extracting

name	extracting
description	Use when extracting evidence from included papers using parallel subagents. TRIGGERS: slr extract, extract evidence, extrair evidências, condense papers, problem method result

Extracting

Parallel evidence extraction from included papers using specialized subagents.

Overview

After screening completes, extract evidence from all INCLUDED papers using parallel subagents to maximize throughput.

Core principle: Dispatch 2 agents per paper sequentially (condense → tag).

Prerequisite: Screening must be complete (scimesh:screening).

Requirement: Papers must have fulltext.pdf available.

Directory Structure

{review_path}/
├── index.yaml           # Protocol + stats
└── papers/
    └── {year}/                  # Organized by publication year
        └── {paper-slug}/
            ├── index.yaml       # Metadata + screening
            ├── fulltext.pdf     # PDF (required)
            └── condensed.md     # Complete extraction with frontmatter

Agents

Agent	Responsibility	Input	Output
paper-briefer	Quick briefing for classification and tagging	PDF	condensed.md (body)
paper-tagger	Add frontmatter with tags and relevance	condensed.md + protocol	condensed.md (with frontmatter)

Workflow

digraph extraction {
    rankdir=TB;
    node [shape=box];

    screen_done [label="Screening complete\n(N included papers)"];
    check_pdf [label="Filter: only papers\nwith fulltext.pdf"];
    dispatch [label="For each paper:\nDispatch condenser"];
    condense [label="paper-briefer\n→ condensed.md (body)"];
    tag [label="paper-tagger\n→ condensed.md (add frontmatter)"];

    screen_done -> check_pdf;
    check_pdf -> dispatch;
    dispatch -> condense;
    condense -> tag;
}

Launching Agents

Step 1: Launch condenser agent for each paper (can run multiple papers in parallel):

# Process multiple papers in parallel - each gets a condenser
Agent(
    subagent_type="scimesh:paper-briefer",
    prompt=f"Extract from: {paper_path}/fulltext.pdf\nWrite to: {paper_path}/condensed.md",
    description=f"Condense: {paper_slug}"
)

Step 2: After condenser completes, launch tagger:

Agent(
    subagent_type="scimesh:paper-tagger",
    prompt=f"""Add frontmatter to condensed paper:
Condensed: {paper_path}/condensed.md
Protocol: {review_path}/index.yaml
Output: {paper_path}/condensed.md (prepend frontmatter)""",
    description=f"Tag: {paper_slug}"
)

Batch Processing

Process papers in batches - condensers can run in parallel, taggers run after their respective condenser:

Batch 1: Papers 1-10
├── Paper 1: [condense] → [tag]
├── Paper 2: [condense] → [tag]
├── Paper 3: [condense] → [tag]
└── ...

# Launch up to 10 condensers in parallel
# Each tagger waits for its condenser to finish

Maximum parallelism: Launch all condensers for a batch in a single message:

# Single message with multiple Agent calls
Agent(subagent_type="scimesh:paper-briefer", prompt=f"...", description=f"Condense: paper1")
Agent(subagent_type="scimesh:paper-briefer", prompt=f"...", description=f"Condense: paper2")
Agent(subagent_type="scimesh:paper-briefer", prompt=f"...", description=f"Condense: paper3")
# ... up to 10 papers

Progress Tracking

Create Tasks for extraction visibility:

for paper in included_papers_with_pdf:
    TaskCreate(
        subject=f"Extract: {paper_title[:40]}...",
        description=f"Condense and tag {paper_slug}",
        activeForm=f"Extracting {paper_slug}..."
    )

Handling Papers Without PDF

Skip papers without PDF. Before starting extraction:

# Use Glob to find papers with PDFs
Glob(pattern="{review_path}/papers/**/fulltext.pdf")

Compare against included papers to determine which are missing PDFs. Papers without PDF are simply skipped during extraction.

Pre-Extraction Check

Ask user before starting:

{
    "question": f"Found {with_pdf_count}/{total_count} papers with PDFs. Extract evidence from {with_pdf_count} papers?",
    "header": "Extract?",
    "options": [
        {"label": f"Yes, extract {with_pdf_count} (Rec)", "description": "Dispatch agents for papers with PDFs"},
        {"label": "Select specific papers", "description": "Choose which papers to extract"},
        {"label": "Skip to synthesis", "description": "Generate PRISMA without extraction"}
    ],
    "multiSelect": False
}

Next Step

After extraction is complete:

• Use scimesh:appraising for deep critical appraisal of included papers (6 opus agents + fact-checker + synthesizer per paper).
• Use scimesh:synthesizing to generate PRISMA and synthesis.