Program and Presentation Details
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Day 1 — Wednesday — October 7, 2026 — Eastern Time (ET)

09:00–09:30 — Welcome and Introduction to Allotrope: Framework and Roadmap
                                    Allotrope Foundation

09:30–10:00 — Keynote: Welcome and Introduction to USP: Welcome and an Overview of USP and the Digital Projects
                                    USP

10:30–11:15 — Advancing ASM for Digital Analytical Methods
                                    Birthe Nielsen (Pistoia Alliance), Benjamin Woolford-Lim (Allotrope), Vinny Antonucci (DAMs WG member), Jeroen De Hass (Laboperator)

The Pistoia Alliance and Allotrope Foundation are collaborating to develop a vendor-neutral, machine-readable representation of analytical methods using the Allotrope Simple Model. The project is testing and refining a general method scaffold against multiple analytical examples, while examining how method procedures, materials, equipment requirements, acceptance criteria and calculations should be represented. Current work includes AI-assisted method mapping, alignment with ISA-88, and early vendor implementation of ASM import and mapping. This session will share progress, key modelling insights and initial implementation learnings, demonstrating how structured digital methods could support method exchange, transfer and future laboratory execution across ELN, LIMS and LES platforms.

11:15–11:45 — From Paper to Digital: USP MethodConnect Enables Machine-Readable USP–NF Methods for the Modern Laboratory 
                                    Kyle Larsen, Sr. Informatics Product Manager (USP)

11:45–12:15 — Future Opportunities Utilizing ASM for Method Standardization, Interoperability, and Automation 
                                    Andy Sasaki, General Manager – R&D Center, Shimadzu Scientific Instruments (Shimadzu)
                                    Minoru Namikawa, Software Liaison, Shimadzu Scientific Instruments (Shimadzu)

As analytical laboratories continue to advance digitalization and automation, there is increasing interest in representing analytical methods in a structured, machine-readable format. In this PoC study, selected LC method parameters were defined in JSON format and converted into a CDS LC method. The work demonstrates the feasibility of digital method representation and provides insights into future opportunities utilizing ASM for method standardization, interoperability, and automation.

01:15–01:45 — Pistoia Alliance Open-Source Instrument Data Converter Repository project 
                                    Nathalie Batoux (Pistoia Alliance), Chris Severs (Benchling)

Interoperability is a critical condition to make use of instrument data results downstream. However, 2 instruments measuring the same result but from different vendors will produce different results file format, blocking direct comparison and use. This Pistoia Alliance project is the continuation and expansion of Benchling's Allotropy repository of open-source instrument data converters to standard formats. With the Pistoia Alliance taking ownership of the Allotropy open source repository, we hope to foster more collaboration and data sharing that is completely vendor neutral.

01:45–02:15 — ASM as the Semantic Contract for a Life Sciences Unified Namespace: An End-to-End Reference Implementation with Ruvu 
                                    Imodoye Abioro, Co-founder/CTO (Healthbotics LLC)

02:15–02:45 — Automating ASM Generation at Scale
                                    Robert H. Williams, Customer Collaboration Director, Automation Productivity Solutions, Productivity Solutions Division (Agilent Technologies)

03:15–04:00 — Connecting the Laboratory and the Manufacturing Process: Allotrope, ISA-88 and ISA-95 
                                    Chris Monchinski (InflexionPoint)

Modern manufacturing increasingly depends on analytical measurements that cross the traditional boundaries between laboratory systems, process automation, and manufacturing operations management. Standards such as ISA 88 and ISA 95 used to describe and execute manufacturing processes do not, by themselves, provide the rich scientific semantics necessary to consistently describe analytical instruments, methods, measurements, samples, and results. This presentation will explore how the Allotrope framework can complement ISA-88 and ISA-95 to bridge this gap and provide a semantic connection between process context and analytical data.
The presentation will examine two use cases to illustrate a broader architectural concept: ISA-88 describes the process context, ISA-95 describes the manufacturing operations context, and Allotrope provides the analytical and scientific context needed to connect measurements and results to both. The combination of these standards offers the potential for a true standards-based semantic foundation spanning laboratory and manufacturing environments.
The session will conclude by exploring how these complementary standards could enable more interoperable architectures for PAT, Quality 4.0, autonomous laboratories, advanced process control, digital manufacturing, and AI—where machines and agents understand the context and meaning of the data they receive.
Details on use cases:
From an ISA-88 perspective, analytical measurements are increasingly becoming integral parts of recipe execution. In-line and at-line technologies such as spectroscopy, chromatography, particle analysis, and other Process Analytical Technology (PAT) instruments may provide measurements that influence recipe transitions, process parameters, hold points, exception handling, and ultimately process outcomes. ISA-88 provides a strong model for recipes, procedural control, equipment, materials, parameters, and execution context, while Allotrope can provide the scientific and analytical context needed to consistently describe the instrument, analytical method, measurement, and resulting data. Connecting these models creates an opportunity to associate analytical results directly with the recipe step, equipment, material, batch, process conditions, and time under which the measurement was produced.
From an ISA-95 perspective, the same challenge extends beyond the process cell and into manufacturing operations and laboratory workflows. A manufacturing operation may generate a requirement for a set of quality tests that must be scheduled, dispatched, executed by an internal or third-party laboratory, and returned to manufacturing. ISA-95 provides models for the production, quality, inventory, and material context surrounding this workflow, including concepts such as test specifications and quality test results. Allotrope can complement this by providing a standardized semantic representation of the scientific data generated during execution of those tests. Together, these models can support a digital thread from a material lot or production order, through sample and test execution, to analytical results, material disposition, inventory status, and ultimately product release.

04:00–04:45 — Industry Panel: How Do We Close the Context Gap?
                                    Moderator: Chris Sigler (Merck)

04:45–05:00 — Wrap-up Day 1

Day 2 — Thursday — October 8, 2026 — Eastern Time (ET)

09:00–09:30 — Welcome & Day 1 Recap
                                    Allotrope Foundation

09:30–10:00 — From Measurement to Decision: Building Context-Aware Analytical Systems for the Pharmaceutical Supply Chain 
                                    Dennis Hall, Vice President, Advanced Manufacturing and Technologies (USP)

10:00–10:30 — Providing Universal Context: The Role of a FAIR Data Registry for Enterprise Product Intelligence
                                    Heiner Oberkampf, CEO & Co-Founder (Accurids)

11:00–11:30 — CMC Results Expansion to AFO
                                    Wes Schafer (Allotrope Product Team)

At the last Connect meeting, work was shown that tested the connected domains hierarchy using stability and polymorph studies used in typical CMC type drug filings. The hierarchy worked well and is a candidate recommendation pending input from the community. Some gaps were found in the AFO however and this presentation proposes solutions to close those gaps, particularly around typical analytical result types typically reported in such filings: identity, structure elucidation, assay, and impurity levels. OWL restrictions are proposed to enhance reasoning and thus further enable AI.

11:30–12:00 — From Analytical Data Interoperability to Operational Validity: Capturing Expert Knowledge for Connected Laboratories
                                    Luis Schachner (Genentech)

Analytical data standards increasingly enable interoperable representation of analytical methods, results, requirements, and data-validity concepts. Yet laboratory scientists also rely on substantial expert knowledge that is rarely captured explicitly: how workflows fail, which signals reveal or obscure those failures, what scientific conclusions may be compromised, and when corrective action or escalation is required. We are developing a structured, provenance-aware approach for eliciting and representing this operational-validity knowledge alongside analytical workflow and decision context. Using bioanalytical workflows as case studies, we separate source-documented content, expert-confirmed knowledge, model-derived hypotheses, and curator-derived representations, with atomic assertions retained in a human-reviewed evidence ledger before graph projection. A primary ELISA case demonstrates how a mature protocol package containing execution instructions, calculations, and classification logic can still be enriched with expert knowledge about epistemic limitations, failure interpretation, observable signals, and conditional decisions. We will discuss how this layer could complement AFO-aligned analytical data representations and support connected-laboratory interoperability without conflating execution completion with scientific validity.

12:00–12:30 — From Lab to Regulatory: Connecting Allotrope with the IDMP Ontology 
                                    Heiner Oberkampf,  CEO & Co-Founder (Accurids)
                                    Aditya Tyagi, (IDMP Ontology Project Lead (Pistoia Alliance)

01:30–02:00 — Introduction to ICH M04 Structured Product Quality Submissions (SPQS)
                                    Rita Algorri (Amgen), Sheetal Gaiki (J&J)

02:00–02:30 — Showcasing a Structured CMC Use Case in the Cloud: FDA Research Collaboration Project PRISM and Its Potential to Support Collaborative Review
                                    Ciby Abraham (Merck)
                                    Vada Perkins, Vice President, Global Head of Regulatory Intelligence & Policy (Boehringer Ingelheim)

The CMC regulatory landscape is undergoing a significant transformation, driven by the ongoing revision of ICH M4Q(R2), the introduction of ICH M16, and increasing discussion across industry and health authorities on the use of cloud-based platforms, structured submissions, and AI/ML-enabled tools in the regulatory environment. Project PRISM provides a practical CMC use case to explore how these emerging capabilities could support more efficient creation, exchange, and review of regulatory information. By showcasing a structured CMC submission approach in a cloud-based environment, this research collaboration with FDA offers an opportunity for the broader community to learn from real-world application, evaluate potential benefits and implementation considerations, and identify how modern digital approaches may enable more collaborative, transparent, and efficient review. Ultimately, this work can help inform the evolution of regulatory processes and support the delivery of the next generation of medicines to patients around the world more efficiently.

02:30–03:00 — Structuring the CMC Submission: AI-Based Structuring of CMC Data from PDF as a Proof of Concept Until an Agreed CMC Data Standard Is Available
                                    Ciby Abraham (Merck)
                                    Vada Perkins, Vice President, Global Head of Regulatory Intelligence & Policy (Boehringer Ingelheim)

In this session, we will provide a deeper look at the CMC submission use case and describe how unstructured information from traditional PDF-based regulatory content can be converted into structured, usable CMC data. The discussion will outline the approach used to identify, extract, organize, and structure key CMC information in the absence of an agreed global CMC data standard, while also highlighting the practical considerations, limitations, and opportunities associated with applying AI-based tools in this context. The session will also include a demonstration of how a cloud-based CMC application can support collaborative review by enabling multiple stakeholders to access structured information, review content in context, and perform data analysis in near real time. Together, these examples will illustrate how structured CMC data and digital review environments may help improve transparency, consistency, and efficiency across submission preparation and regulatory assessment.

03:15–03:45 — Presentation (TBD)

03:45–04:30 — Group Discussion, Workshop Wrap-up, What's Next