Allotrope in the News
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
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:
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
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 the NFDI4chem website https://knowledgebase.nfdi4chem.de/knowledge_base/docs/topics/ontology/
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