claude-scientific-skills/scientific-thinking/scientific-writing/SKILL.md

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scientific-writing

Comprehensive toolkit for writing, structuring, and formatting scientific research papers, manuscripts, and academic documents. This skill should be used when drafting or revising scientific manuscripts, structuring research papers using IMRAD format, formatting citations and references, creating effective figures and tables, applying reporting guidelines (CONSORT, STROBE, PRISMA), writing abstracts or specific paper sections, adhering to journal submission requirements, or improving scientific writing clarity and precision. Supports multiple citation styles (APA, AMA, Vancouver, Chicago), provides field-specific reporting standards, and ensures compliance with academic writing conventions across biomedical, life sciences, engineering, and physical sciences disciplines.

Scientific Writing

Overview

Scientific writing is a specialized form of communication that requires precision, clarity, and adherence to established conventions. This skill provides comprehensive guidance for creating high-quality scientific manuscripts, from initial structure to final submission. Whether drafting a research article, review paper, case report, or thesis, this skill ensures writing meets the rigorous standards of academic and scientific publishing.

When to Use This Skill

Invoke this skill when:

• Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
• Structuring a research paper using IMRAD or other standard formats
• Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)
• Creating, formatting, or improving figures, tables, and data visualizations
• Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews)
• Drafting abstracts that meet journal requirements (structured or unstructured)
• Preparing manuscripts for submission to specific journals
• Improving writing clarity, conciseness, and precision
• Addressing reviewer comments and revising manuscripts

Core Capabilities

1. Manuscript Structure and Organization

IMRAD Format: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes:

• Introduction: Establish research context, identify gaps, state objectives
• Methods: Detail study design, populations, procedures, and analysis approaches
• Results: Present findings objectively without interpretation
• Discussion: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to references/imrad_structure.md.

Alternative Structures: Support discipline-specific formats including:

• Review articles (narrative, systematic, scoping)
• Case reports and case series
• Meta-analyses and pooled analyses
• Theoretical/modeling papers
• Methods papers and protocols

2. Section-Specific Writing Guidance

Abstract Composition: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

Introduction Development: Build compelling introductions that:

• Establish the research problem's importance
• Review relevant literature systematically
• Identify knowledge gaps or controversies
• State clear research questions or hypotheses
• Explain the study's novelty and significance

Methods Documentation: Ensure reproducibility through:

• Detailed participant/sample descriptions
• Clear procedural documentation
• Statistical methods with justification
• Equipment and materials specifications
• Ethical approval and consent statements

Results Presentation: Present findings with:

• Logical flow from primary to secondary outcomes
• Integration with figures and tables
• Statistical significance with effect sizes
• Objective reporting without interpretation

Discussion Construction: Synthesize findings by:

• Relating results to research questions
• Comparing with existing literature
• Acknowledging limitations honestly
• Proposing mechanistic explanations
• Suggesting practical implications and future research

3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to references/citation_styles.md.

Major Citation Styles:

• AMA (American Medical Association): Numbered superscript citations, common in medicine
• Vancouver: Numbered citations in square brackets, biomedical standard
• APA (American Psychological Association): Author-date in-text citations, common in social sciences
• Chicago: Notes-bibliography or author-date, humanities and sciences
• IEEE: Numbered square brackets, engineering and computer science

Best Practices:

• Cite primary sources when possible
• Include recent literature (last 5-10 years for active fields)
• Balance citation distribution across introduction and discussion
• Verify all citations against original sources
• Use reference management software (Zotero, Mendeley, EndNote)

4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to references/figures_tables.md.

When to Use Tables vs. Figures:

• Tables: Precise numerical data, complex datasets, multiple variables requiring exact values
• Figures: Trends, patterns, relationships, comparisons best understood visually

Design Principles:

• Make each table/figure self-explanatory with complete captions
• Use consistent formatting and terminology across all display items
• Label all axes, columns, and rows with units
• Include sample sizes (n) and statistical annotations
• Follow the "one table/figure per 1000 words" guideline
• Avoid duplicating information between text, tables, and figures

Common Figure Types:

• Bar graphs: Comparing discrete categories
• Line graphs: Showing trends over time
• Scatterplots: Displaying correlations
• Box plots: Showing distributions and outliers
• Heatmaps: Visualizing matrices and patterns

5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to references/reporting_guidelines.md.

Key Guidelines:

• CONSORT: Randomized controlled trials
• STROBE: Observational studies (cohort, case-control, cross-sectional)
• PRISMA: Systematic reviews and meta-analyses
• STARD: Diagnostic accuracy studies
• TRIPOD: Prediction model studies
• ARRIVE: Animal research
• CARE: Case reports
• SQUIRE: Quality improvement studies
• SPIRIT: Study protocols for clinical trials
• CHEERS: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to references/writing_principles.md.

Clarity:

• Use precise, unambiguous language
• Define technical terms and abbreviations at first use
• Maintain logical flow within and between paragraphs
• Use active voice when appropriate for clarity

Conciseness:

• Eliminate redundant words and phrases
• Favor shorter sentences (15-20 words average)
• Remove unnecessary qualifiers
• Respect word limits strictly

Accuracy:

• Report exact values with appropriate precision
• Use consistent terminology throughout
• Distinguish between observations and interpretations
• Acknowledge uncertainty appropriately

Objectivity:

• Present results without bias
• Avoid overstating findings or implications
• Acknowledge conflicting evidence
• Maintain professional, neutral tone

7. Journal-Specific Formatting

Adapt manuscripts to journal requirements:

• Follow author guidelines for structure, length, and format
• Apply journal-specific citation styles
• Meet figure/table specifications (resolution, file formats, dimensions)
• Include required statements (funding, conflicts of interest, data availability, ethical approval)
• Adhere to word limits for each section
• Format according to template requirements when provided

8. Common Pitfalls to Avoid

Top Rejection Reasons:

1. Inappropriate, incomplete, or insufficiently described statistics
2. Over-interpretation of results or unsupported conclusions
3. Poorly described methods affecting reproducibility
4. Small, biased, or inappropriate samples
5. Poor writing quality or difficult-to-follow text
6. Inadequate literature review or context
7. Figures and tables that are unclear or poorly designed
8. Failure to follow reporting guidelines

Writing Quality Issues:

• Mixing tenses inappropriately (use past tense for methods/results, present for established facts)
• Excessive jargon or undefined acronyms
• Paragraph breaks that disrupt logical flow
• Missing transitions between sections
• Inconsistent notation or terminology

Workflow for Manuscript Development

Stage 1: Planning

1. Identify target journal and review author guidelines
2. Determine applicable reporting guideline (CONSORT, STROBE, etc.)
3. Outline manuscript structure (usually IMRAD)
4. Plan figures and tables as the backbone of the paper

Stage 2: Drafting

1. Start with figures and tables (the core data story)
2. Write Methods (often easiest to draft first)
3. Draft Results (describing figures/tables objectively)
4. Compose Discussion (interpreting findings)
5. Write Introduction (setting up the research question)
6. Craft Abstract (synthesizing the complete story)
7. Create Title (concise and descriptive)

Stage 3: Revision

1. Check logical flow and "red thread" throughout
2. Verify consistency in terminology and notation
3. Ensure figures/tables are self-explanatory
4. Confirm adherence to reporting guidelines
5. Verify all citations are accurate and properly formatted
6. Check word counts for each section
7. Proofread for grammar, spelling, and clarity

Stage 4: Final Preparation

1. Format according to journal requirements
2. Prepare supplementary materials
3. Write cover letter highlighting significance
4. Complete submission checklists
5. Gather all required statements and forms

Integration with Other Scientific Skills

This skill works effectively with:

• Data analysis skills: For generating results to report
• Statistical analysis: For determining appropriate statistical presentations
• Literature review skills: For contextualizing research
• Figure creation tools: For developing publication-quality visualizations

References

This skill includes comprehensive reference files covering specific aspects of scientific writing:

• references/imrad_structure.md: Detailed guide to IMRAD format and section-specific content
• references/citation_styles.md: Complete citation style guides (APA, AMA, Vancouver, Chicago, IEEE)
• references/figures_tables.md: Best practices for creating effective data visualizations
• references/reporting_guidelines.md: Study-specific reporting standards and checklists
• references/writing_principles.md: Core principles of effective scientific communication

Load these references as needed when working on specific aspects of scientific writing.