# Enhanced ontology engineering through a Web-based, Cloud-based software architecture

> **NIH NIH R01** · STANFORD UNIVERSITY · 2021 · $236,100

## Abstract

PROJECT SUMMARY/ABSTRACT
This proposal is submitted to supplement grant R01 LM013498-01, “The Metadata Powerwash - Integrated
tools to make biomedical data FAIR.” The parent grant proposes to study methods to standardize the
metadata in online datasets to make the corresponding data more findable, accessible, interoperable, and
reusable. The goal is to transform the metadata that annotate experimental datasets online to a form that
adheres to standard reporting guidelines and that uses terms from standard ontologies. The parent grant
supports research that depends on the availability of a wide range of biomedical ontologies—standard
collections of terms that describe the entities in different application areas. In our work, nearly all the
ontologies that we use are created and maintained via a software tool known as Protégé, a system developed
in our laboratory that is the most widely used open-source tool for ontology engineering in the world. These
ontologies represent the development work of third parties or of members of the team participating in the
research supported by the parent grant. Protégé currently exists in two forms: (1) a desktop version written as
a Java application, and (2) a version that operates over the Web. We propose substantial, new software
engineering to improve the performance and long-term sustainability of the Protégé system.
To support our needs for ontology engineering in conjunction with our existing NLM R01 grant, we propose two
specific aims: (1) We will convert WebProtégé to a modern, microservice-based architecture, adding new
microservices—including the availability of a plug-in architecture that will allow third parties to contribute novel
additions to the WebProtégé code base. We will use a software-development approach that will allow us to
implement the new architecture in a controlled, incremental manner. (2) We will modernize WebProtégé to
make it Cloud-native. We will take advantage of the NIH STRIDES initiative, containerizing the system for
deployment in the Google Cloud Platform (GPC) and adapting the software to operate with Cloud-based third-
party software for data storage, data queueing, and search. We also will migrate all current WebProtégé users
and their projects to the Cloud-based system. Our work will benefit the biomedical community at large, while
enhancing our capabilities for ontology engineering as required by our existing grant.

## Key facts

- **NIH application ID:** 10405968
- **Project number:** 3R01LM013498-01S1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Mark A Musen
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $236,100
- **Award type:** 3
- **Project period:** 2021-05-01 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10405968

## Citation

> US National Institutes of Health, RePORTER application 10405968, Enhanced ontology engineering through a Web-based, Cloud-based software architecture (3R01LM013498-01S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10405968. Licensed CC0.

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