bio-task-system

name	bio-task-system
description	Step 2 of the bio-manuscript pipeline: design the task system. Use when identifying the dominant task taxonomy in a field and organizing it into a staged Level 1-4 difficulty ladder to prepare for downstream dataset and metric design.

bio-task-system

Step 2: Task system design (任务体系构建)

Identify the main task categories in the field and organize them into a staged difficulty ladder.

Purpose

1. Find the dominant task taxonomy in the target field
2. Define Level 1-4 task tiers
3. Ensure the task ladder increases in difficulty
4. Prepare the task system for downstream dataset and metric design

Input Format

topic: [research topic]
paper_count: [number of related papers from Step 1]

Workflow

Step 2.1: Task taxonomy search

If there is substantial prior work, extract tasks from existing papers.

If there is not enough prior work, borrow the taxonomy from a parent domain and adapt it.

Typical adaptation logic:

• single-cell multi-omics -> spatial multi-omics
• modality alignment -> spatial-cell alignment
• batch integration -> cross-sample integration

Step 2.2: Task tier design

Define four levels:

• Level 1: basic validation task
• Level 2: intermediate application task
• Level 3: challenge task
• Level 4: flagship innovation task

Increase across three dimensions:

1. Data complexity
2. Technical difficulty
3. Biological value

Step 2.3: Standardize task descriptions

For each task, write:

• definition
• difficulty level
• data requirements
• technical focus
• biological value
• representative methods
• mapped figure

Output Format

# Task System Design

## Task Sources
- Extracted from related papers:
- Borrowed from parent domain:

## Tier Overview
| Level | Task type | Difficulty | Figure |
|-------|-----------|------------|--------|
| 1 | ... | low | Figure 2 |
| 2 | ... | medium | Figure 3 |
| 3 | ... | high | Figure 4 |
| 4 | ... | highest | Figure 5 |

## Detailed Task Descriptions

### Task 1: [task name]
- Definition:
- Difficulty:
- Data requirements:
- Technical focus:
- Biological value:
- Representative methods:
- Mapped figure:

### Task 2: ...

## Progression Rationale
1. Data complexity rises across tasks
2. Technical difficulty rises across tasks
3. Biological value rises across tasks

## Next Step
- Use the task system to search for datasets in Step 3

Example Ladder

• Level 1: vertical integration
• Level 2: horizontal / cross-slice integration
• Level 3: mosaic integration with missing modalities
• Level 4: diagonal integration across platform / resolution / cohort

Usage

/bio-task-system "spatial multi-omics integration | paper_count: 5"

Notes

1. Keep the ladder interpretable to reviewers.
2. Avoid adding too many tasks; four well-designed tiers are usually enough.
3. Make sure each task can later be tied to datasets, metrics, and figures.