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Allotrope in the News

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 integrations lab systems. It mentions focused on all aspects of running a lab. 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.

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/

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

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 

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 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

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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

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  

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