
+---
+name: pubmed-database
+description: Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
+origin: community
+---
+
+# PubMed Database
+
+Use this skill when a task needs biomedical literature from PubMed rather than
+general web search.
+
+## When to Use
+
+- Searching MEDLINE or life-sciences literature.
+- Building PubMed queries with MeSH terms, field tags, dates, or article types.
+- Looking up PMIDs, abstracts, publication metadata, or related citations.
+- Running systematic-review search passes that need repeatable search strings.
+- Using NCBI E-utilities directly from Python, shell, or another HTTP client.
+
+## Query Construction
+
+Start with the research question, split it into concepts, then combine concepts
+with Boolean operators.
+
+```text
+concept_1 AND concept_2 AND filter
+synonym_a OR synonym_b
+NOT exclusion_term
+```
+
+Useful PubMed field tags:
+
+- `[ti]`: title
+- `[ab]`: abstract
+- `[tiab]`: title or abstract
+- `[au]`: author
+- `[ta]`: journal title abbreviation
+- `[mh]`: MeSH term
+- `[majr]`: major MeSH topic
+- `[pt]`: publication type
+- `[dp]`: date of publication
+- `[la]`: language
+
+Examples:
+
+```text
+diabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt] AND 2023:2026[dp]
+(metformin[nm] OR insulin[nm]) AND diabetes mellitus, type 2[mh] AND randomized controlled trial[pt]
+smith ja[au] AND cancer[tiab] AND 2026[dp] AND english[la]
+```
+
+## MeSH and Subheadings
+
+Prefer MeSH when the concept has a stable controlled-vocabulary term. Combine
+MeSH with title/abstract terms when the topic is new or terminology varies.
+
+Correct subheading syntax puts the subheading before the field tag:
+
+```text
+diabetes mellitus, type 2/drug therapy[mh]
+cardiovascular diseases/prevention & control[mh]
+```
+
+Use `[majr]` only when the topic must be central to the paper. It can improve
+precision but may miss relevant work.
+
+## Filters
+
+Publication types:
+
+- `clinical trial[pt]`
+- `meta-analysis[pt]`
+- `randomized controlled trial[pt]`
+- `review[pt]`
+- `systematic review[pt]`
+- `guideline[pt]`
+
+Date filters:
+
+```text
+2026[dp]
+2020:2026[dp]
+2026/03/15[dp]
+```
+
+Availability filters:
+
+```text
+free full text[sb]
+hasabstract[text]
+```
+
+## E-utilities Workflow
+
+NCBI E-utilities supports repeatable API workflows:
+
+1. `esearch.fcgi`: search and return PMIDs.
+2. `esummary.fcgi`: return lightweight article metadata.
+3. `efetch.fcgi`: fetch abstracts or full records in XML, MEDLINE, or text.
+4. `elink.fcgi`: find related articles and linked resources.
+
+Use an email and API key for production scripts. Store API keys in environment
+variables, never in committed files or command history.
+
+```python
+import os
+import time
+import requests
+
+BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
+
+
+def esearch(query: str, retmax: int = 20) -> list[str]:
+    params = {
+        "db": "pubmed",
+        "term": query,
+        "retmode": "json",
+        "retmax": retmax,
+        "tool": "ecc-pubmed-search",
+        "email": os.environ.get("NCBI_EMAIL", ""),
+    }
+    api_key = os.environ.get("NCBI_API_KEY")
+    if api_key:
+        params["api_key"] = api_key
+
+    response = requests.get(f"{BASE}/esearch.fcgi", params=params, timeout=30)
+    response.raise_for_status()
+    time.sleep(0.35)
+    return response.json()["esearchresult"]["idlist"]
+
+
+pmids = esearch("hypertension[mh] AND randomized controlled trial[pt] AND 2024:2026[dp]")
+print(pmids)
+```
+
+For batches, prefer NCBI history server parameters (`usehistory=y`,
+`WebEnv`, `query_key`) instead of passing very long PMID lists through URLs.
+
+## Output Discipline
+
+For each search pass, record:
+
+- exact search string
+- database searched
+- date searched
+- filters used
+- result count
+- export format
+- any manual exclusions
+
+Example:
+
+```markdown
+| Database | Date searched | Query | Filters | Results |
+| --- | --- | --- | --- | ---: |
+| PubMed | 2026-05-11 | `sickle cell disease[mh] AND CRISPR[tiab]` | 2020:2026[dp], English | 42 |
+```
+
+## Review Checklist
+
+- Are field tags valid PubMed tags?
+- Are MeSH terms paired with free-text synonyms for newer topics?
+- Is the date range explicit and appropriate?
+- Does the search log include enough detail to reproduce the query?
+- Are API keys loaded from the environment?
+- Does HTTP code call `raise_for_status()` or otherwise handle non-200
+  responses before parsing?
+- Are rate limits respected?
+
+## References
+
+- [PubMed help](https://pubmed.ncbi.nlm.nih.gov/help/)
+- [NCBI E-utilities documentation](https://www.ncbi.nlm.nih.gov/books/NBK25501/)
+- [NCBI API key guidance](https://support.nlm.nih.gov/kbArticle/?pn=KA-05317)
+- NCBI support: <eutilities@ncbi.nlm.nih.gov>
--- a/skills/scientific-thinking-literature-review/SKILL.md
+++ b/skills/scientific-thinking-literature-review/SKILL.md
@@ -0,0 +1,192 @@
+---
+name: literature-review
+description: Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.
+origin: community
+---
+
+# Literature Review
+
+Use this skill when the task is to find, screen, synthesize, and cite a body of
+academic or technical literature.
+
+## When to Use
+
+- Building a systematic, scoping, or narrative literature review.
+- Synthesizing the state of the art for a research question.
+- Finding gaps, contradictions, or future-work directions.
+- Preparing citation-backed background sections for papers or reports.
+- Comparing evidence across peer-reviewed papers, preprints, patents, and
+  technical reports.
+
+## Review Types
+
+- **Narrative review**: broad synthesis; useful for orientation.
+- **Scoping review**: maps concepts, methods, and evidence gaps.
+- **Systematic review**: predefined protocol, reproducible search, explicit
+  screening and exclusion.
+- **Meta-analysis**: systematic review plus quantitative effect aggregation.
+
+Ask the user which level of rigor is needed. If unspecified, default to a
+scoping review for exploratory work and a systematic review for publication or
+clinical claims.
+
+## Workflow
+
+### 1. Define the Question
+
+Convert the prompt into a searchable research question.
+
+For clinical or biomedical work, use PICO:
+
+- Population
+- Intervention or exposure
+- Comparator
+- Outcome
+
+For technical work, use:
+
+- system or domain
+- method or intervention
+- comparison baseline
+- evaluation metric
+
+### 2. Plan the Search
+
+Create a search protocol before collecting sources:
+
+- databases to search
+- date range
+- languages
+- publication types
+- inclusion criteria
+- exclusion criteria
+- exact search strings
+
+Minimum useful database set:
+
+- PubMed for biomedical and life-sciences literature.
+- arXiv for CS, math, physics, quantitative biology, and preprints.
+- Semantic Scholar or Crossref for broad academic discovery.
+- Domain-specific sources when relevant, such as clinical-trial registries,
+  patent databases, standards bodies, or official technical docs.
+
+### 3. Search and Log Evidence
+
+Keep a search log that makes the review reproducible:
+
+```markdown
+| Database | Date searched | Query | Filters | Results | Export |
+| --- | --- | --- | --- | ---: | --- |
+| PubMed | 2026-05-11 | `("CRISPR"[tiab] OR "Cas9"[tiab]) AND "sickle cell"[tiab]` | 2020:2026, English | 86 | PMID list |
+| arXiv | 2026-05-11 | `CRISPR sickle cell gene editing` | q-bio, 2020:2026 | 9 | BibTeX |
+```
+
+Save raw IDs, URLs, DOIs, abstracts, and notes separately from the final prose.
+
+### 4. Deduplicate
+
+Deduplicate in this order:
+
+1. DOI
+2. PMID or arXiv ID
+3. exact title
+4. normalized title plus first author and year
+
+Record how many duplicates were removed.
+
+### 5. Screen Sources
+
+Screen in stages:
+
+1. title
+2. abstract
+3. full text
+
+For systematic work, record exclusion reasons:
+
+- wrong population
+- wrong intervention
+- wrong outcome
+- not primary research
+- duplicate
+- unavailable full text
+- outside date range
+
+### 6. Extract Data
+
+Use a structured extraction table:
+
+```markdown
+| Study | Design | Population/Data | Method | Comparator | Outcome | Key finding | Limitations |
+| --- | --- | --- | --- | --- | --- | --- | --- |
+| Author Year | RCT/cohort/review/etc. | sample or corpus | method | baseline | measured outcome | result | caveat |
+```
+
+For technical papers, include dataset, benchmark, metric, baseline, and
+reproducibility notes.
+
+### 7. Synthesize
+
+Group evidence by theme rather than summarizing papers one by one.
+
+Useful synthesis lenses:
+
+- strongest evidence
+- conflicting evidence
+- methodological weaknesses
+- population or dataset limits
+- recency and replication
+- practical implications
+- unanswered questions
+
+Separate claims by confidence:
+
+- **High confidence**: replicated, high-quality evidence across sources.
+- **Medium confidence**: plausible but limited by sample, method, or recency.
+- **Low confidence**: early, speculative, single-source, or weakly measured.
+
+### 8. Verify Citations
+
+Before finalizing:
+
+- verify DOI, PMID, arXiv ID, or official URL
+- check author names and publication year
+- do not cite a paper for a claim it does not make
+- mark preprints as preprints
+- distinguish reviews from primary evidence
+
+## Output Template
+
+```markdown
+# Literature Review: <Topic>
+
+Generated: <date>
+Review type: <narrative | scoping | systematic | meta-analysis>
+Search window: <dates>
+Databases: <list>
+
+## Research Question
+
+## Search Strategy
+
+## Inclusion and Exclusion Criteria
+
+## Evidence Summary
+
+## Thematic Synthesis
+
+## Gaps and Limitations
+
+## References
+
+## Search Log
+```
+
+## Pitfalls
+
+- Do not treat search snippets as evidence.
+- Do not mix preprints, reviews, and primary studies without labeling them.
+- Do not omit negative or conflicting findings.
+- Do not claim systematic-review rigor without a reproducible protocol.
+- Do not use a single database for a broad claim unless the scope is explicitly
+  limited to that database.
--- a/skills/scientific-thinking-scholar-evaluation/SKILL.md
+++ b/skills/scientific-thinking-scholar-evaluation/SKILL.md
@@ -0,0 +1,160 @@
+---
+name: scholar-evaluation
+description: Structured scholarly-work evaluation for papers, proposals, literature reviews, methods sections, evidence quality, citation support, and research-writing feedback.
+origin: community
+---
+
+# Scholar Evaluation
+
+Use this skill to evaluate academic or scientific work with a repeatable rubric.
+
+## When to Use
+
+- Reviewing a research paper, proposal, thesis chapter, or literature review.
+- Checking whether claims are supported by cited evidence.
+- Evaluating methodology, study design, analysis, or limitations.
+- Comparing two or more papers for quality or relevance.
+- Producing structured feedback for revision.
+
+## Evaluation Scope
+
+Start by identifying the artifact:
+
+- empirical research paper
+- theoretical paper
+- technical report
+- systematic or narrative literature review
+- research proposal
+- thesis or dissertation chapter
+- conference abstract or short paper
+
+Then choose scope:
+
+- **comprehensive**: all rubric dimensions
+- **targeted**: one or two dimensions, such as method or citations
+- **comparative**: rank multiple works against the same rubric
+
+## Rubric
+
+Score each applicable dimension from 1 to 5:
+
+- 5: excellent; clear, rigorous, and publication-ready
+- 4: good; minor improvements needed
+- 3: adequate; meaningful gaps but usable
+- 2: weak; substantial revision needed
+- 1: poor; major validity or clarity problems
+
+Use `N/A` for dimensions that do not apply.
+
+### 1. Problem and Research Question
+
+- Is the problem clear and specific?
+- Is the contribution meaningful?
+- Are scope and assumptions explicit?
+- Does the question match the claimed contribution?
+
+### 2. Literature and Context
+
+- Is relevant prior work covered?
+- Does the work synthesize rather than merely list sources?
+- Are gaps accurately identified?
+- Are recent and foundational sources balanced?
+
+### 3. Methodology
+
+- Does the method answer the research question?
+- Are design choices justified?
+- Are variables, datasets, participants, or materials described clearly?
+- Could another researcher reproduce the work?
+- Are ethical and practical constraints acknowledged?
+
+### 4. Data and Evidence
+
+- Are data sources credible and appropriate?
+- Is sample size or corpus coverage adequate?
+- Are inclusion, exclusion, and preprocessing decisions documented?
+- Are missing data and bias risks discussed?
+
+### 5. Analysis
+
+- Are statistical, qualitative, or computational methods appropriate?
+- Are baselines and controls fair?
+- Are uncertainty, sensitivity, or robustness checks included when needed?
+- Are alternative explanations considered?
+
+### 6. Results and Interpretation
+
+- Are results clearly presented?
+- Do claims stay within the evidence?
+- Are figures, tables, and metrics understandable?
+- Are negative or null results handled honestly?
+
+### 7. Limitations and Threats to Validity
+
+- Are limitations specific rather than generic?
+- Are internal, external, construct, and conclusion-validity risks addressed?
+- Does the paper distinguish speculation from demonstrated results?
+
+### 8. Writing and Structure
+
+- Is the argument easy to follow?
+- Are sections organized around the research question?
+- Are definitions and notation clear?
+- Is the tone precise and scholarly?
+
+### 9. Citations
+
+- Do cited papers support the claims attached to them?
+- Are primary sources used where possible?
+- Are reviews labeled as reviews?
+- Are preprints labeled as preprints?
+- Are citation metadata and links correct?
+
+## Review Process
+
+1. Read the abstract, introduction, figures, and conclusion for claimed
+   contribution.
+2. Read methods and results for evidence quality.
+3. Check the strongest claims against cited sources.
+4. Score each applicable dimension.
+5. Separate critical blockers from revision suggestions.
+6. End with concrete next edits.
+
+## Output Template
+
+```markdown
+# Scholar Evaluation: <Artifact>
+
+## Overall Assessment
+
+- Overall score: <1-5 or N/A>
+- Confidence: <high | medium | low>
+- Summary: <3-5 sentences>
+
+## Dimension Scores
+
+| Dimension | Score | Evidence | Revision priority |
+| --- | ---: | --- | --- |
+| Problem and question |  |  |  |
+| Literature and context |  |  |  |
+| Methodology |  |  |  |
+| Data and evidence |  |  |  |
+| Analysis |  |  |  |
+| Results and interpretation |  |  |  |
+| Limitations |  |  |  |
+| Writing and structure |  |  |  |
+| Citations |  |  |  |
+
+## Critical Issues
+
+## Recommended Revisions
+
+## Evidence Checks Needed
+```
+
+## Pitfalls
+
+- Do not use the score as a substitute for concrete feedback.
+- Do not penalize a paper for omitting a dimension outside its scope.
+- Do not treat citation count, venue, or author reputation as proof of quality.
+- Do not accept unsupported claims just because they appear in the abstract.