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Allotrope in the News
How to jumpstart innovation in R&D? Biotech must solve the instrument connectivity challeng
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.
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:
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File format standards
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Interconnect standards of messaging and exchange data standards
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Modular systems with easy integration blocks
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Stable operating system environment
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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
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.
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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
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Benchling's blog: https://www.benchling.com/blog/benchling-connect
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"allotropy", open source, Python library repository on GitHub: https://github.com/Benchling-Open-Source/allotropy
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LinkedIn post: https://www.linkedin.com/posts/benchling_benchlingconnect-github-benchlingconnect-activity-7109907679673790468-bGoC
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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.
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The press release is available at: https://www.benchling.com/news/benchling-open-source-library-lab-instrument-data-converters
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The LinkedIn post is available at: https://www.linkedin.com/posts/benchling_benchling-creates-open-source-library-of-activity-7064195283236048896-xdU6
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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
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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
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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:
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:
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
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
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
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