codeply-cli 0.3.1 → 0.4.0

package/skills/scientific-thinking-literature-review/SKILL.md

@@ -1,193 +1,193 @@
----
-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.
-metadata:
-  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.
+---
+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.
+metadata:
+  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.