The Rise of the Allotrope Simple Model and Allotrope Foundation’s Evolution

In the article “The Rise of the Allotrope Simple Model” published in Drug Discovery Today, ZONTAL Data Scientists discuss the details of the new format and outline a path to successful adoption [1]. Here we review some highlights.

The Allotrope Foundation, established in 2012 by pharmaceutical companies, instrument vendors, and software firms, has been on a mission to solve the data exchange challenge plaguing analytical laboratories. After a decade of work, the Foundation has released several products that are now finding adoption across various companies. Most notably, the recently developed Allotrope Simple Model (ASM) is expediting and broadening the adoption of Allotrope standards.

As a result, the Foundation has expanded into the chemical industry in recent years and is revamping its business model to lower the barrier to entry for smaller companies. This article presents the proceedings from the 2023 Fall Allotrope Connect conference and summarizes the Foundation’s technical and organizational developments since 2020.

Allotrope Product Suite Updates

The original Allotrope product suite comprised the Allotrope Foundation Ontologies (AFO), the Allotrope Data Format (ADF), and the Allotrope Data Model (ADM). While the AFO usage has tripled over the past three years, indicating its growing acceptance, the adoption of the complex ADF format has been sluggish.

To address this, the Foundation introduced the Allotrope Simple Model (ASM) – a lightweight, JSON-based format with a semantically controlled vocabulary but significantly less ontological overhead compared to ADF. The ASM has witnessed rapid adoption and is undergoing swift expansion across various techniques like chromatography, qPCR, and mass spectrometry.

Introducing the Allotrope Simple Model

The ASM represents an evolution of the Foundation’s extensive development efforts, transitioning into a phase of widespread adoption beyond the initial pharmaceutical industry. The user-friendly JSON format and compatibility with existing tools have been key drivers of the ASM’s rapid acceptance.

The ASM operates with three components: an Instance Data file containing the experimental data, a Manifest file linking to ontologies and schemas, and a JSON schema defining the data structure. It leverages the flexibility of JSON while maintaining a standards-based framework governed by the Foundation’s ontologies.

The ASM’s close relationship with the Allotrope Data Model (ADM) has facilitated a smooth transition, as the tabular ADM structure aligns well with the ASM’s key-value pairs. The ASM supports both simple and aggregated tabular models, enabling efficient data representation across multiple samples and replicates.

Creating a New ASM Model

Developing a new ASM model involves forming a working group, collecting example data, mapping terms to existing ontologies (or creating new ones if needed), defining JSON schemas, and undergoing Allotrope review. This iterative process ensures comprehensive coverage and adherence to Allotrope standards – see Figure 1.

Figure 1 Allotrope simple model creation process chart

Allotrope Connect 2023: Key Discussions

Among multiple presentations, the United States Pharmacopeia (USP) highlighted its efforts to integrate Allotrope models, employing natural language processing tools to convert monograph documents into Allotrope formats in collaboration with ZONTAL.

A New Business Model for Broader Adoption

Recognizing the growing membership outside of the pharmaceutical industry, the Allotrope Board of Directors announced plans to develop a new business model that lowers the entry barrier for smaller companies. The proposed model aims to reduce membership fees, allowing for broader participation from diverse organizations and fostering a more inclusive, community-driven approach to development.

Conclusion

The Allotrope Foundation is undergoing a significant technological and organizational transition, marked by the success of the Allotrope Simple Model and a strategic shift towards broader cross-industry adoption. With its user-friendly format, standards-based framework, and an evolving business model that encourages community participation, the Foundation is poised to play a pivotal role in reshaping the digital laboratory landscape across various sectors.

With ZONTAL being on the forefront of delivering digital transformation to the laboratory, reach out to our team to discuss which strategy will lead you into a successful future.

The full article can be read here: https://authors.elsevier.com/a/1ioAU4r9RkrPQq

Sources:

1. Haynie C, Gardiner S, Della Corte D., Rise of the Allotrope Simple Model: update from 2023 Fall Allotrope Connect. Drug Discovery Today. 2024:103944.