[Paper Review] Open Chemistry: RESTful Web APIs, JSON, NWChem and the Modern Web Application

Marcus D. Hanwell, Wibe A. de Jong+1 more|arXiv (Cornell University)|Jul 13, 2017

Scientific Computing and Data Management12 references4 citations

TL;DR

This paper presents an open-source, web-native platform for chemical and materials research that integrates computational and experimental data using RESTful APIs, JSON data formats, and the NWChem quantum chemistry code. By leveraging modern web technologies—including HTML5, JavaScript, and JSON-LD—the platform enables interactive, cross-device visualization and analysis of 3D molecular structures, electronic properties, and vibrational modes, with extensible, standardized data exchange across distributed, federated instances.

ABSTRACT

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers a highly interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing (HPC) resources, and offer command-line tools to automate interaction---connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web---going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript web client.

Motivation & Objective

• To address the fragmentation of chemical data by creating a unified, open platform that integrates computational and experimental results.
• To enable interactive, cross-device visualization and analysis of complex chemical data using modern web technologies.
• To develop a standardized, human- and machine-readable data format (Chemical JSON) for computational chemistry outputs, replacing legacy formats.
• To support federated deployment of the platform across research institutions, allowing customization and decentralized data storage.
• To extend the reach of high-performance computing (HPC) resources through lightweight, RESTful web APIs and command-line tools for automation.

Proposed method

• Built a server-side component in Python 3 exposing RESTful APIs to manage data access, trigger calculations, and support authentication.
• Used JSON as the primary data interchange format, extending it with semantic annotations via JSON-LD to enable machine-readable meaning and linked data capabilities.
• Developed a single-page HTML5/JavaScript web client that consumes the REST API for real-time, interactive visualization of 3D molecular structures and properties.
• Integrated open-source visualization libraries (e.g., for 3D rendering and charting) and extended Avogadro 2 and NWChem to natively output data in the new JSON format.
• Enabled command-line and desktop client integration via the same RESTful endpoints, supporting automated workflows and HPC job submission.
• Deployed the platform using Ansible and Ubuntu-based cloud images, with all source code hosted on GitHub for open collaboration and reproducibility.

Experimental results

Research questions

• RQ1 How can computational and experimental chemical data be unified in a single, accessible, and interactive platform?
• RQ2 Can RESTful web APIs and JSON-based data formats enable efficient, scalable, and interoperable data exchange across diverse chemistry software tools?
• RQ3 To what extent can modern web technologies (HTML5, WebGL, JavaScript) support high-performance, interactive visualization of complex 3D chemical data on multiple devices?
• RQ4 How can semantic web standards (e.g., JSON-LD) be leveraged to add machine-understandable meaning to chemical data in a lightweight, extensible format?
• RQ5 What architectural patterns enable federated deployment of scientific platforms while maintaining data consistency and user autonomy?

Key findings

• The platform successfully demonstrated end-to-end integration of NWChem computational outputs with a web-based visualization interface using a new JSON-based data format.
• The use of RESTful APIs enabled seamless interaction between web, desktop, and command-line clients, supporting automated workflows and HPC integration.
• The Chemical JSON format, derived from NWChem log files via a custom converter, proved effective in representing complex data such as 3D structures, electronic states, and vibrational modes.
• The web client achieved high interactivity and responsiveness, even on low-bandwidth connections, by minimizing server round-trips and performing most rendering client-side.
• Federated deployment of the platform was validated through modular, containerized deployment using Ansible and Ubuntu images, enabling site-specific customization.
• The adoption of JSON-LD was shown to be a viable path toward semantic enrichment of chemical data, with potential for future transformation into RDF triples and knowledge graph integration.