How-to Guides

How can I add other new embedding models?

FANTASIA is modular by design. To integrate a new protein language model such as Ankh:

  1. Declare the model in the constants.yaml file under sequence_embedding_types.

  2. Implement the corresponding Python module in: protein_information_system/operation/embedding/proccess/sequence/new_model.py

  3. Register the model in your runtime configuration (config.yaml) using embedding.types.

📘 Full guide: Adding Embedding Models

How is the functional lookup table generated and populated?

FANTASIA supports several pathways to build the functional lookup table, including:

  • Automatic accession fetching from UniProt using search criteria.

  • Manual import from CSV lists.

  • Local annotation processing via custom TOPGO files.

Each mode is fully configurable.

📘 Full guide: Lookup Table Generation