Allotrope in the News

Digital Evolution: Novo Nordisk's Shift to Ontology-Based Data Management

An article that discusses the way Novo Nordisk Research & Early Development leverages an Ontology-Based Data Management (OBDM) strategy for digital transformation was published on arXiv, an open curated research-sharing platform. It presents a Virtual Knowledge Graph approach while consuming the Allotrope Foundation Ontology (AFO).
The article can be viewed at Link
A PDF version can be downloaded at Link

Digital Evolution: Novo Nordisk's Shift to Ontology-Based Data Management

The 2024 Allotrope Connect Workshop is happening right now in Boston, hosted by Thermo Fisher Scientific!

This event brings together industry leaders, innovators, and collaborators from the scientific data ecosystem to explore the latest advancements in data standardization, interoperability, and digital lab transformation.
Read the post on LinkedIn

Vendor-Neutral Electronic Lab Notebook (ELN) Data Model Released in Allotrope Foundation’s Q4 Release!

An Allotrope vendor-neutral ELN data model is a pivotal step forward in enabling seamless data integration and fostering collaboration across systems. With the introduction of this first ELN Working Group milestone, Allotrope aims to broaden its domain coverage beyond its primary focus on the measurement domain to include the experiment authoring domain.
Read the post on LinkedIn

Optimizing Pharmaceutical Operations: A Deep Dive into an E2E Request-to-Result Workflow

An article published by SciY discusses the importance of streamlining laboratory workflows in the pharmaceutical industry to enhance efficiency and data integrity. It emphasizes the role of standardized data formats and interoperability in achieving seamless data exchange across various laboratory processes. The Allotrope Foundation's initiatives, particularly the development of the ADF and the ASM, are highlighted as pivotal in creating vendor-agnostic, fully traceable workflows. These standards facilitate the creation of self-reporting data assets, enabling automation, process optimization, and improved compliance within pharmaceutical operations.
Read the article at Link

From research to manufacturing: Overcoming data challenges in the drug development lifecycle

A white paper, produced by Scientific Computing World in partnership with Siemens Digital Industries, follows a recent online roundtable event where experts across the drug development lifecycle shared insights on improving data collection, storage, retrieval, and analysis. It highlights the critical role of standardized formats, metadata, and data ontologies in enabling efficient processes, fostering collaboration, and ensuring seamless technology transfer. The paper also mentions the work of the Allotrope Foundation in developing open data formats to facilitate sharing between diverse laboratory instruments and systems, enhancing interoperability and streamlining data usage in pharmaceutical R&D and manufacturing.
Download the white paper from Scientific Computing World at: Link

Data collection and formats in drug discovery

An article and white paper that were published on Scientific Computing World and sponsored by Siemens Digital Industries, emphasizes the importance of a common language in accelerating pharmaceutical research. It highlights the role of the Allotrope Foundation in advancing data interoperability and standardization, enabling seamless integration and analysis of diverse datasets to support more efficient drug discovery processes.
Read the article and download the white paper at Link

Read the post on LinkedIn

Allotrope’s Role in Advancing FAIR Data with LADS OPC UA at NFDI4Chem

A recent LinkedIn post highlights how Allotrope Foundation's technologies are instrumental in bridging the gap between "data at rest" (files and databases) and "data in motion" (e.g., OPC UA protocols). This synergy, showcased in a NFDI4Chem YouTube channel, underscores the value of Allotrope's contributions to enabling FAIR data principles in modern lab automation and connectivity.
Read the post on LinkedIn. Watch the presentation on NFDI4Chem YouTube channel

Day 2 of the 2024 Allotrope Connect Workshop is Happening Now!

Day 1 was packed with engaging sessions. Today promises even more exciting insights and discussions as we continue driving innovation and standardization across the scientific data landscape. Stay tuned for updates!
Read the post on LinkedIn

Robust "ELN in a future data-centric ecosystem" discussion now in progress at Allotrope Connect Workshop in Boston!

Robust "ELN in a future data-centric ecosystem" discussion now in progress at Allotrope Connect Workshop in Boston.
Read the post on LinkedIn

The 2024 Allotrope Connect Workshop is happening right now in Boston, hosted by Thermo Fisher Scientific!

Streamlining Analytical Method Validation for ICH Compliance with ASM, eCTD Submissions, GAMP5 Qualification, and Standardized Data Integration: By PharmaLex at Fall 2024 Allotrope Connect in Boston

PharmaLex experts will discuss an important aspect of CMC activities on how to streamline analytical method validation, and automatically generate ICH Q2(R2)-compliant reports, ready for eCTD submission. Pharmalex created a platform for GAMP5-qualified environment that can integrate diverse data sources via ASM format.
Read the post on LinkedIn

Instrument Integration to Knowledge Graph Development journey - To enable seamless flow of data in Laboratory Space with Allotrope: By Merck at Fall 2024 Allotrope Connect in Boston

Merck to explore the process of integrating instruments data into knowledge graph development, highlighting the critical role of Allotrope, a standardized data framework in the scientific lab space.
Read the post on LinkedIn

How Agilent will use Allotrope Data Format to improve Laboratory Efficiency? - By Agilent Digital Lab Innovation Team at Fall 2024 Allotrope Connect in Boston

Agilent Digital Labs Innovations Team showcases how they are helping scientific organizations boost productivity by digitalizing labs and leveraging AI/ML.
Read the post on LinkedIn

Enabling Automated End-to-End Chromatographic Data Workflows and Accelerated Data Insights with ASM Vendor-Neutral Data Format at Fall 2024 Allotrope Connect in Boston

Merck experts present how the Allotrope Simple Model (ASM) automates chromatographic data workflows. By standardizing data, ASM improves scalability in data movement, transformation, and integration, enabling advanced visualizations and AI/ML pipeline support for innovative insights.
Read the post on LinkedIn

ZONTAL, a SciY company, is making in the Fairdata space

ZONTAL, a SciY company and Allotrope Foundation member, is making in the Fairdata space, particularly integrating and standardizing data from different chromatography Data Systems (CDS)
Read the post on LinkedIn

Enabling Automated End-to-End Chromatographic Data Workflows and Accelerated Data Insights with the Allotrope Simple Model (ASM) Vendor-Neutral Data Format

Bio-IT World Conference & Expo, April 2025 preliminary agenda, features a Merck presentation on Enabling Automated End-to-End Chromatographic Data Workflows and Accelerated Data Insights with the Allotrope Simple Model (ASM) Vendor-Neutral Data Format.
Read the preliminary agenda on Bio-IT World

Unlock Chromatography Data with FAIR Data Standards

ZONTAL enhances chromatography by integrating data from various Chromatography Data Systems (CDS) into a vendor-neutral format using Allotrope Foundation’s ASM. Supporting liquid chromatography and mass spectrometry workflows, ZONTAL enables organizations to compare methods and results, access predictive and prescriptive analytics, and streamline FAIR data.
Read about it at Link

How ASM connectors drive AI/ML to accelerate wet & dry lab workflows by Benchling at Fall 2024 Allotrope Connect in Boston

Benchling will provide an overview of how Allotrope data models are being used to automate instrument data capture, analytics & AI/ML to accelerate wet & dry lab workflows.
Read the post on LinkedIn

Unlocking Scalable Data and AI Power by Scitara at Fall 2024 Allotrope Connect in Boston

A strategy to unlock scalable data value will be presented by Scitara Corporation, focusing on leveraging a connectivity framework. The role of the Allotrope Simple Model (ASM) in enhancing data extraction will be discussed, along with the transformative impact of AI in laboratory environments.
Read the post on LinkedIn

Unlocking the Power of Scientific Data with Scitara DLX Streaming Capabilities

Scitara DLX leverages advanced streaming capabilities to help laboratories overcome challenges in data management and achieve FAIR principles (Findable, Accessible, Interoperable, Reusable). By automating workflows and transforming data into standardized formats like JSON, the platform enhances interoperability with support for standards like the Allotrope Simple Model (ASM), fostering a more connected and efficient laboratory environment.
Read the blog at Link and on LinkedIn

OpenChrom at Fall 2024 Allotrope Connect in Boston

Lablicate will be showcasing OpenChrom at the 2024 Allotrope Connect event. OpenChrom enables advanced data analysis for chromatography, spectrometry, and molecular biology.
Read the post on LinkedIn

Lablicate Supports Open Data Standards with Allotrope and OpenChrom

Lablicate supports open data standards like Allotrope ADF and ASM with OpenChrom!
Read the post on LinkedIn

2024 Fall Allotrope Connect event is hosted by Thermo Fisher Scientific

2024 Fall Allotrope Connect event is now open! Hosted by Thermo Fisher Scientific, the event will take place on November 19-20 at the Boston Long Wharf Marriott. Join members of the Allotrope Foundation and the wider scientific community to explore advancements in data standardization and insights within labs and manufacturing.
Read the post on LinkedIn

Reimagining the Future of Biopharmaceutical Digitalization

BioProcess International, an Informa Connect publication, featured an article covering a conference organized by the University College London (UCL) – Accenture Innovation Partnership and the UCL Future Targeted Healthcare Manufacturing (FTHM) Hub. The event emphasized the increasing digitalization in the biopharmaceutical industry to boost efficiency and product quality. It also discussed the interoperability challenges in systems like Electronic Laboratory Notebooks (ELNs), Laboratory Information Management Systems (LIMS), and Manufacturing Execution Systems (MES), highlighting the Allotrope framework as a vendor-driven solution for modular, standardized approaches.

The article further notes how AI and automation will strengthen quality-by-design (QbD) initiatives, ensuring consistent product quality and reducing risks. This marks a significant step toward Industry 4.0 with smart, agile operations.
Read the full article at Link and on LinkedIn

Be Open to Abstract Concepts such as Ontologies and Metadata Standards

Prof. Norbert Kockmann, from the Faculty of Bio and Chemical Engineering at TU Dortmund University, leads the "Apparatus Design" working group. Along with his team, Prof. Kockmann develops tools and training materials to support the documentation of research data, which are incorporated into the "NFDI4Cat" initiative. This initiative is part of the National Research Data Infrastructure (NFDI) and is focused on advancing the management of research data within the fields of catalysis and process engineering.

In a recent Q&A, Prof. Kockmann discusses the development and advantages of standardized vocabularies in scientific research. He emphasizes how the use of common vocabularies facilitates collaboration and data reuse across different disciplines. Additionally, TU Dortmund has acknowledged the critical role that ontologies and metadata standards play in the scientific landscape, further demonstrated by its decision to join the Allotrope Foundation, a global initiative that promotes the use of such frameworks.

For further insights from Prof. Kockmann, you can read the discussion (in German) at TU Dortmund and on LinkedIn

Xendat Data Deep Dive: Ontologies and Drug Discovery - Chemistry

Xendat Data & Analytics presents the role of ontologies in drug discovery and their transformative impact on chemistry. They brief how ontologies organize complex chemical data, making it findable, accessible, interoperable, and reusable (FAIR) for researchers globally. Highlighting ontologies like ChEBI, ChEMBL, and the Allotrope Foundation Ontology (AFO), they discuss how they are advancing drug discovery, environmental science, and chemical research.
Watch it on YouTube

MALDI-TOF MS Peaks

In a recent blog on Open Source Spectrometry, Lablicate indicated its plans to model a Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry peaks using the Allotrope Simple Model (ASM). This model will be applied to the Lablicate OpenChrom Allotrope Plugins, aiming to make Mass Spectrometry data more accessible in a JSON format.

Read the blog on Open Source Spectrometry or the related post on LinkedIn

OpenChrom Allotrope Plugins

A recent Lablicate blog describes the new developed OpenChrom Allotrope Plugins to support open standards in analytical chemistry. These plugins enable the use of the Allotrope Simple Model (ASM) and Allotrope Data Format (ADF) allowing seamless conversion and analysis of data across multiple formats, and ensuring long-term accessibility and compatibility for data-driven applications in science.
Read the entire blog at Link or the post on LinkedIn

OpenChrom Allotrope Plugins explained

Read the recent Lablicate post on LinkedIn where the OpenChrom Allotrope Plugins are explained

Data Centricity: The Key to Successful Digital Labs

Read the recent Zontal post on LinkedIn, where the Data centricity places data at the core of operations and decision-making. This means treating data as a key asset, ensuring it is self-describing, and using open formats like the Allotrope Data Format (ADF) from Allotrope Foundation for interoperability.

Generating knowledge graphs through text mining of catalysis research related literature

A recent work led by the department of Biochemical and Chemical Engineering, Laboratory of Equipment Design, TU Dortmund University, Germany, was published on the Royal Society of Chemistry journal.
The work highlights the importance of structured research data management in catalysis, guided by FAIR principles. It combines ontology learning and named entity recognition to automate the extraction and organization of key data into a machine-readable knowledge graph. The Allotrope Foundation Ontology (AFO) plays a central role as the primary ontology, facilitating the extension of knowledge graphs with precise definitions and relationships, thereby enhancing the usability and compatibility of catalysis research data.
Read the paper at Link or download a PDF version from Link

Introducing the 2024/Q2 Allotrope Release: New Solution NMR and Electrophoresis Models Plus More!

LinkedIn post introducing the 2024/Q2 Allotrope release:
• New Solution NMR model
• New Electrophoresis model
• New Chromatography Column model
• New Plate Reader Kinetics model
• Modularization updates
Read the post on LinkedIn

The landscape of ontologies in materials science and engineering: A survey and evaluation

The Karlsruhe Institute of Technology's Institute of Applied Informatics and Formal Description Methods has published a paper on arXiv analyzing 60 ontologies used in Materials Science and Engineering (MSE). This study evaluates and compares these ontologies, providing a comprehensive overview and quality metrics that have been lacking in previous surveys. The paper highlights the strengths and weaknesses of these ontologies, including those related to the Allotrope framework, to help experts select and incorporate suitable ontologies for their work.
Read the paper on arXiv

A Controlled Vocabulary and Taxonomy for the Submission of Quality Attributes for Therapeutic Proteins Solutions

Authored by members of the U.S. FDA's Center for Drug Evaluation and Research, this paper presents a controlled vocabulary and structured taxonomical naming approach for the quality attributes of therapeutic proteins. This systematic harmonized naming is essential for the successful implementation of structured data systems in regulatory submissions, addressing challenges posed by the lack of a standardized taxonomy. The approach supports emerging products and advanced technologies, aligning with the digital transformation known as Pharma 4.0 or Industry 4.0, and mentions various structured data approaches, including those by the Allotrope Foundation.
Read more at SpringerOpen or download at Link

Realizing the benefits of AI in Biopharma: Collaborative open source projects for data management

A recent Benchling blog emphasizes that for the biopharma industry to fully harness the benefits of AI, companies must collaborate to build the necessary data management functions.

The blog highlights several open-source software projects focused on data management, including:
• HELM (Hierarchical Editing Language for Macromolecules): A Pistoia Alliance project that enables the representation of a wide range of biomolecules. GitHub Link
• allotropy: A Python library developed by Benchling for converting instrument data into the Allotrope Simple Model (ASM). GitHub Link
• Nextflow: A workflow system for creating scalable, portable, and reproducible workflows. GitHub Link
Read the entire blog at Link
Read the post on LinkedIn

Agilent’s Environmental, Social, and Governance (ESG) Report: Advancing Great Science with Sustainable Solutions

Agilent published on July 2024 its 2023 Environmental, Social, and Governance (ESG) Report: Pursuing Advancing Great Science with Sustainable Solutions. It names Allotrope Foundation as one of the industry groups it is associated.

The report can be downloaded at Link

Digital Standards: A Path to Sustainable and Interoperable Chemical Data Exchange

A workshop led by International Union of Pure and Applied Chemistry (IUPAC), the International Chemical Identifier (InChI) Trust, and the Cambridge Crystallographic Data Center (CCDC) focused on developing sustainable and interoperable digital standards for chemical data exchange. It highlighted the need for machine-readable data, sustainable business models, and stakeholder engagement. Participants discussed existing standards and future strategies, aiming to foster collaboration and ensure the relevance and adoption of digital standards in chemistry. The dialogue also explored how digital standards could impact related disciplines and industries, especially in artificial intelligence and machine learning. They listed the Allotrope Data Framework for analytical data as one of the examined standards.
Read about the workshop on ResearchGate, Gruyter, or LinkedIn. Download at Link or the IUPAC Chemistry International July 2024 issue at Link

SLAM – A thin-client for interoperable annotation and biomedical signal handling

An article published on Science Direct introduces SLAM, a free and open-source software designed for managing complex biosignals, such as EEG. This software utilizes precise and interoperable annotations stored in an HDF5 file with RDF, inspired by the architecture of the Allotrope Data Format (ADF). This web-based tool addresses the challenge of diverse annotation protocols in multi-center medical environments, enabling high-performance I/O and data aggregation across different acquisition modalities. It facilitates the integration of biosignal data analysis within a medical context, leveraging machine learning for precise and reusable annotations.

The work was supported by the French Agence Nationale de la Recherche and the American Memorial Hospital Foundation (AMHF).
The article is available on Science Direct or for download at Link

Market Report: Biotechnology Instruments Market Size to Touch USD 132.80 Billion by 2033

According to a market report published in July 2024, the biotechnology instruments market, valued at over USD 90.06 billion in 2023, is projected to reach approximately USD 132.80 billion by 2033. This growth is driven by advancements in research and development, increasing demand for personalized medicine, and rising investments in the biotechnology sector. The report highlights Benchling's active role in the Allotrope Partner Network (APN) and their development of free, open-source converters to transform data into the Allotrope Simple Model (ASM) format, promoting industry standards.
Read about the report at: Towards Healthcare and BioSpace.com

Allotrope plugin for OpenChrom has been published

Allotrope ASM/ADF plugin for OpenChrom has been published. It offers file format conversion, data processing and archiving as well as special viewers for both Allotrope Data Format and Allotrope Simple Model to deep dive into the ontology. Huge thanks to the Allotrope Foundation for technical support and allowing our usual "free for students" with their proprietary technology as well.
View the post on LinkedIn

Technology Trends in Separation Science: Data Handling

A discussion on technology trends in separation science, focusing on "Data Handling", featured insights from leaders of prominent chromatography instrumentation companies (Agilent, Shimadzu, Thermo Fisher, and Waters). They addressed five questions:

What is currently the biggest problem in data management for chromatographers?
What is the future of data handling solutions for chromatographers?
What one recent development in “Big Data” is most important for chromatographers from a practical perspective?
What obstacles do you think stand in the way of chromatographers adopting new data solutions?
What was the biggest accomplishment or news in 2023-2024 for Data Handling?

The Allotrope Simple Model (ASM) was highlighted for its growing popularity and role in standardizing data formats in a vendor-neutral way.
Read the discussion on LCGC International and on LinkedIn

NFDI4Cat 2.0: International Partners

NFDI4Cat an initiative to shape the digital future of catalysis, funded by the German Research Foundation (DFG), published in a Letter of Intent its NFDI4Cat 2.0 goals and noted the Allotrope Foundation for partnership.

View the letter (page12) at Link

True Instrument Integration Requires More Standardization

Introducing BASF's evolution in instrument connection and why standardization with LADS/OPC-UA and the Allotrope Simple Model (ASM) is key to success. Don't miss this presentation, given at the 2024 Spring Allotrope Connect Workshop. View the post on LinkedIn

Unlocking the automation potential via open standards

Introducing BASF's motivation for adoption of the Allotrope Simple Models (ASM) with concrete use cases, as well the need for data quality for AI applications to be effective.

Don't miss this presentation, given at the 2024 Spring Allotrope Connect Workshop.

View the post on LinkedIn

Natural Language Processing-Based Extension of the Allotrope Foundation Ontology

Introducing the extension of the Allotrope Foundation Ontology (AFO) with new concepts derived from scientific literature was presented by was presented by TU Dortmund University at the 2024 Spring Allotrope Connect Workshop. Using Natural Language Processing (NLP)-based concept extraction, the ontology is expanded with new classes and relations. This approach facilitates the generation of knowledge graphs through NLP-assisted text mining, enabling the reuse of AFO entities and structured querying of the extracted knowledge.
Don't miss this presentation, given at the 2024 Spring Allotrope Connect Workshop.
View the post on LinkedIn

Lessons from Shape Therapeutics: How to harness AI for R&D success

Shape Therapeutics joined Benchling on BIO to talk about what it means to have AI-ready data, AI-enabled scientists, and how they’re approaching all of this at ShapeTX. Benchling's initiative with the Allotrope Foundation is a major step to support it.

The blog can be viewed at Link

View the post on LinkedIn

Pharmaceutical CMC ISA-88 Process Ontology

Introducing the pharmaceutical CMC process ontology, based on the ISA88/95 framework, to standardize lab and plant production recipes. It enhances digital technology transfers, integrates with execution systems, and captures structured process data for material lot tracking and advanced analytics. Explore the ontology current status, relationship with Allotrope Framework Ontology (AFO), and sample data applications.
Don't miss this presentation, given at the 2024 Spring Allotrope Connect Workshop.
View the post on LinkedIn: Post-1 Post-2

Pharma 4.0 Market: Global Industry Assessment & Forecast

Vantage Market Research published a Pharma 4.0 market forecast for the years 2024 – 2032. It mentions the Allotrope Foundation work to create an open source format and enables data interoperability and contextualization for the pharmaceutical manufacturing.

View the highlights of this market research at Link

Resetting R&D for AI: Biotech’s Path to AI-Ready Data & AI-Enabled Scientists

ShapeTX joined Benchling on BIO to talk about what it means to have AI-ready data, AI-enabled scientists, and how they’re approaching all of this at ShapeTX. The discussion mentions Benchling's initiative with the Allotrope Foundation as the right direction for the industry to support those goals.
Watch the webinar on BIO at Link
View the post on LinkedIn

AFO and IDMP-O; showcasing the federation of ontologies

AFO and IDMP-O; showcasing the federation of ontologies to facilitate broad end-to-end adoption for real-world problems spanning multiple data domains, and see how the solution is realized through concrete implementation.

Don't miss this presentation, given at the 2024 Spring Allotrope Connect Workshop.

View the post on LinkedIn: Post-1, Post-2

Using ChatGPT for automatic asset onboarding for Industrial IoT projects

How generative AI can potentially automate asset modeling, which remains a time-consuming aspect of Industrial IoT projects, and followed a showcase of how OPC-UA based Laboratory Agnostic Device Standard (LADS) and the Allotrope Simple Model (ASM) enable seamless integration and data accessibility across diverse laboratory devices.
Don't miss this Microsoft presentation, given at the 2024 Spring Allotrope Connect Workshop.
View the post on LinkedIn

Combining standardized lab instrument communication with standardized data formats is now a reality

Using OPC-UA based Laboratory Agnostic Device Standard (LADS) and the Allotrope Simple Model (ASM), we can achieve seamless integration and data accessibility across diverse laboratory devices. Don't miss this presentation, given at the 2024 Spring Allotrope Connect Workshop.
View the post on LinkedIn

Digital Evolution: Novo Nordisk's Shift to Ontology-Based Data Management

Bringing OPC-UA and Allotrope ASM together to enable real automation in the analytical lab

Bringing OPC-UA (communication standard) and Allotrope ASM (data format standard) together to enable real automation in the analytical lab, was presented at the 2024 Spring Allotrope Connect Workshop.

View the post on LinkedIn

Unleashing lab connectivity presentation at the 2024 Spring Allotrope Connect was live at LADShack

Agilent Technologies presentation titled "LADS and ASM Revolutionizing Seamless Lab Integration and Data Flow" at the 2024 Spring Allotrope Connect workshop was streamed simultaneously at the LADS OPC-UA LADShack event.

View the post on LinkedIn

Lablicate shared their latest advancements using Allotrope Foundation data models

During the 2024 Spring Allotrope Connect, Lablicate shared the latest advancements using Allotrope Foundation data models in OpenChrom.

View the post on LinkedIn

ZONTAL's Summary of the 2024 Spring Allotrope Connect

ZONTAL's brief overview and key takeaways from the 2024 Spring Allotrope Connect can be viewed in the following LinkedIn posts: Post-1, Post-2

Growing value of data standardization: Allotrope Foundation Connect Workshop Proceedings

Drug Discovery Today, an online magazine of ScienceDirect published on May 2024 an article that discusses the recent Allotrope Foundation (AF) Connect Workshops (2021–2023). It showcased some of the latest advancements in data standardization for analytical data in the pharmaceutical industry. The article was written by Henning Kayser (Bayer) and Miu-Ling Lau (Merck).

The article is available at this Link or at PubMed Link

How to jumpstart innovation in R&D? Biotech must solve the instrument connectivity challenge

Benchling published a white paper that discusses the lab instrumentation connectivity challenges and proposed solutions with a forward-looking data strategy, making it ready for incorporation of AI, ML and Large language models (LLMs). It proposes the use of the Allotrope Simple Model (ASM) to allow the use of standardize data and prevent vendor lock-in by mapping all instrument output to ASM, and making the converter codes open source and freely available on GitHub.
The white paper can be downloaded at Link

An Introduction to Scientific Data Standards

propharma a Research Consulting Organization (RCO), published "An Introduction to Scientific Data Standards". It mentions the work done by the Pistoia Alliance and the Allotrope Foundation to support the FAIR principles for data
Standardization and lists several data file format standards, including the Allotrope Data Format (ADF).
The brief flyer is available at Link

Exciting news for the Allotrope community! The 2024/Q1 release is here, featuring new Spectrophotometry and Multi Analyte Profiling models, and much more!

Some of the release highlights include:
* New Spectrophotometry model for UV-VIS-NIR spectrophotometers.
* New Multi Analyte profiling model for immunological assays.
* Additional support for external Chromatography detectors
* Modularization updates to existing models like Tensile Test, Stirring, and more.

Read about it on LinkedIn

Join the Allotrope Foundation on an Exciting Journey to Standardize Flow Cytometry Data Analysis!

The Allotrope Foundation, lauded for its mission of breaking silos in data analysis, shapes the future of Flow Cytometry analysis with its new working group. With expert minds from Genentech, Merck, GSK, and others, it strives to create a modular standard bridging across various techniques and domains. Read about it on LinkedIn

BASF Digital Solutions hosts the Allotrope Foundation's Allotrope Connect Spring 2024 event in Ludwigshafen, Germany

BASF Digital Solutions hosts the Allotrope Foundation's Allotrope Connect Spring 2024 event in Ludwigshafen, Germany.
Experts from industry leading companies, solution providers and instrument manufacturers will join up to discuss on and advance the standardization of data in laboratories.
Stay tuned for more information about how to register for the event! Link

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

ZONTAL team review in a blog some of the highlights from the article “The Rise of the Allotrope Simple Model” that was published in Drug Discovery Today, where ZONTAL Data Scientists discuss the details of the new format and outline a path to successful adoption.

View a related LinkedIn post about ASM revolutionizing the data exchange in the lab at Link

Pharmaceutical CMC process ontology Community of Interest Meeting

The Pharmaceutical CMC process ontology is a Pistoia project aims to build the appropriate ontology based on the ISA88/95 framework to standardize laboratory and plant production process recipes to establish standardized definitions, facilitate digital technology transfers, and integration with execution systems in order to capture structured process data for material lot genealogy tracking, streamlined technology transfers, and advanced process analytics, thereby enhancing efficiency and transparency throughout the pharmaceutical production lifecycle. It integrates the Allotrope Foundation Ontology (AFO).
Listen to the community of interest recording at Link

"A lot is happening in terms of communication standardization and data formats next to the Rhine river in Germany this year!"

Matthias Schuh from Essentim posted on LinkedIn the fact that the Allotrope 2024 Spring Connect Workshop at BASF is happening simultaneity with Spectaris LADSHack next to the Rhine river in Germany.

Rise of the Allotrope Simple Model: update from 2023 Fall Allotrope Connect

Drug Discovery Today, an online magazine of ScienceDirect, published on March 2024 an article that presents the proceedings from the 2023 Fall Allotrope Connect conference and describes the technical and organizational developments in recent years. In particular, it describes the Allotrope Simple Model (ASM) that was developed to broaden the adoption.

The article is available at this Link or at PubMed Link

Lablicate Demonstrated OpenChrome with the Allotrope Simple Model

As part of the opening of FutureLab.NRW at IUTA, Lablicate demonstrated with OpenChrom the advantages of open standards such as the Allotrope Simple Model (ASM). Link

Inside the Minds of SLAS Scientists: Bridging the Gap in Data Standardization

New Matter, the official Society for Laboratory Automation and Screening (SLAS) podcasts site, published on Feb 2024 an interview with Glenwood Barbee, product marketer for automation and analytics at Benching. Glenwood talks about Benchling Connect, a platform designed to accelerate connectivity and automation in the lab.
He discusses the goal to make the platform natively compatible with an industry standard and the case of FAIR data, where they started by using the Allotrope Simple model (ASM) as well as building an open source repository of instruments data converters to accelerate the adoption of the data standard.
The podcast and the transcript are available at this Link

Delivering a Standards Based Framework that Enables the Lab of the Future: Interoperability & Connectivity

Joseph Pease, Senior Director at Genentech, will be delivering a presentation titled "Delivering a Standards Based Framework that Enables the Lab of the Future: Interoperability & Connectivity" on behalf of the Allotrope Foundation at the Lab of the Future USA event in Boston, MA. As one of the founding board members of Allotrope Foundation, Joseph will highlight the power of the framework, especially Allotrope Simple Models (ASM). This insightful session will explore the evolution of the Allotrope Foundation, components of the framework and how they enable frictionless data sharing, including AI/ML!, and real-world Examples of the framework in action.

Be sure to catch this insightful presentation on the event's second day, March 12th, 2024, from 14:25 to 14:35 ET: Link

allotropy: Python package for converting instrument data into ASM is on PyPI

allotropy, an open-source Python library for converting instrument data into the Allotrope Simple Model (ASM) is available on the Python Package Index (PyPI) repository at https://pypi.org/project/allotropy/,

The objective of this library is to read text or Excel based instrument software output and return a JSON representation that conforms to the published ASM schema.

Panel Discussion: Leaders in Biotech and Engineering

Women Who Code, a global organization with the vision of "Empowering diverse women to excel in technology careers", conducted a Panel Discussion on "Leaders in Biotech and Engineering". Alyss Weissglass, Software Engineer at Benchling, talks about the important work by Allotrope professionals from across the biotech sphere who are dedicated to standardizing the data formats that comes off of lab machines, and how Benchling has committed to building a suite of open source connectors to adapt into the single unified Allotrope format.

The panel discussion is available at this Link and on YouTube.

5 changes underway for R&D IT shifting to advanced modalities and biologics

pharmaphorum, an online healthcare and pharmaceutical industry news site, published on January 2024, an article that discusses the shift to new and advance modalities in the lab, how bringing biologics from the lab to patients requires more complex data, and greater need for collaboration across specializations. It requires R&D IT to evolve the systems and processes of the lab.

The article mentions the publicly available data standards for lab instruments using the Allotrope Simple Model (ASM), as well as the recent Benchling launched of Connect, which automates instrument data capture and management using a unique open source approach, mapping all instrument output to the ASM, and making the converter codes open source and freely available on GitHub.

The article is available at this link.

Pharmaceutical CMC Process Ontology

Pistoia Alliance updated its project plans on "Pharmaceutical CMC Process Ontology". It outlines an advanced semantic architectural design for a Process Ontology, featuring seamless integration with the established Product (IDMP-O), Analytical (AFO, Allotrope Foundation Ontology), and Unit of Measure (QUDT) ontologies.

Ontologies4Cat: Investigating the Landscape of Ontologies for Catalysis Research Data Management

The Journal of Cheminformatics is reviewing for publication a paper, written by the Laboratory of Equipment Design, Faculty of Biochemical and Chemical Engineering, TU-Dortmund University, that investigates the landscape of ontologies for catalysis research data management. It demonstrates the mapping of ontology classes with Allotrope Foundation Ontology (AFO).

A review of the paper is available at link.

Data Centricity: Key for the Successful Digital Journey towards a Digital Lab

Zontal posted on January 2024, an article that discusses how data centricity is important for the operations and decision-making processes with the digital lab evolution. It mentions the Allotrope Data Format (ADF) and the Allotrope Simple Model (ASM), as non-proprietary data standards for laboratories which are crucial in the digital lab.

The article is available at this link.

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2023 - Allotrope in the News

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Biopharma Industry Struggles to Embrace IoT, but Collaboration and Investment Offer a Path Forward

itsforhome, an online news site on technology products and solutions, published on December 2023, an article about the biopharmaceutical industry that has been slower to adopt the Internet of Things (IoT) compared to other industries. It discusses a path to move forward. It mentions Allotrope as one of the efforts to standardize data in order to facilitate connectivity.
The article is available at this link.

Biopharma Yet to Fully Benefit from the Internet of Things

Genetic Engineering & Biotechnology News (GEN) published on December 2023, an article that discusses the reality that drug makers are yet to benefit by connecting manufacturing tech through Internet of Things (IoT). It mentions Allotrope as one of the efforts to standardize data in order to facilitate connectivity.
The article is available at this link, and the DNS Africa Resource Centre (DARC) at this link.

The Challenges and Opportunities of Implementing IoT in Biopharmaceutical Manufacturing

ISP.PAGE an online technology and connectivity news, posted on December 2023, an article that discusses the challenges and opportunities of implementing Internet of Things (IoT) in biopharmaceutical manufacturing. It mentions Allotrope as one of the efforts to standardize data in order to facilitate connectivity.

The article is available at this link.

How Benchling is powering an open source approach to data standardization with Allotrope Benchling

Benchling posted a blog on December 2023, that describes their strategy for powering data standardization in the lab, based on the Allotrope Simple Model (ASM). It summarizes some of the hurdles they have encountered along the way, how they are working to make open source a reality, and the implementation of Benchling Connect which is a service for exchanging instruments data.

The blog is available at this link.

The Benchling Connect datasheet can be downloaded at this link.

The LinkedIn post is available at this link.

Proprietary data formats are killing your AI initiative

TetraScience posted a blog on December 2023, that describes how organizations need to dramatically simplify data and metadata harmonization efforts before they can start realizing the tremendous potential of AI in science. It mentions the Allotrope Simple Model (ASM) as a way to standardize the structure of instrument data.

The blog is available at this link.

Discover the Allotrope Framework for Modeling Information

Toolify.ai an online directory for AI tools, published on December 2023 an article that describes how the Allotrope Framework provides a comprehensive solution for modeling information in various domains.
The article is available at this link.

Words we lived by in 2023: A year in review at Benchling

Benchling posted a blog on December 2023, that reviews the yearly effort to bring the scientific data from lab instruments and systems together into one platform for end-to-end data management and analysis. It describes the launch of Benchling Connect and the alignment with the Allotrope Simple Model (ASM).
The blog is available at this link.

5 changes underway for R&D IT shifting to biologics

Benchling posted a blog on December 2023, that discusses how bringing biologics from the lab to patients requires more complex data, and greater need for collaboration across specializations. It requires R&D IT to evolve the systems and processes of the lab.
The blog mentions the publicly available data standards for lab instruments using the Allotrope Simple Model (ASM), as well as the recent Benchling launched of Connect, which automates instrument data capture and management using a unique open source approach, mapping all instrument output to the ASM, and making the converter codes open source and freely available on GitHub.
The blog is available at this link.

Interoperability of Clinical Data from the VODANBR Project to FHIR Standard

UNIRIO Central Library - Federal University of the State of Rio de Janeiro, published a paper that discuses semantic interoperability in the field of clinical data. It presents the identification and analysis of Knowledge Organization Systems used by the Virus Outbreak Data Network project, Brazil. It lists the AFO as one of the ontologies that make up the WHO COVID-19 semantic model.
The paper is available (in Portuguese) for download at link.

‘Industry first’ for instant secure transfer of analytical methods and results data

The Chemical Industry Journal published an article about the cloud-based collaborative tool now enables the instant transfer and overlaying of analytical methods and results data in a single platform, and between different instrument hardware and software vendors. The proof of concept has been successfully implemented at GSK and will be deployed to the global open-access non-GMP fleet.
The Pistoia Alliance collaborative Methods Hub project, is a digital tool that enables the instant transfer and overlaying of analytical methods. The alliance collaborated with Allotrope Foundation, using the Allotrope Framework technology stack to ensure interoperability.
The article is available at this link.

Five Necessary Elements for Integrating Lab Systems

Lab Manager an online publication focused on aspects of running a lab, posted on November 2023 an article that discusses the elements necessary for integration of the analytical lab systems:

File format standards
Interconnect standards of messaging and exchange data standards
Modular systems with easy integration blocks
Stable operating system environment
User community commitment

It mentions the Allotrope Foundation as pharmaceutical companies' initiative that may provide some direction.
The article is available at: https://www.labmanager.com/five-necessary-elements-for-integrating-lab-systems-where-we-are-vs-where-we-need-to-be-15941

Allotrope Connect

Industrial internet of things: What does it mean for the bioprocess industries?

Biochemical Engineering Journal published on October 2023 a paper that analyzes the role and status of Industrial Internet of Things (IIoT) in the bioprocess industries. The paper mentions the Allotrope Foundation as a platform that offers a standardized framework to obtain uniform data and minimize data loss, as well as facilitate connectivity.

The paper is available at: https://www.sciencedirect.com/science/article/pii/S1369703X23003170

Lab AI: Instrument Integration

Published on Medium on October 2023, the article investigates a way to capture serial lab device data directly into a browser web page. It also suggests converting the data to a standard Allotrope ASM JSON format for easy digital lab exchange of information. Part 2 of the article describes one possible end-to-end solution to create an Allotrope ASM JSON data object for a simple lab weighing task.
The article is available at: https://medium.com/@colin.rebello/lab-ai-instrument-integration-78c0b4047ff4

Part 2 of the article is available at: https://medium.com/@colin.rebello/lab-ai-instrument-integration-2-ee62fae5fa98

Part 2 of the article is also available on LinkedIn

Benchling Connect: Tackling Lab Instrument Connectivity and Data Management with New Open Standards

SAN FRANCISCO, Sept. 19, 2023 /PRNewswire/.

Benchling unveiled its new platform for lab instrument connectivity and data management, Benchling Connect. With Connect, Benchling confronts industry-wide challenges with proliferation of proprietary instrument data models and vendor lock-in by mapping all instrument output to the Allotrope Simple Model (ASM), and making the converter codes open source and freely available on GitHub.

The press release is available at: https://www.prnewswire.com/news-releases/introducing-benchling-connect-tackling-lab-instrument-connectivity-and-data-management-with-new-open-standards-and-a-flexible-platform-301931715.html
Benchling's blog: https://www.benchling.com/blog/benchling-connect
"allotropy", open source, Python library repository on GitHub: https://github.com/Benchling-Open-Source/allotropy
LinkedIn post: https://www.linkedin.com/posts/benchling_benchlingconnect-github-benchlingconnect-activity-7109907679673790468-bGoC
Product Brief on the data conversion to ASM: here

GSK and Pistoia Alliance announce laboratory tech to improve reproducibility

Manufacturing Chemist (https://www.manufacturingchemist.com) an online publication platform published on September 2023 an article that describes the Pistoia Alliance collaborative Methods Hub project, a digital tool that enables the instant transfer and overlaying of analytical methods. The alliance collaborated with Allotrope Foundation, using the Allotrope Framework technology stack to ensure interoperability.
The article is available at: https://www.manufacturingchemist.com/news/article_page/GSK_and_Pistoia_Alliance_announce_laboratory_tech_to_improve_reproducibility/211308

Allotrope Foundation Releases a Vendor Agnostic and an Industry Interoperable Data Model for Laboratory Walk-up Liquid Chromatography/Mass Spectrometry Instrumentation

WASHINGTON (PRNewswire-PRWeb) Sept. 07, 2023.

Developed by members of the Allotrope scientific community, the Walk-up Liquid Chromatography/Mass Spectrometry model leverages Allotrope's Simple Model technology to enable easy integration with downstream analytical applications as well as the collection and conversion of scientific information from a broad range of laboratory instruments into a unified human-readable FAIR data format.

The press release is available at: https://www.prweb.com/releases/allotrope-foundation-releases-a-vendor-agnostic-and-an-industry-interoperable-data-model-for-laboratory-walk-up-liquid-chromatographymass-spectrometry-instrumentation-301921447.html

Introduction to Pharmaceutical Data Items and Their Structure

Astrix, a company dedicated digital transformation, published on September 2023, an article that discusses the structuring of data used in pharmaceutical reporting and the motivation in reduction of errors in Chemistry, Manufacturing, and Controls (CMC) reporting. It mentions the Allotrope Foundation work to standardize ontologies.

The article is available at: https://astrixinc.com/introduction-to-pharmaceutical-data-items-and-their-structure/

Creating Data in Allotrope® Simple Model (ASM) at scale

TetraScience, a member of the Allotrope Partner Network (APN) has published a fact sheet describing how their JSON-based Intermediate Data Schema (IDS) can be used to transform your data into the ASM.

Agilent’s Environmental, Social, and Governance (ESG) Report: Pursuing ESG objectives while advancing sustainability for our customers

Agilent published on July 2023 its 2022 Environmental, Social, and Governance (ESG) Report: Pursuing ESG objectives while advancing sustainability for our customers. It names Allotrope Foundation as one of the industry groups it collaborates to advance innovation
The report can be downloaded at: https://www.agilent.com/about/esg/en/2022-agilent-esg-report.pdf

6 Key Areas for the Laboratory of the Future - The Evolution of Laboratories

LABOR PRAXIS (Laboratory Practice) an online German specialist medium for laboratories and analytics, published on July 2023, a guest article that points to six key areas for the laboratory of the future. It mentions Allotrope Foundation as one of the digital standards to improve communication by exchanging homogenized data.

The article can be translated by the web browser and is available at: https://www.laborpraxis.vogel.de/labor-der-zukunft-6-schluesselbereiche-a-5defc484bba04df74fdc93bc0d9efcd8/

Using Paraphrasers to Detect Duplicities in Ontologies

A research team from the faculty of Information Technology, Czech Technical University, the faculty of Biochemical and Chemical Engineering at TU Dortmund University, and the Institute of Computer Science, Czech Academy of Sciences, published a paper on scitepress, a digital library for science and technology publications, that presents a machine-learning-based approach to detect duplicities in ontologies. An experimental validation was performed with the Allotrope Foundation Ontology (AFO).

The paper is available for download at: link.

Ontology extension with NLP-based concept extraction for domain experts in catalytic sciences

SpringerLink an online publication of Springer Nature, published on July 2023 an article that presents a processing workflow for automatic ontology extension with NLP-based concept extraction for domain experts in catalytic sciences. The method was exercised using the Allotrope Foundation Ontology (AFO). It was developed at the Laboratory of Equipment Design, Faculty of Biochemical and Chemical Engineering, TU-Dortmund University, in Germany.

The article is available at: https://link.springer.com/article/10.1007/s10115-023-01919-1 and also https://www.researchsquare.com/article/rs-2457909/v1

Improving protein therapeutic development through cloud-based data integration

SLAS Technology, an online journal covering topics that reveal how scientists adapt technological advancements for life sciences exploration and experimentation in biomedical research and development, published on July 2023 an article that presents how automated cloud-based data capture and processing are key for pharmaceutical digital evolution. The article presents an implementation with qPCR methods. It mentions the Allotrope Foundation ontologies and format as an optional standard for the instrument data.

The article is available at: https://slas-technology.org/article/S2472-6303(23)00046-8/fulltext

Don't hold back lab digital transformation

pharmaphorum, an online healthcare and pharmaceutical industry news site, published on July 2023 a discussion with Mike Tarselli, the chief scientific and knowledge officer at TetraScience, that analyzes why so many labs are behind the times, and what can be done to bring them up to speed. The discussion mentions the work toward data interoperability done by Allotrope.

The article is available at: https://pharmaphorum.com/digital/dont-hold-back-lab-digital-transformation

Current challenges and recent advances on the path towards continuous biomanufacturing

Members of NIST, published a paper that discusses the challenges and recent advances in the adoption of continuous biomanufacturing compared to traditional batch manufacturing. It mentions the Allotrope framework for analytical measurements in laboratories and the Allotrope Foundation Ontology (AFO) that describes analytical processes together with a data model to enable interoperability.

Which challenges in the laboratory are solved with data standards?

Adesso Group, a large German IT service provider, published on June 2023 an article which discusses "Which challenges in the laboratory are solved with data standards?" It summarizes the principles to ensure data integrity and mentions the standardization work done by Allotrope.

The article is available at: https://www.adesso.de/de/news/blog/welche-herausforderungen-im-labor-werden-mit-datenstandards-geloest.jsp

Benchling Creates Open Source Library of Lab Instrument Data Converters

SAN FRANCISCO, May 16, 2023 (Announced at the Bio-IT World Conference).

Benchling partners with Allotrope, backing industry standards and making library of open source industry data converters freely available to the scientific community. Benchling is contributing to industry standards as an active member of the Allotrope Foundation Partner Network (APN) and is also creating a library of open source converters that format instrument-generated data to the Allotrope Simple Model (ASM) standard to help organizations to put these standards into practice.

The press release is available at: https://www.benchling.com/news/benchling-open-source-library-lab-instrument-data-converters
The LinkedIn post is available at: https://www.linkedin.com/posts/benchling_benchling-creates-open-source-library-of-activity-7064195283236048896-xdU6
An article on Scientific Computing World is available at: https://www.scientific-computing.com/press-releases/eln-provider-creates-open-source-library-laboratory-instrument-data-converters
An article on Laboratory Talk is available at: https://laboratorytalk.com/article/2093440/lab-roundup-22-may-data-conversion-dna-synthesis-bbb-preeclampsia-testing-and-more
A summary on BioIT World is available at: https://www.bio-itworld.com/news/2023/05/24/dna-printing-bioengineered-kidney-constructs-in-space-revvity-s-big-pharma-agreements-more

Opening Panel: Mastering the Data Quality and Interoperability Pain Point.

Dr. Gang Xue, Allotrope Board member, representing Johnson & Johnson, discusses data quality and interoperability and how the efforts at Allotrope to standardize terminology and ontology, enables meaningful data aggregation and harmonization.

The panel discussion takes place at a RE•WORK event that brings together the latest technological advancements as well as practical examples to apply AI to solve challenges in business and society: Link

Data Description & Annotation: Metadata and Minimum Information

The NFDI4chem project for Knowledge Base, discusses within the topic of Data description and Annotation, the need for Minimum Information for Chemical Investigations. It mentions the Allotrope Data Format (ADF) as a format with corresponding ontologies or controlled vocabularies: Link

The Pistoia Alliance welcomes the news that the Allotrope Foundation has made its interoperable laboratory data standards available to all

February 2023.

The Pistoia Alliance welcomes the news that the Allotrope Foundation has made its interoperable laboratory data standards available to all, and fully supports open collaboration and data standardization across the scientific and life sciences ecosystem.

The LinkedIn post is available at: https://www.linkedin.com/posts/pistoia-alliance-inc-_allotrope-foundation-further-expands-access-activity-7033411188713496577-5qcW

Allotrope Foundation Further Expands Access to Interoperable Laboratory Data Standards with Public JSON-based Analytical Data Models

WASHINGTON (PRWEB) FEBRUARY 08, 2023.

The Allotrope Simple Models (ASMs) enable the collection and conversion of scientific information from a broad range of laboratory instruments into a unified human-readable FAIR data format.

The press release is available at: http://www.prweb.com/releases/2023/2/prweb19153189.htm

Text-to-Ontology Mapping via Natural Language Processing with Application to Search for Relevant Ontologies in Catalysis

Multidisciplinary Digital Publishing Institute (MDPI), a publisher of open-access scientific journals, published a research paper that presents a machine-learning based approach to text-to-ontology mapping. The research performs an empirical validation in catalysis using the Allotrope Foundation Ontology (AFO).
The paper is available at link.

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2022 - Allotrope in the News

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Lab Interoperability with DLX using ASM-JSON Format

A new whitepaper written by Daniel DeAlmeida, Scitara’s Head of Product Management, was published on November 2022. The paper discusses the language of automated science. It provides the advantages of using Scitara DLX’s ability to provide data mobility and transform data in flight in combination with the Allotrope’s ASM for the structure of instrument data. By using this mechanism, result data can be automatically standardized before storage in data lakes without the need of further interpretation.

The paper is available at: https://scitara.com/allotrope/

Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening

A new project paper was published in ChemRxiv on September 2022. The paper named "Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening", presents an open-source Python project called MOCCA (Multivariate Online Contextual Chromatographic Analysis) for the analysis of open-format HPLC–DAD (photodiode array detector) raw data.

The project includes the use of the Allotrope Framework as well as a Python library that was developed by the HDF5 Group and named h5ld (It enables to read the ADF file Data Description using Python https://github.com/HDFGroup/h5ld).

The paper is available at: https://chemrxiv.org/engage/chemrxiv/article-details/6310f9f9bc257bf6a0d7e5a0

MOCCA documentation is available at: https://mocca.readthedocs.io

The article is also available on the ACS Publications at: https://pubs.acs.org/doi/full/10.1021/acscentsci.2c01042

Trends and Developments in Data Handling 2022: Key trends and developments in data handling according to selected panelists from the chromatography sector

A selected group of panelists from the chromatography sector answers a set of questions on The Column, on October 2022 and discusses: "Trends and Developments in Data Handling 2022."

The panel answers questions on data management and handling solutions for chromatographers, as well as the importance of recent developments in “Big Data” and others. Allotrope Foundation is referenced as an initiative to address some of the challenges.

The discussion is available at:

https://cdn.sanity.io/files/0vv8moc6/chroma/ca19542d443eb5c447eb6515828f72b412180a3e.pdf/Vol18_Issue10_TheColumn_October2022_Europe%26Asia.pdf

Text-to-Ontology mapping via natural language processing models: Attempts to solve text-to-ontology mapping challenges

A new research paper was published in the CEUR-WS.org which is an online publication service for editors of scientific proceedings, on September 2022: "Text-to-Ontology Mapping via Natural Language Processing Models." The paper presents the work in attempting to solve text-to-ontology mapping challenges and mentions the Allotrope Foundation Ontology as one of the ontologies that were used during the experiments. The paper is available at:

http://ceur-ws.org/Vol-3226/paper3.pdf

Data format standards in analytical chemistry

The Karlsruhe Institute of Technology (KIT), a research university in Germany, published a paper that summarizes the different data format standards that are available in analytical chemistry. It names Allotrope Foundation and the related products as one of the standardization efforts and bodies in chemistry.

The paper is available at the following link.

Details can be found at: link.

Digitalization of paper-based processes against standardized ontologies: Project digitizes sharing of data to support machine learning and boost cyber resilience

A new article was published in the R&D World Magazine on June 2022: "The Pistoia Alliance is announcing that it has successfully completed a proof of concept (PoC) on the digital transfer via cloud of analytical High Performance Liquid Chromatography (HPLC) methods, proving it is possible to move analytical methods securely between two different vendors and Chromatography Data Systems (CDS) vendors with ease...The Pistoia Alliance collaborated with the Allotrope Foundation, using the Allotrope Framework technology stack to ensure interoperability." The article is available at https://www.rdworldonline.com/pistoia-alliance-project-digitizes-sharing-of-analytical-methods-data-to-support-machine-learning-and-boost-cyber-resilience/

Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic

A new article was published in the Journal of Biomedical Semantics on April 2022: “Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic”. It was written by a team in the Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. The article discusses the fragmentation of health data that is not interoperable for analysis with the various heterogeneous information systems that are used in hospitals. It suggests applying the Findable, Accessible, Interoperable and Reusable (FAIR) principles. As part of the suggested metadata modelling, it references and uses properties from the Allotrope Foundation Ontology (AFO). The article can be downloaded freely from the Journal of Biomedical Semantics publications at: https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-022-00263-7.pdf

American Chemical Society: Now Is the Time to Build a National Data Ecosystem for Materials Science and Chemistry Research Data

A new article was published in ACS Omega on April 2022: “Now Is the Time to Build a National Data Ecosystem for Materials Science and Chemistry Research Data”. The article makes a viewpoint about the urgent need of a long-term solution in the United States for data in chemistry and materials. It is giving the Allotrope Foundation as an example in the pharmaceutical industry. The article can be downloaded freely from the ACS Omega publications at: https://pubs.acs.org/doi/pdf/10.1021/acsomega.2c00905

From Platform to Knowledge Graph: Evolution of Laboratory Automation

The University of Cambridge (The department of Chemical Engineering and Biotechnology and Cambridge Centre for Advanced Research and Education in Singapore – CARES ), an Allotrope APN member, recently published an extensive paper: "From Platform to Knowledge Graph: Evolution of Laboratory Automation". The paper references the Allotrope products in several cases. It can be downloaded freely from the American Chemical Society publication website at https://pubs.acs.org/doi/10.1021/jacsau.1c00438

Methods Database PoC: Fully Automated and Interoperable Import and Export of HPLC-UV Methods

In its April 2022 newsletter, the Pistoia Alliance published that it has successfully completed a PoC on the digital transfer of analytical HPLC-UV methods between two different Chromatographic Data Systems (CDS) based on a data standard and ontology for semantic representation of the method parameters along with adapters allowing for seamless transfer of analytical method information.

The work started in 2019 when Pistoia Alliance, jointly with the Allotrope Foundation, built a data model for HPLC-UV method parameters (the ‘Methods Database’). Further information is available at https://www.pistoiaalliance.org/methods/april-2022-methods-database-hplc-uv-methods/

Automation & Control Trends: The Digitalization Dozen

Automation.com a subsidiary of ISA, the International Society of Automation published a special 2021 summary report and analysis on "Automation & Control Trends: The Digitalization Dozen"

Allotrope work is mentioned under the 5th trend "Open Standards: Essential for Innovation". The report can be downloaded from the Automation.com website at

https://www.automation.com/getmedia/c27f055a-02f7-4a98-8d09-b61871e42bda/Acom-Trends-2021-Final.pdf?ext=.pdf

Nature Chemistry: Making the collective knowledge of chemistry open and machine actionable

New article was published in Nature Chemistry in April 2022: "Making the collective knowledge of chemistry open and machine actionable”. The article mentions the effort spreadheaded by the pharmaceutical industry to develop a unified data model where the Allotrope data format is mentioned.

The article can be downloaded freely from the Nature Chemistry website at

https://www.nature.com/articles/s41557-022-00910-7.pdf

Data integrity within the biopharmaceutical sector in the era of Industry 4.0

The Biotechnology Journal published a paper that outlines how Data Integrity (DI) in the highly regulated biopharmaceutical sector is of paramount importance to ensure decisions on meeting product specifications are accurate and hence assure patient safety and product quality. The paper aims to identify DI risks and mitigation strategies in biopharmaceutical manufacturing facilities as the sector moves towards Industry 4.0. It mentions the Allotrope solution that uses a standard data framework to facilitate the storage, as well as use and integration of analytical data into a single file regardless of the data complexity to help avoid data loss and misinterpretation risks.

The article can be downloaded freely from the Wiley online library at

https://onlinelibrary.wiley.com/doi/full/10.1002/biot.202100609

NFDI4chem: Analysis of Chemical Ontologies

The NFDI4chem is an initiative to build an open and FAIR infrastructure for research data management in chemistry. It is funded by the German Research Foundation – DFG. An analysis of chemical ontologies was published where the comprehensive coverage of the Allotrope Foundation Ontology - AFO is demonstrated in the graphical chart.

The analysis can be found at

https://www.degruyter.com/document/doi/10.1515/pac-2021-2007/html?lang=en

Research Ideas and Outcomes Journal: Towards a National Research Data Infrastructure for Chemistry in Germany

The Research Ideas and Outcomes Journal published a grant proposal that describes the vision of the NFDI4chem initiative to digitize all key steps in chemical research. Part of its strategy is to develop standards and interfaces for data exchange in cooperation with organizations such as Allotrope Foundation. The grant proposal can be downloaded freely from the Research Ideas and Outcomes Journal at

https://riojournal.com/article/55852/download/pdf/

Delivering Digital Transformation with Self-reporting Data Assets

SpringerLink an online publication of Springer Nature, published in 2022 a paper that review the current challenges for the digital transformation of the pharma enterprise and offer a solution in form of a data centric architecture powered by a digital hub and Self-reporting data assets (SRDAs)

The paper can be downloaded from https://link.springer.com/chapter/10.1007/978-3-030-89906-6_62

Self-reporting data assets and their representation in the pharmaceutical industry

Drug Discovery Today an online magazine of ScienceDirect, published in January 2022 a paper that introduce the concept of self-reporting data assets (SRDAs), which preserve data and contextual information. The paper evaluates a few options in common use cases within the pharmaceutical industry and shows that the Allotrope Data Format (ADF) is the most suitable format for the implementation of SRDAs.

The paper can be downloaded from https://www.sciencedirect.com/science/article/abs/pii/S1359644621003287