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2020 Fall Allotrope™ Connect


(Update: Public session recordings can be found here.)

(Update: Click on each presentation title to view & download .pdf)

All times in EDT (GMT-4) and are 30-minute sessions.

Allotrope Connect Agenda

Sept. 30th

10:00am - Introduction & Product Team Update with a Roadmap To Recognizing Value

Presenters and Co-Authors

  • Vinny Antonucci (Allotrope Foundation Chair, Director of Informatics, Merck)

  • Matthew Fox (Product Dir., Allotrope Foundation)


Vinny Antonucci                   Matthew Fox

Abstract / Summary​

  • Allotrope Connect introduction and presentation on a roadmap to recognizing value within your company with key decision points to consider in order to move forward with adopting the Allotrope Framework.

  • Introductions to new Allotrope Partners

    • Intel​ - Stephanie Cope

    • Benchling - Stella Howard

    • dotmatics - Charles Fracchia

Stephanie Cope                       Stella Howard                           Charles Fracchia


10:30am - A Path Towards Allotrope Adoption through Cloud-based Data Harmonization: A qPCR Plate Reader Case Study

Presenters* and Co-Authors​

  • George Van Den Driessche* (Strategic Analytics, Analytical Development, Biogen)

  • Evan Anderson* (TetraScience)

  • Devin Bailey (Strategic Analytics, Analytical Development, Biogen)

  • Spin Wang (TetraScience)

  • Len Blackwell (Strategic Analytics, Analytical Development, Biogen)

George Van Den Driessche                 Evan Anderson

Abstract / Summary

  • File standards offer pharmaceutical companies enhanced data integrity, new opportunities for analytical insights, and independence from instrument vendor software. Allotrope Foundation standardizes analytical instrument outputs by developing Allotrope Foundation Ontologies (AFOs) and Allotrope Data Format (ADF) file structures. However, the immediate value of adopting Allotrope standards requires a data architecture that captures the diversity of a company’s instrument portfolio. An ideal data architecture should utilize cloud-based data harmonization and transform instrument data into an open, interoperable format. Once data is harmonized, the adoption of Allotrope standards may be achieved with data conversion services to generate ADF files, ADF archiving, and implementing triple store technologies.

Here, we will demonstrate a process that prepares qPCR plate reader files for Allotrope adoption, supported by the Tetra Data Platform.

Currently, Biogen has multiple qPCR plate readers that store instrument outputs as individual entities on a corporate shared drive where files are siloed in location and format. The qPCR assay supports Biogen’s platform host cell DNA impurity method for large molecule pharmaceutical biologics programs. An interoperable harmonized data infrastructure enabled automated qPCR data analysis, such as experiment result reporting and control charting with python-based data science tools. Additionally, these efforts catalyzed the collaborative development of a first-draft qPCR Allotrope Tabular Model with the Allotrope Modeling Working Group. 


11:00am - Making the Digital Lab a Reality at Novartis with ZONTAL - An Allotrope Framework based FAIR Data hub

Presenters and Co-Authors​

  • Wolfgang Colsman (CEO, ZONTAL)

  • Ralph Haefeli (Senior IT-Manager, Novartis)

  • Olivia Woolley Meza (Senior Data Scientist, Novartis)

Wolfgang Colsman                Ralph Haefeli                Olivia Woolley Meza

Abstract / Summary

  • Novartis adopted a FAIR data strategy with focus on advanced analytics to help scientists focus again on science. In order to achieve their goals, Novartis selected ZONTAL as a FAIR data hub to deliver the enabling IT platform – powered by the Allotrope Data Format. In a joint presentation, we will review the driving use cases and highlight the enabling aspects of the Allotrope Data Format. 


11:30am - Publishing and Resolving Modularized Ontologies with Accurids - Use-Case Presentation and Demo

Presenters and Co-Authors​

  • Heiner Oberkampf (Head of Data Governance, OSTHUS)

  • Heiko Fessenmayr (R&D Lab Informatics System Architect, Agilent)

Heiner Oberkampf                   Heiko Fessenmayr

Abstract / Summary

  • The presentation describes the functional capabilities for integrated publication of Allotrope Foundation Ontologies with vendor-specific extensions. The concrete use-case is prepared in collaboration with Agilent on analytical methods. In addition to the presentation, we give a software demonstration of a PoC realization of the use-case with the Accurids product, which combines terminology browsing capabilities with PURL mechanisms.

Oct. 5th

10:00am - 

Supporting the Allotrope Foundation with Scientific Publications – An open invite

Presenters and Co-Authors​

  • Dennis Della Corte (Brigham Young University)

Dennis Della Corte

Abstract / Summary

  • Della Corte lab at BYU is a member of the APN and contributes to the scientific visibility of the consortium. In 2020, two publications introducing or highlighting the Allotrope Data Format were accepted. Both will shortly be presented. A third publication is currently underway to demonstrate the superiority of a semantic data format over other formats, like JSON or AnIML. We will discuss the differentiating factors between the formats and key use cases empowered by the Allotrope Data Format. In conclusion, we will invite Pharma to join this initiative with additional user stories and insights.


10:30am - Extending the Allotrope Framework: An Ontological Representation and Analysis of Process Chemistry

Presenters and Co-Authors​

  • Oliver He (University of Michigan)

  • Wes Schafer (Merck)

Yongqun (Oliver) He                     Wes Schafer

Abstract / Summary

  • In order to fully utilize our analytical data, the data needs to be associated with the context of the samples it represents. Process chemistry is an important domain in pharmaceutical development, and the source of many samples is covered by Allotrope. While Allotrope covers some aspects of synthetic chemistry, it is not a comprehensive process chemistry ontology. An extensive survey showed that there are only vocabularies that cover operations and to some extent the chemical processes themselves. To logically represent the entities related to process chemistry and the relations among these entities, we are developing a process chemistry domain ontology named OPC, which stands for Ontology of Process Chemistry. The ontology enables state of the art semantic data mining and predictive analysis of the experimental conditions in process research, synthetic route development, optimization and validation. To maintain interoperability, OPC is being developed according to the Allotrope style guide including the usage of the Basic Formal Ontology (BFO) as the upper-level ontology, and it is consistent with the OBO foundry ontology development principles. The OPC hierarchical structure aligns all the process chemistry-related topics and terms under BFO. Design patterns are designed to logically and semantically interlink different terms under different sub-branches together. Example use cases include batch release, impurity control, fate and purge, and DoE (design of experiments). OPC  maintains its interoperability with Allotrope ontologies. OPC could be developed as a standalone ontology or become part of Allotrope Ontology. 


11:00am - Seamless Integration of OpenLab CDS with ZONTAL Space – Implementing the Pistoia Method Model

Presenters and Co-Authors​

  • Ralph Mueller (Agilent)

  • Wolfgang Colsman (CEO, ZONTAL)

  • Heiko Fessenmayr (R&D Lab Informatics System Architect, Agilent)

Ralph Mueller                    Wolfgang Colsman                 Heiko Fessenmayr

Abstract / Summary

  • Agilent and Zontal will demonstrate together, how a potential way of sharing analytical methods within and beyond a single laboratory could work effectively over the Pistoia MethodDB approach supported by ADF as exchange format.

  • An essential feature for its usability will be the seamless integration of OpenLab CDS and ZONTAL Space (MethodDB).

  • In this joint presentation, Agilent and ZONTAL will provide background on this initiative, and a live demonstration of the interaction between both systems.


11:30am - MassSpec ADF: a full data “round-trip” - From raw data conversion from Sciex Analyst to reopen ADF

Presenters and Co-Authors​

  • Blair C. James (Chief Architect, Aftermarket Solutions, SCIEX)

  • Henning Kayser (Digital Transformation Lead, Crop Science Small Molecules Technologies, Bayer)

  • Paul-James Jones Ph. D. (IT Lead Business Consultant, RDM-E, Boehringer Ingelheim)

Blair C. James               Henning Kayser               Paul-James Jones

Abstract / Summary

  • Making laboratory data - in this case Triple-quad mass spec data – FAIR to comply with current and future regulatory requirements as long-term availability of “live data”  and its reuse is the driving theme of the present work. In this talk we will explain how we addressed this challenge by implementing a SCIEX Analyst ADF Exporter in a collaborative approach between Boehringer Ingelheim, Bayer and SCIEX. Paving the way towards a fully integrated workflow and data round-trip we want to share our latest achievements to display MassSpec raw data stored in ADF, as well as insights on technical implementation and demo.


12:00pm - Leveraging millions of ADF files and enabling Data Science in Pharma with Python and R

Presenters and Co-Authors​

  • Zach Pitluk (Vice President Life Sciences Business Development, Paradigm4)

Zach Pitluk

Abstract / Summary

  • Discuss attributes of SciDB that enable data analytics with large collections of ADF files.

  • The REVEAL: Allotrope AGILE Data Sciences Platform enables data selection and scientific computation over the imported ADF files using Python and R. The software stack includes high-level interfaces, via R Shiny and R connecting to the data engine, SciDB, which runs on cloud or on premises servers.  Examples of analysis of DoE and storage/peak matching from a large HDF5 metabolite atlas will be presented.

Oct. 7th 

10:00am - Implementing the Allotrope Framework at Biotechs – A case study between MacroMoltek and ZONTAL

Presenters and Co-Authors​

  • Dennis Della Corte (ZONTAL)

  • Monica Berrondo (Macromoltek)

Dennis Della Corte                    Monica Berrondo

Abstract / Summary

  • Small to midsize biotech companies are highly agile and dynamic. With rapidly changing headcounts, growing laboratory capabilities, and complex interactions with contract partners, they need a reliable data strategy to avoid loss of data and IP. In a joint presentation, with MacroMoltek CEO Monica Berrondo, we will highlight the major data challenges and opportunities of a small biotech. We will showcase how Allotrope Framework-based data management in ZONTAL enables machine learning based Data Science and increases efficiency and value.


10:30am - Rapid Converter Framework - An approach to ultra-fast converter development

Presenters* and Co-Authors​

  • Paul-James Jones*, Ph. D. (IT Lead Business Consultant, RDM-E, Boehringer Ingelheim)

  • Justin Van Duine* (Pfizer)

  • Bo Du (Pfizer)

Paul-James Jones                    Justin VanDuine

Abstract / Summary

  • Creating ADF files from vendor-proprietary data is one potential, although largely unrealized use of the Allotrope Framework.  We present a general approach to creating converters for vendor data with an emphasis on speed, scalability and standardization.  An overview of the process is presented, then we will build and execute a converter in real time using the BIP RapidADF Framework.


11:00am - Leveraging Basic Formal Ontology (BFO) by Allotrope Foundation Ontology (AFO) to Achieve Data Interoperability (Technical Session)


  • Amnon Ptashek (Tech. Dir., Allotrope Foundtion)

Amnon Ptashek

Abstract / Summary

  • Common vocabulary and data interoperability is a fundamental key to transform the acquisition, exchange, and management of laboratory data throughout its complete lifecycle. The top-level ontology Basic Formal Ontology (BFO) 2.0 which recently became an ISO/IEC standard, solves a major problem for knowledge graphs which is the tendency to generate silos where different groups create vocabularies to suit their own domain. The AFO suite leverages BFO, and was designed from the ground up to align with it at the upper layer. The presentation will cover the fundamentals of BFO consisting of very general and domain neutral terms. It will demonstrate the AFO alignment across its different domains.


11:30am - Tools for Managing Ontology Quality (Technical Session)

Presenters and Co-Authors​

  • Karin Colsman (OSTHUS)​

Abstract / Summary

  • An introduction to the Allotrope Developer Operations Tools and their manual and automated usage. We will look at a selection of our tools and how they can be used to notify ontologists about styleguide violations and other issues.


12:00pm - Panel Discussion of Allotrope Community Leaders

  • Several Allotrope Board Members and a co-Lead of the Allotrope Partner Network with a facilitator. Leaders to share their takeaways from the Connect and answer live questions from the attendees.

  • Facilitator: 

    • Peter Boogaard​ - External examiner at Rotterdam University of Applied Sciences

  • Panelists: 

    • Janet Cheetham - (Executive Director, Analytical Research and Development, Amgen)​

    • Len Blackwell - (Strategic Analytics, Analytical Development, Biogen)

    • Vinny Antonucci - (Allotrope Foundation Chair, Director of Informatics, Merck)

    • Graham McGibbons - Director, Strategic Partnerships at Advanced Chemistry Development, Inc., (ACD/Labs)

Peter Boogaard                Janet Cheetham         







Len Blackwell         Vinny Antonucci         Graham McGibbon

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