protocoling

name	protocoling
description	Use when starting a systematic literature review to define the research protocol. TRIGGERS: slr init, protocol, PICO, SPIDER, define criteria, start review, iniciar revisao, definir protocolo, criterios de inclusao, criterios de exclusao

Protocoling

Define research protocol for systematic literature review using PICO, SPIDER, or Custom framework.

Overview

Guide users through defining a complete SLR protocol before any search. This is an interactive skill - use AskUserQuestion to gather all protocol information.

Core principle: No search without protocol. Use uvx scimesh workspace init --type slr to create the workspace with protocol.

Iron Rules

1. NO search without protocol - Protocol MUST exist BEFORE any search
2. NO autonomous query building - Query construction is INTERACTIVE; user approves each component
3. Use workspace commands - Always use uvx scimesh workspace commands for SLR

Workflow

Use AskUserQuestion to gather protocol info. All questions need 2-4 options.

Step 1: Framework Selection (FIRST QUESTION)

Question 1: Framework

{
    "question": "Which framework do you want to use for your research question?",
    "header": "Framework",
    "options": [
        {"label": "PICO", "description": "Population, Intervention, Comparison, Outcome - quantitative/clinical research"},
        {"label": "SPIDER", "description": "Sample, Phenomenon, Design, Evaluation, Research type - qualitative research"},
        {"label": "Custom", "description": "Build your own from building blocks - flexible for any domain"}
    ],
    "multiSelect": False
}

Step 2: Framework-Specific Questions

If PICO Selected

Ask for PICO components:

• Population: Who or what is being studied?
• Intervention: What treatment, method, or exposure?
• Comparison: What is the alternative (if any)?
• Outcome: What effects or results are measured?

If SPIDER Selected

Ask for SPIDER components:

• Sample: Who are the participants?
• Phenomenon of Interest: What experience or behavior?
• Design: What research design (interviews, focus groups, etc.)?
• Evaluation: What outcomes or findings?
• Research type: What type (qualitative, mixed-methods)?

If Custom Selected

Ask the following building block questions:

Question 2a: Context fields

{
    "question": "Which CONTEXT fields do you need? (what/who is being studied)",
    "header": "Context",
    "options": [
        {"label": "Population", "description": "Group or entities being studied"},
        {"label": "Sample", "description": "Specific subset or participants"},
        {"label": "Setting", "description": "Environment or location"},
        {"label": "Domain", "description": "Field or application area"}
    ],
    "multiSelect": True
}

Question 2b: Action fields

{
    "question": "Which ACTION fields do you need? (what is being done/studied)",
    "header": "Action",
    "options": [
        {"label": "Intervention", "description": "Treatment or method applied"},
        {"label": "Method", "description": "Technique or algorithm"},
        {"label": "Phenomenon", "description": "Experience or behavior of interest"},
        {"label": "Mechanism", "description": "How something works"}
    ],
    "multiSelect": True
}

Question 2c: Result fields

{
    "question": "Which RESULT fields do you need? (what is measured/evaluated)",
    "header": "Result",
    "options": [
        {"label": "Outcome", "description": "Effects or results measured"},
        {"label": "Metrics", "description": "Specific measures used"},
        {"label": "Evaluation", "description": "Assessment criteria"}
    ],
    "multiSelect": True
}

Step 3: Framework-Independent Questions

These questions apply to ALL frameworks:

Question 3: Year range

{
    "question": "What year range should papers be from?",
    "header": "Years",
    "options": [
        {"label": "Last 5 years (Recommended)", "description": "Dynamic: based on current year"},
        {"label": "Last 10 years", "description": "Dynamic: based on current year"},
        {"label": "Last 3 years", "description": "Dynamic: based on current year"},
        {"label": "Custom range", "description": "You specify"}
    ],
    "multiSelect": False
}

Note: Compute the actual year range dynamically from the current date. For example, if today is 2026, "Last 5 years" means "2021-2026".

Question 4: Languages

{
    "question": "What languages are acceptable?",
    "header": "Languages",
    "options": [
        {"label": "English only (Recommended)", "description": "Most common in academia"},
        {"label": "English + Portuguese", "description": "Include PT papers"},
        {"label": "Any language", "description": "No language filter"}
    ],
    "multiSelect": False
}

Question 5: Study types to include

{
    "questions": [
        {
            "question": "Which study types to include?",
            "header": "Include",
            "options": [
                {"label": "Primary research", "description": "Original experiments, empirical studies"},
                {"label": "Systematic reviews", "description": "Systematic reviews, meta-analyses"},
                {"label": "Conference papers", "description": "Full papers from conferences"},
                {"label": "Preprints", "description": "arXiv, bioRxiv, medRxiv, SSRN"}
            ],
            "multiSelect": True
        },
        {
            "question": "Which study types to EXCLUDE?",
            "header": "Exclude",
            "options": [
                {"label": "Conference abstracts", "description": "Abstracts without full text"},
                {"label": "Editorials/letters", "description": "Opinion pieces, letters to editor"},
                {"label": "Commentaries", "description": "Short commentaries on other papers"},
                {"label": "Protocols", "description": "Study protocols without results"}
            ],
            "multiSelect": True
        }
    ]
}

Question 6: Minimum citations

{
    "question": "Set a minimum citation threshold?",
    "header": "Citations",
    "options": [
        {"label": "No minimum (Recommended)", "description": "Include all papers regardless of citations"},
        {"label": "At least 5 citations", "description": "Filter out very low-impact papers"},
        {"label": "At least 10 citations", "description": "Moderate impact threshold"},
        {"label": "At least 50 citations", "description": "High impact only"}
    ],
    "multiSelect": False
}

Question 7: Data/Code availability

{
    "question": "Require open data or code?",
    "header": "Open science",
    "options": [
        {"label": "No requirement (Recommended)", "description": "Include all papers"},
        {"label": "Prefer open data/code", "description": "Prioritize but don't exclude"},
        {"label": "Must have open data", "description": "Exclude papers without available data"},
        {"label": "Must have open code", "description": "Exclude papers without available code"}
    ],
    "multiSelect": False
}

Question 8: Search providers

{
    "question": "Which providers to search?",
    "header": "Providers",
    "options": [
        {"label": "OpenAlex (Recommended)", "description": "200M+ works, open metadata, citation counts."},
        {"label": "Semantic Scholar", "description": "AI/ML focus, citation graph, abstracts."},
        {"label": "arXiv", "description": "Preprints in CS, Physics, Math. Free full-text PDFs."},
        {"label": "Scopus", "description": "Comprehensive coverage. Requires SCOPUS_API_KEY environment variable."}
    ],
    "multiSelect": True
}

Question 9: Target pool size

{
    "question": "How many papers do you want to screen?",
    "header": "Pool size",
    "options": [
        {"label": "30-100 (Recommended)", "description": "Focused review"},
        {"label": "100-200", "description": "Comprehensive review"},
        {"label": "200-500", "description": "Exhaustive review"}
    ],
    "multiSelect": False
}

Question 10: Research question (free text)

{
    "question": "Describe your research question:",
    "header": "Research Q",
    "options": [
        {"label": "Example: How does X affect Y?", "description": "Cause-effect question"},
        {"label": "Example: What methods exist for X?", "description": "Survey question"}
    ],
    "multiSelect": False
}
# User will select "Other" and type their actual question

Create Workspace with Protocol

After gathering all information via AskUserQuestion, create the workspace in two steps:

Step 1: Initialize the workspace

uvx scimesh workspace init {review_path}/ \
  --type slr \
  --question "Research question here" \
  --framework pico \
  --databases "arxiv,openalex,semantic_scholar" \
  --year-range "2021-2026"

Available flags for workspace init:

• --type: slr, exploration, collection (required for SLR)
• --question: Research question
• --framework: pico, spider, custom
• --databases: Comma-separated provider list
• --year-range: Year range string

Step 2: Add inclusion and exclusion criteria

# Add inclusion criteria (one call with all criteria)
uvx scimesh workspace add-inclusion {review_path}/ \
  "First inclusion criterion" \
  "Second inclusion criterion"

# Add exclusion criteria
uvx scimesh workspace add-exclusion {review_path}/ \
  "First exclusion criterion" \
  "Second exclusion criterion"

Step 3: Set framework-specific fields

The workspace init creates the workspace with an empty framework. To populate framework fields (PICO, SPIDER, or Custom), edit the index.yaml directly using the Edit tool:

For PICO Framework

Edit {review_path}/index.yaml to set:

framework:
  type: pico
  fields:
    population: "Description of population"
    intervention: "Description of intervention"
    comparison: "Description of comparison"
    outcome: "Description of outcome"

For SPIDER Framework

Edit {review_path}/index.yaml to set:

framework:
  type: spider
  fields:
    sample: "Description of sample"
    phenomenon: "Description of phenomenon"
    design: "Description of design"
    evaluation: "Description of evaluation"
    research_type: "qualitative"

For Custom Framework

Edit {review_path}/index.yaml to set:

framework:
  type: custom
  fields:
    population: "Description"
    method: "Description"
    outcome: "Description"

Directory Structure

The workspace creates this structure:

{review_path}/
├── index.yaml       # Workspace config + stats
├── log.yaml         # Search history (queries, results)
├── papers.yaml      # Paper list with search_ids
└── papers/
    └── {year}/              # Organized by publication year
        └── {paper-slug}/
            ├── index.yaml   # Paper metadata + screening status
            └── fulltext.pdf # PDF (if downloaded)

Note: {review_path} is user-defined. Examples: ./reviews/my-slr/, ~/Documents/reviews/transformers-2024/

Workspace File Structure

index.yaml - Workspace config and stats:

SLR Workspace (actual structure)

type: slr
question: "Research question here"
framework:
  type: pico
  fields:
    population: ""
    intervention: ""
    comparison: ""
    outcome: ""
constraints:
  databases:
    - arxiv
    - openalex
    - semantic_scholar
  year_range: "2021-2026"
inclusion:
  - "criterion 1"
exclusion:
  - "criterion 1"
stats:
  total: 0
  included: 0
  excluded: 0
  maybe: 0
  unscreened: 0
  with_pdf: 0

log.yaml - Search history:

- id: b135ec76a5e4
  type: search
  query: "TITLE(attention) AND PUBYEAR > 2022"
  providers: [arxiv, openalex]
  executed_at: "2026-01-30T10:00:00Z"
  results:
    total: 50
    unique: 45

papers.yaml - Paper list with traceability:

- path: 2024/yang-simulating-hard-attention
  doi: "10.1234/example"
  title: "Simulating Hard Attention..."
  status: unscreened
  search_ids: [b135ec76a5e4]

Modifying Protocol

After init, use these commands to modify:

# Modify workspace-level fields
uvx scimesh workspace set {review_path}/ --question "New RQ" --year-range "2020-2024"

# Add inclusion criteria
uvx scimesh workspace add-inclusion {review_path}/ "Must use deep learning"

# Add exclusion criteria
uvx scimesh workspace add-exclusion {review_path}/ "Survey papers"

# For framework-specific fields, edit index.yaml directly with the Edit tool

Validation

Before proceeding to search (scimesh:searching), verify:

• Workspace exists with index.yaml
• Framework is specified (pico, spider, or custom) with fields populated
• At least 1 inclusion criterion defined
• At least 1 exclusion criterion defined
• Research question is filled

If validation fails: Run workspace init --type slr or use workspace set/add-*/Edit to complete protocol.

Next Step

After protocol is complete, use scimesh:searching to build and execute the query.