PlanGexQ

PlanGexQ encodes planarian morphologies as mathematical graphs and registers gene expression patterns to produce ontology-linked standardized datasets for curation and mechanistic analysis.

Key Features:

• Morphology encoding: Encodes reference morphologies using mathematical graphs linked to the planarian anatomy ontology.
• Reference morphology generation: Automatically generates reference morphologies from encoded graphs and ontology terms.
• Gene expression registration: Registers gene expression pattern images to the encoded reference morphologies for spatial mapping.
• Ontology-based annotation: Automatically generates annotations using planarian anatomy ontology terms by analyzing spatial expression patterns and associated textual descriptions.
• Standardized dataset creation: Encodes morphological outcomes and gene expression patterns into a centralized, standardized format to support knowledge extraction and mechanistic model development.

Scientific Applications:

• Spatial phenotype formalization: Formalizes spatial phenotypes and gene expression patterns for comparative analysis and data integration in developmental and regenerative biology.
• Mechanistic model support: Provides standardized, ontology-linked datasets to support reverse-engineering and development of mechanistic models.
• Perturbation analysis: Enables unambiguous description and interpretation of experimental outcomes from genetic, surgical, or pharmacological perturbations in planarians and other regenerative organisms.

Methodology:

Worm morphologies are encoded as mathematical graphs tied to anatomical ontology terms; reference morphologies are automatically generated from these encodings; gene expression patterns are registered to the reference morphologies and integrated into a centralized standardized dataset.