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NAMO Paper Curation Guides

This directory contains comprehensive guides for curating different types of NAM (New Approach Methodology) research papers into the NAMO data model. Each guide provides step-by-step instructions tailored to the specific characteristics and requirements of different model types.

Available Guides

📧 How to Curate an Organoid Paper

Learn to curate organoid research papers with focus on: - Biological complexity: Self-organization, differentiation protocols - Culture systems: Matrix composition, growth factors, cost optimization
- Validation strategies: Morphological, functional, and molecular assessment - Example: Takahashi et al. cost-reduced intestinal organoid drug screening

Key Features: - Step-by-step walkthrough from abstract to final YAML - Emphasis on biological differentiation and self-organization - Culture optimization and cost-reduction strategies - Organoid-specific validation metrics

🔬 How to Curate an Organ-on-Chip Paper

Learn to curate organ-on-chip and microphysiological system papers with focus on: - Technical engineering: Microfluidic design, flow control, sensor integration - System architecture: Multi-channel, layered, and complex geometries - Performance metrics: Throughput, automation, reproducibility - Example: Zhu et al. dynamic multi-organ drug screening platform

Key Features: - Detailed microfluidic design parameter extraction - Enum validation for technical specifications - Multi-organ system integration approaches - Engineering-focused validation strategies

General Curation Principles

Universal Best Practices

  1. Start with Paper Structure
  2. Abstract: Identifies model type and key innovation
  3. Methods: Technical protocols and parameters
  4. Results: Performance data and validation

  5. Discussion: Context and limitations

  6. Schema Mapping

  7. Use appropriate ontology IDs (UBERON for anatomy, CL for cell types)
  8. Ensure controlled vocabulary compliance
  9. Check enum values against schema definitions

  10. Validate required fields for each model class

  11. Technical Accuracy

  12. Extract quantitative measurements and performance metrics
  13. Capture innovation and unique features
  14. Document validation approaches and results

  15. Include comprehensive literature references

  16. Quality Assurance

  17. Run just test to ensure YAML validates
  18. Verify all required fields are complete
  19. Check enum values are correct
  20. Test against the schema after curation

Model Type Decision Tree

Is it a microfluidic device?
├─ Yes: Use OrganOnChip or TissueOnChip guide
│   ├─ Focus on organ physiology → OrganOnChip
│   └─ Focus on tissue function → TissueOnChip
└─ No: Is it self-organizing from stem cells?
    ├─ Yes: Use Organoid guide
    └─ No: Consider other NAM model types
        ├─ 3D cell culture without microfluidics → ThreeDCellCulture
        ├─ Computational model → MLModel, QSARModel, etc.
        └─ Animal model → AnimalModel

Schema Classes Summary

Model Class Abstract? Key Features Required Fields
Organoid No Self-organizing, stem cell-derived organ_modeled, cell_source
OrganOnChip No Microfluidic, organ physiology organ_modeled, microfluidic_design
TissueOnChip No Microfluidic, tissue function tissue_modeled, microfluidic_design
MicrophysiologicalSystem Yes Use concrete subclasses above N/A
ThreeDCellCulture No 3D without microfluidics three_d_architecture

Common Enum Values

Complexity Levels

  • LOW: Simple, single-parameter models
  • MODERATE: Multi-parameter with some interactions
  • HIGH: Complex, multi-system interactions

Architecture Types

  • Microfluidic: SINGLE_CHANNEL, MULTI_CHANNEL, LAYERED
  • 3D Culture: SPHEROID, SCAFFOLD_BASED, HYDROGEL_EMBEDDED

Flow Control

  • SYRINGE_PUMP, PRESSURE_DRIVEN, GRAVITY_DRIVEN, PERISTALTIC_PUMP

Troubleshooting

Common Validation Errors

  1. Unknown enum code: Check schema for valid enum values
  2. Missing required field: Add mandatory fields for model class
  3. Invalid class name: Use concrete classes, not abstract ones
  4. Incorrect file naming: Use ClassName-example-ID.yaml format

Getting Help

  • Check existing examples in tests/data/valid/
  • Validate with just test after changes
  • Review schema definitions in src/namo/schema/namo.yaml
  • Consult class-specific guides for detailed instructions

These guides ensure comprehensive, accurate curation while maintaining consistency with the NAMO data model across different types of NAM research.