Reuse the existing website interface

Oct 13, 2025 by wbrum.org 11 views

Overview

Our website currently interfaces with a knowledge graph database focused on SRA information, but we have an upcoming database about obelisks, a previously unrecognized class of viroid-like elements identified in human gut metatranscriptomic data. To support this and potentially future databases, we need a feature that allows us to swap or integrate different databases/knowledge graphs seamlessly. This will enable us to replicate the website interface for other use cases, such as obelisks, without requiring significant redevelopment.

Background / Context

The current website interface is tightly coupled with the SRA knowledge graph, which limits its adaptability for other datasets or knowledge graphs. Key challenges include:

Lack of Modularity: The interface is not designed to handle multiple databases or knowledge graphs, making it difficult to extend to new use cases like obelisks.
Code Duplication: Without a reusable framework, replicating the interface for new databases would require significant code duplication and maintenance overhead.
Scalability Issues: As we expand to include additional databases (e.g., obelisks), the current architecture may become unwieldy and difficult to manage.

By developing a feature to swap or integrate databases/knowledge graphs, we can:

Reuse the existing website interface for new datasets, such as the obelisks database.
Reduce development time and effort for future projects.
Create a modular and scalable architecture that supports multiple use cases.

Hypothesis

Implementing a feature to swap or integrate databases/knowledge graphs will enable us to replicate the website interface for other use cases, such as obelisks, while maintaining a modular and scalable architecture.

Experiment

To achieve this goal, we propose the following experiment:

Design Modular Architecture:

Define a standardized schema or interface for databases/knowledge graphs to ensure compatibility with the website.
Create a configuration system to specify which database or knowledge graph to use (e.g., SRA, obelisks).

Develop Database Swapping Feature:

Implement a backend mechanism to dynamically load and switch between different databases/knowledge graphs based on user selection or configuration.
Ensure the frontend can adapt to the structure and content of the active database (e.g., filters, modules, visualizations).

Integrate Obelisks Database:

Adapt the obelisks database to conform to the standardized schema or interface.
Test the website interface with the obelisks database to ensure compatibility and functionality.

Testing:

Test the database swapping feature with multiple datasets to ensure it works as expected.
Validate that the website interface adapts correctly to the structure and content of each database.

Controls

To ensure the success of this experiment, we will:

Ensure backward compatibility with the existing SRA knowledge graph and website interface.
Validate that the database swapping feature does not introduce performance bottlenecks or errors.

Expected Outcome

The expected outcome of this experiment is:

A modular feature that allows seamless swapping or integration of databases/knowledge graphs.
The website interface can be replicated for new use cases, such as the obelisks database, with minimal redevelopment.
A scalable architecture that supports future expansion to additional datasets.

Open Questions

Some open questions that need to be addressed include:

Should the database swapping feature be user-configurable (e.g., a dropdown menu) or controlled via backend configuration?
How should we handle differences in schema or structure between databases (e.g., missing fields, additional data types)?

References

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Designing a Modular Architecture

To design a modular architecture, we need to define a standardized schema or interface for databases/knowledge graphs. This will ensure compatibility with the website and enable seamless swapping or integration of databases.

Standardized Schema or Interface

A standardized schema or interface will provide a common structure for databases/knowledge graphs, making it easier to integrate and swap between them. This schema or interface should include:

Data types: Define the data types that will be used in the database, such as strings, integers, and dates.
Fields: Define the fields that will be used in the database, such as name, description, and metadata.
Relationships: Define the relationships between fields and data types, such as one-to-one, one-to-many, and many-to-many.

Configuration System

A configuration system will allow us to specify which database or knowledge graph to use, such as SRA or obelisks. This system should include:

Database selection: Allow users to select which database or knowledge graph to use.
Configuration options: Provide options for configuring the database or knowledge graph, such as filtering and sorting.

Developing a Database Swapping Feature

To develop a database swapping feature, we need to implement a backend mechanism to dynamically load and switch between different databases/knowledge graphs based on user selection or configuration.

Backend Mechanism

The backend mechanism should include:

Database connection: Establish a connection to the selected database or knowledge graph.
Data retrieval: Retrieve data from the selected database or knowledge graph.
Data processing: Process the retrieved data to ensure compatibility with the website.

Frontend Adaptation

The frontend should be able to adapt to the structure and content of the active database, including:

Filters: Allow users to filter data based on specific criteria.
Modules: Provide modules for visualizing and interacting with data.
Visualizations: Provide visualizations for displaying data, such as charts and graphs.

Integrating the Obelisks Database

To integrate the obelisks database, we need to adapt it to conform to the standardized schema or interface.

Adapting the Obelisks Database

The obelisks database should be adapted to conform to the standardized schema or interface, including:

Data type mapping: Map the data types in the obelisks database to the standardized schema or interface.
Field mapping: Map the fields in the obelisks database to the standardized schema or interface.
Relationship mapping: Map the relationships between fields and data types in the obelisks database to the standardized schema or interface.

Testing the Database Swapping Feature

To test the database swapping feature, we need to test it with multiple datasets to ensure it works as expected.

Testing Scenarios

The testing scenarios should include:

Happy path: Test the database swapping feature with a valid dataset.
Error path: Test the database swapping feature with an invalid dataset.
Edge cases: Test the database swapping feature with edge cases, such as large datasets and complex relationships.

Conclusion

Q: What is the current challenge with the website interface?

A: The current website interface is tightly coupled with the SRA knowledge graph, which limits its adaptability for other datasets or knowledge graphs. Key challenges include lack of modularity, code duplication, and scalability issues.

Q: What is the goal of implementing a feature to swap or integrate databases/knowledge graphs?

A: The goal is to enable the website interface to be replicated for new use cases, such as the obelisks database, with minimal redevelopment, while maintaining a modular and scalable architecture.

Q: How will the database swapping feature be implemented?

A: The database swapping feature will be implemented using a backend mechanism to dynamically load and switch between different databases/knowledge graphs based on user selection or configuration.

Q: What is the standardized schema or interface for databases/knowledge graphs?

A: The standardized schema or interface will provide a common structure for databases/knowledge graphs, including data types, fields, and relationships.

Q: How will the obelisks database be integrated?

A: The obelisks database will be adapted to conform to the standardized schema or interface, including data type mapping, field mapping, and relationship mapping.

Q: What are the testing scenarios for the database swapping feature?

A: The testing scenarios will include happy path, error path, and edge cases, such as large datasets and complex relationships.

Q: What are the expected outcomes of implementing the database swapping feature?

A: The expected outcomes include a modular feature that allows seamless swapping or integration of databases/knowledge graphs, the website interface can be replicated for new use cases, and a scalable architecture that supports future expansion to additional datasets.

Q: What are the open questions that need to be addressed?

A: Some open questions that need to be addressed include whether the database swapping feature should be user-configurable or controlled via backend configuration, and how to handle differences in schema or structure between databases.

Q: What are the references for this project?

A: [placeholder]

Q: What is the expected timeline for implementing the database swapping feature?

A: The expected timeline will be determined based on the complexity of the project and the resources available.

Q: What are the resources required to implement the database swapping feature?

A: The resources required will include a team of developers, a project manager, and a database administrator.

Q: What are the risks associated with implementing the database swapping feature?

A: The risks associated with implementing the database swapping feature include data loss, system downtime, and security breaches.

Q: How will the database swapping feature be maintained and updated?

A: The database swapping feature will be maintained and updated through regular software updates, bug fixes, and feature enhancements.

Q: What are the benefits of implementing the database swapping feature?

A: The benefits of implementing the database swapping feature include increased flexibility, reduced development time, and improved scalability.

Q: How will the database swapping feature be tested and validated?

A: The database swapping feature will be tested and validated through a combination of unit testing, integration testing, and user acceptance testing.

Q: What are the next steps for implementing the database swapping feature?

A: The next steps will include designing the modular architecture, developing the database swapping feature, and integrating the obelisks database.

Q: What are the key performance indicators (KPIs) for measuring the success of the database swapping feature?

A: The KPIs will include metrics such as user adoption, system uptime, and data quality.