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Zulfiqar M, Crusoe MR, König-Ries B, Steinbeck C, Peters K, Gadelha L. Implementation of FAIR Practices in Computational Metabolomics Workflows-A Case Study. Metabolites 2024; 14:118. [PMID: 38393009 PMCID: PMC10891576 DOI: 10.3390/metabo14020118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using the Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using a CWL description on WorkflowHub. During the submission process on WorkflowHub, a CWL description is used for packaging MAW using the Workflow RO-Crate profile, which includes metadata in Bioschemas. Researchers can use this narrative discussion as a guideline to commence using FAIR practices for their bioinformatics or cheminformatics workflows while incorporating necessary amendments specific to their research area.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Michael R. Crusoe
- ELIXIR (The European Life-Sciences Infrastructure for Biological Information) Germany, Institute of Bio- and Geosciences (IBG-5)—Computational Metagenomics, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
| | - Birgitta König-Ries
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Institute for Informatics, Friedrich Schiller University Jena, 07743 Jena, Germany
- iDiv—German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, 04103 Leipzig, Germany;
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Kristian Peters
- iDiv—German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, 04103 Leipzig, Germany;
- Geobotany and Botanical Gardens, Martin-Luther University of Halle-Wittenberg, 06108 Halle, Germany
- Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Luiz Gadelha
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Institute for Informatics, Friedrich Schiller University Jena, 07743 Jena, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Kuhn S, Kolshorn H, Steinbeck C, Schlörer N. Twenty years of nmrshiftdb2: A case study of an open database for analytical chemistry. Magn Reson Chem 2024; 62:74-83. [PMID: 38112483 DOI: 10.1002/mrc.5418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023]
Abstract
In October 2003, 20 years ago, the open-source and open-content database NMRshiftDB was announced. Since then, the database, renamed as nmrshiftdb2 later, has been continuously available and is one of the longer-running projects in the field of open data in chemistry. After 20 years, we evaluate the success of the project and present lessons learnt for similar projects.
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Affiliation(s)
- Stefan Kuhn
- Institute of Computer Science, University of Tartu Tartu Estonia and School of Computer Science and Informatics, De Montfort University, Leicester, UK
| | - Heinz Kolshorn
- Department Chemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Nils Schlörer
- NMR-Plattform, Friedrich-Schiller-Universität Jena, Jena, Germany
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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Zulfiqar M, Stettin D, Schmidt S, Nikitashina V, Pohnert G, Steinbeck C, Peters K, Sorokina M. Untargeted metabolomics to expand the chemical space of the marine diatom Skeletonema marinoi. Front Microbiol 2023; 14:1295994. [PMID: 38116530 PMCID: PMC10728474 DOI: 10.3389/fmicb.2023.1295994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/31/2023] [Indexed: 12/21/2023] Open
Abstract
Diatoms (Bacillariophyceae) are aquatic photosynthetic microalgae with an ecological role as primary producers in the aquatic food web. They account substantially for global carbon, nitrogen, and silicon cycling. Elucidating the chemical space of diatoms is crucial to understanding their physiology and ecology. To expand the known chemical space of a cosmopolitan marine diatom, Skeletonema marinoi, we performed High-Resolution Liquid Chromatography-Tandem Mass Spectrometry (LC-MS2) for untargeted metabolomics data acquisition. The spectral data from LC-MS2 was used as input for the Metabolome Annotation Workflow (MAW) to obtain putative annotations for all measured features. A suspect list of metabolites previously identified in the Skeletonema spp. was generated to verify the results. These known metabolites were then added to the putative candidate list from LC-MS2 data to represent an expanded catalog of 1970 metabolites estimated to be produced by S. marinoi. The most prevalent chemical superclasses, based on the ChemONT ontology in this expanded dataset, were organic acids and derivatives, organoheterocyclic compounds, lipids and lipid-like molecules, and organic oxygen compounds. The metabolic profile from this study can aid the bioprospecting of marine microalgae for medicine, biofuel production, agriculture, and environmental conservation. The proposed analysis can be applicable for assessing the chemical space of other microalgae, which can also provide molecular insights into the interaction between marine organisms and their role in the functioning of ecosystems.
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Affiliation(s)
- Mahnoor Zulfiqar
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Daniel Stettin
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Saskia Schmidt
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Vera Nikitashina
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Christoph Steinbeck
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Kristian Peters
- iDiv - German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Leipzig, Germany
- Geobotany and Botanical Gardens, Martin-Luther University of Halle-Wittenberg, Halle, Germany
- Institute of Plant Biochemistry, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Maria Sorokina
- Faculty of Chemistry and Earth Sciences, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Pharmaceuticals Division, Research & Development, Data Science and Artificial Intelligence, AG Bayer, Berlin, Germany
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Chandrasekhar V, Sharma N, Schaub J, Steinbeck C, Rajan K. Cheminformatics Microservice: unifying access to open cheminformatics toolkits. J Cheminform 2023; 15:98. [PMID: 37845745 PMCID: PMC10577930 DOI: 10.1186/s13321-023-00762-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net . The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice .
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Affiliation(s)
- Venkata Chandrasekhar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Nisha Sharma
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Jonas Schaub
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
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Rajan K, Brinkhaus HO, Agea MI, Zielesny A, Steinbeck C. Author Correction: DECIMER.ai: an open platform for automated optical chemical structure identification, segmentation and recognition in scientific publications. Nat Commun 2023; 14:6034. [PMID: 37758729 PMCID: PMC10533819 DOI: 10.1038/s41467-023-41814-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Affiliation(s)
- Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - M Isabel Agea
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
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Rajan K, Brinkhaus HO, Agea MI, Zielesny A, Steinbeck C. DECIMER.ai: an open platform for automated optical chemical structure identification, segmentation and recognition in scientific publications. Nat Commun 2023; 14:5045. [PMID: 37598180 PMCID: PMC10439916 DOI: 10.1038/s41467-023-40782-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
The number of publications describing chemical structures has increased steadily over the last decades. However, the majority of published chemical information is currently not available in machine-readable form in public databases. It remains a challenge to automate the process of information extraction in a way that requires less manual intervention - especially the mining of chemical structure depictions. As an open-source platform that leverages recent advancements in deep learning, computer vision, and natural language processing, DECIMER.ai (Deep lEarning for Chemical IMagE Recognition) strives to automatically segment, classify, and translate chemical structure depictions from the printed literature. The segmentation and classification tools are the only openly available packages of their kind, and the optical chemical structure recognition (OCSR) core application yields outstanding performance on all benchmark datasets. The source code, the trained models and the datasets developed in this work have been published under permissive licences. An instance of the DECIMER web application is available at https://decimer.ai .
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Affiliation(s)
- Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - M Isabel Agea
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
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Brinkhaus HO, Rajan K, Schaub J, Zielesny A, Steinbeck C. Open data and algorithms for open science in AI-driven molecular informatics. Curr Opin Struct Biol 2023; 79:102542. [PMID: 36805192 DOI: 10.1016/j.sbi.2023.102542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 02/19/2023]
Abstract
Recent years have seen a sharp increase in the development of deep learning and artificial intelligence-based molecular informatics. There has been a growing interest in applying deep learning to several subfields, including the digital transformation of synthetic chemistry, extraction of chemical information from the scientific literature, and AI in natural product-based drug discovery. The application of AI to molecular informatics is still constrained by the fact that most of the data used for training and testing deep learning models are not available as FAIR and open data. As open science practices continue to grow in popularity, initiatives which support FAIR and open data as well as open-source software have emerged. It is becoming increasingly important for researchers in the field of molecular informatics to embrace open science and to submit data and software in open repositories. With the advent of open-source deep learning frameworks and cloud computing platforms, academic researchers are now able to deploy and test their own deep learning models with ease. With the development of new and faster hardware for deep learning and the increasing number of initiatives towards digital research data management infrastructures, as well as a culture promoting open data, open source, and open science, AI-driven molecular informatics will continue to grow. This review examines the current state of open data and open algorithms in molecular informatics, as well as ways in which they could be improved in future.
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Affiliation(s)
- Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
| | - Jonas Schaub
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
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Zulfiqar M, Gadelha L, Steinbeck C, Sorokina M, Peters K. MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry. J Cheminform 2023; 15:32. [PMID: 36871033 PMCID: PMC9985203 DOI: 10.1186/s13321-023-00695-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC-MS) to achieve a high-throughput profile of metabolites from complex biological resources, only a small fraction of these metabolites can be annotated with confidence. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds such as in silico generated spectra and molecular networking. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data to further facilitate and automate the complex annotation by combining tandem mass spectrometry (MS2) input data pre-processing, spectral and compound database matching with computational classification, and in silico annotation. MAW takes the LC-MS2 spectra as input and generates a list of putative candidates from spectral and compound databases. The databases are integrated via the R package Spectra and the metabolite annotation tool SIRIUS as part of the R segment of the workflow (MAW-R). The final candidate selection is performed using the cheminformatics tool RDKit in the Python segment (MAW-Py). Furthermore, each feature is assigned a chemical structure and can be imported to a chemical structure similarity network. MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub ( https://github.com/zmahnoor14/MAW ). The performance of MAW is evaluated on two case studies. MAW can improve candidate ranking by integrating spectral databases with annotation tools like SIRIUS which contributes to an efficient candidate selection procedure. The results from MAW are also reproducible and traceable, compliant with the FAIR guidelines. Taken together, MAW could greatly facilitate automated metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany.
| | - Luiz Gadelha
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany.
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany.,Data Science and Artificial Intelligence, Research and Development, Bayer Pharmaceuticals, 13353, Berlin, Germany
| | - Kristian Peters
- iDiv - German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Leipzig, 04103, Germany. .,Geobotany and Botanical Gardens, Martin-Luther University of Halle-Wittenberg, 06108, Halle, Germany. .,Leibniz Institute of Plant Biochemistry, 06120, Halle, Germany.
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Herres-Pawlis S, Bach F, Bruno IJ, Chalk SJ, Jung N, Liermann JC, McEwen LR, Neumann S, Steinbeck C, Razum M, Koepler O. Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices. Angew Chem Int Ed Engl 2022; 61:e202203038. [PMID: 36347644 DOI: 10.1002/anie.202203038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/11/2022]
Abstract
Research data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.
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Affiliation(s)
- Sonja Herres-Pawlis
- Institut für Anorganische Chemie, RWTH Aachen University, Landoltweg 1A, 52074, Aachen, Germany
| | - Felix Bach
- E-Research, FIZ Karlsruhe-Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ian J Bruno
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK
| | - Stuart J Chalk
- Department of Chemistry, University of North Florida, 1 UNF Drive, Jacksonville, FL 32224, USA
| | - Nicole Jung
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Johannes C Liermann
- Johannes Gutenberg University Mainz, Department of Chemistry, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Leah R McEwen
- Cornell University Library, 293 Clark Hall, Ithaca, NY 14853-2501, USA
| | - Steffen Neumann
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 1, 07743, Jena, Germany
| | - Matthias Razum
- E-Research, FIZ Karlsruhe-Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Oliver Koepler
- Lab Linked Scientific Knowledge, TIB-Leibniz Information Centre for Science and Technology, Welfengarten 1B, 30173, Hannover, Germany
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11
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Lai A, Schaub J, Steinbeck C, Schymanski EL. An algorithm to classify homologous series within compound datasets. J Cheminform 2022; 14:85. [PMID: 36510332 PMCID: PMC9746203 DOI: 10.1186/s13321-022-00663-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
Homologous series are groups of related compounds that share the same core structure attached to a motif that repeats to different degrees. Compounds forming homologous series are of interest in multiple domains, including natural products, environmental chemistry, and drug design. However, many homologous compounds remain unannotated as such in compound datasets, which poses obstacles to understanding chemical diversity and their analytical identification via database matching. To overcome these challenges, an algorithm to detect homologous series within compound datasets was developed and implemented using the RDKit. The algorithm takes a list of molecules as SMILES strings and a monomer (i.e., repeating unit) encoded as SMARTS as its main inputs. In an iterative process, substructure matching of repeating units, molecule fragmentation, and core detection lead to homologous series classification through grouping of identical cores. Three open compound datasets from environmental chemistry (NORMAN Suspect List Exchange, NORMAN-SLE), exposomics (PubChemLite for Exposomics), and natural products (the COlleCtion of Open NatUral producTs, COCONUT) were subject to homologous series classification using the algorithm. Over 2000, 12,000, and 5000 series with CH2 repeating units were classified in the NORMAN-SLE, PubChemLite, and COCONUT respectively. Validation of classified series was performed using published homologous series and structure categories, including a comparison with a similar existing method for categorising PFAS compounds. The OngLai algorithm and its implementation for classifying homologues are openly available at: https://github.com/adelenelai/onglai-classify-homologues .
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Affiliation(s)
- Adelene Lai
- grid.16008.3f0000 0001 2295 9843Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg ,grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessing Strasse 8, 07743 Jena, Germany
| | - Jonas Schaub
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessing Strasse 8, 07743 Jena, Germany
| | - Christoph Steinbeck
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessing Strasse 8, 07743 Jena, Germany
| | - Emma L. Schymanski
- grid.16008.3f0000 0001 2295 9843Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
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12
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Schaub J, Zander J, Zielesny A, Steinbeck C. Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). J Cheminform 2022; 14:79. [PMID: 36357931 PMCID: PMC9650898 DOI: 10.1186/s13321-022-00656-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022] Open
Abstract
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day.
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Affiliation(s)
- Jonas Schaub
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743 Jena, Germany
| | - Julian Zander
- grid.454254.60000 0004 0647 4362Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Achim Zielesny
- grid.454254.60000 0004 0647 4362Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Christoph Steinbeck
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743 Jena, Germany
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13
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Herres‐Pawlis S, Bach F, Bruno IJ, Chalk SJ, Jung N, Liermann JC, McEwen LR, Neumann S, Steinbeck C, Razum M, Koepler O. Mindestinformationsstandards in der Chemie: Ein Appell zum besseren Umgang mit Forschungsdaten. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sonja Herres‐Pawlis
- Institut für Anorganische Chemie RWTH Aachen University Landoltweg 1A 52074 Aachen Deutschland
| | - Felix Bach
- E-Research FIZ Karlsruhe – Leibniz Institute for Information Infrastructure Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Ian J. Bruno
- Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ UK
| | - Stuart J. Chalk
- Department of Chemistry University of North Florida 1 UNF Drive Jacksonville FL 32224 USA
| | - Nicole Jung
- Institute of Biological and Chemical Systems (IBCS) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Johannes C. Liermann
- Johannes Gutenberg University Mainz Department of Chemistry Duesbergweg 10–14 55128 Mainz Deutschland
| | - Leah R. McEwen
- Cornell University Library 293 Clark Hall Ithaca NY 14853-2501 USA
| | - Steffen Neumann
- Bioinformatics and Scientific Data Leibniz Institute of Plant Biochemistry Weinberg 3 06120 Halle Deutschland
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry Friedrich-Schiller-University Jena Lessingstr. 1 07743 Jena Deutschland
| | - Matthias Razum
- E-Research FIZ Karlsruhe – Leibniz Institute for Information Infrastructure Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Oliver Koepler
- Lab Linked Scientific Knowledge TIB – Leibniz Information Centre for Science and Technology Welfengarten 1B 30173 Hannover Deutschland
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14
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Brinkhaus HO, Zielesny A, Steinbeck C, Rajan K. DECIMER-hand-drawn molecule images dataset. J Cheminform 2022; 14:36. [PMID: 35681226 PMCID: PMC9185882 DOI: 10.1186/s13321-022-00620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/25/2022] [Indexed: 12/01/2022] Open
Abstract
The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER — Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field.
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Affiliation(s)
- Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
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15
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Brinkhaus HO, Rajan K, Zielesny A, Steinbeck C. RanDepict: Random chemical structure depiction generator. J Cheminform 2022; 14:31. [PMID: 35668480 PMCID: PMC9169273 DOI: 10.1186/s13321-022-00609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others. Here we present RanDepict, a toolkit for the creation of diverse sets of chemical structure depictions. The diversity of the image features is generated by making use of all available depiction parameters in the depiction functionalities of the CDK, RDKit, and Indigo. Furthermore, there is the option to enhance and augment the image with features such as curved arrows, chemical labels around the structure, or other kinds of distortions. Using depiction feature fingerprints, RanDepict ensures diversely picked image features. Here, the depiction and augmentation features are summarised in binary vectors and the MaxMin algorithm is used to pick diverse samples out of all valid options. By making all resources described herein publicly available, we hope to contribute to the development of deep learning-based OCSR systems.
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Affiliation(s)
- Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, D-45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
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16
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Rutz A, Sorokina M, Galgonek J, Mietchen D, Willighagen E, Gaudry A, Graham JG, Stephan R, Page R, Vondrášek J, Steinbeck C, Pauli GF, Wolfender JL, Bisson J, Allard PM. The LOTUS initiative for open knowledge management in natural products research. eLife 2022; 11:e70780. [PMID: 35616633 PMCID: PMC9135406 DOI: 10.7554/elife.70780] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/22/2022] [Indexed: 12/17/2022] Open
Abstract
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.
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Affiliation(s)
- Adriano Rutz
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University JenaJenaGermany
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the CASPragueCzech Republic
| | - Daniel Mietchen
- Ronin InstituteMontclairUnited States
- Leibniz Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, Maastricht UniversityMaastrichtNetherlands
| | - Arnaud Gaudry
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - James G Graham
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Ralf Stephan
- Ontario Institute for Cancer Research (OICR), University Ave SuiteTorontoCanada
| | | | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the CASPragueCzech Republic
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University JenaJenaGermany
| | - Guido F Pauli
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Jonathan Bisson
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
- Department of Biology, University of FribourgFribourgSwitzerland
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17
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Abstract
Chemical structure generators are used in cheminformatics to produce or enumerate virtual molecules based on a set of boundary conditions. The result can then be tested for properties of interest, such as adherence to measured data or for their suitability as drugs. The starting point can be a potentially fuzzy set of fragments or a molecular formula. In the latter case, the generator produces the set of constitutional isomers of the given input formula. Here we present the novel constitutional isomer generator surge based on the canonical generation path method. Surge uses the nauty package to compute automorphism groups of graphs. We outline the working principles of surge and present benchmarking results which show that surge is currently the fastest structure generator. Surge is available under a liberal open-source license.
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Affiliation(s)
- Brendan D McKay
- School of Computing, Australian National University, Canberra, ACT, 2601, Australia.
| | - Mehmet Aziz Yirik
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany
| | - Christoph Steinbeck
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany.
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18
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Sorokina M, Barth E, Zulfiqar M, Kwantes M, Pohnert G, Steinbeck C. Draft genome assembly and sequencing dataset of the marine diatom Skeletonema cf. costatum RCC75. Data Brief 2022; 41:107931. [PMID: 35242913 PMCID: PMC8866145 DOI: 10.1016/j.dib.2022.107931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the Skeletonema genus. Here we present a draft assembly of the Skeletonema cf. costatum RCC75 genome, obtained from PacBio and Illumina NovaSeq data. This dataset will expand the knowledge of the Bacillariophyceae genetics and contribute to the global understanding of phytoplankton's physiological, ecological, and environmental functioning.
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Affiliation(s)
- Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, Jena, Germany
- Corresponding authors.
| | - Emanuel Barth
- Bioinformatics Core Facility, Friedrich Schiller University, Leutragraben 1, Jena, Germany
| | - Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, Jena, Germany
| | - Michiel Kwantes
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, Jena, Germany
- Corresponding authors.
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19
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Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN, Minotto A, Moreno P, Nainala VC, O'Donovan C, Pireddu L, Roger P, Shaw F, Steinbeck C, Weber RJM, Sansone SA, Rocca-Serra P. ISA API: An open platform for interoperable life science experimental metadata. Gigascience 2021; 10:giab060. [PMID: 34528664 PMCID: PMC8444265 DOI: 10.1093/gigascience/giab060] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab-a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, the JSON serialization ISA-JSON was developed. RESULTS In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters, and its growing user community. CONCLUSIONS The ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.
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Affiliation(s)
- David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
- Department of Informatics and Media, Uppsala University, Box 513, 75120 Uppsala, Sweden
| | - Dominique Batista
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Keeva Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Robert P Davey
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Anthony Etuk
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
- Science and Technology Facilities Council, Scientific Computing Department, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Genome Research Limited, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Massimiliano Izzo
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Martin Larralde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas N Lawson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alice Minotto
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Venkata Chandrasekhar Nainala
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Luca Pireddu
- Distributed Computing Group, CRS4: Center for Advanced Studies, Research & Development in Sardinia, Pula 09050, Italy
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Felix Shaw
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christoph Steinbeck
- Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
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20
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Sorokina M, McCaffrey KS, Deaton EE, Ma G, Ordovás JM, Perkins-Veazie PM, Steinbeck C, Levi A, Parnell LD. A Catalog of Natural Products Occurring in Watermelon- Citrullus lanatus. Front Nutr 2021; 8:729822. [PMID: 34595201 PMCID: PMC8476801 DOI: 10.3389/fnut.2021.729822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Sweet dessert watermelon (Citrullus lanatus) is one of the most important vegetable crops consumed throughout the world. The chemical composition of watermelon provides both high nutritional value and various health benefits. The present manuscript introduces a catalog of 1,679 small molecules occurring in the watermelon and their cheminformatics analysis for diverse features. In this catalog, the phytochemicals are associated with the literature describing their presence in the watermelon plant, and when possible, concentration values in various plant parts (flesh, seeds, leaves, roots, rind). Also cataloged are the chemical classes, molecular weight and formula, chemical structure, and certain physical and chemical properties for each phytochemical. In our view, knowing precisely what is in what we eat, as this catalog does for watermelon, supports both the rationale for certain controlled feeding studies in the field of precision nutrition, and plant breeding efforts for the development of new varieties with enhanced concentrations of specific phytochemicals. Additionally, improved and comprehensive collections of natural products accessible to the public will be especially useful to researchers in nutrition, cheminformatics, bioinformatics, and drug development, among other disciplines.
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Affiliation(s)
- Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
| | | | - Erin E. Deaton
- Department of Horticulture, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Guoying Ma
- Department of Horticulture, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - José M. Ordovás
- Nutrition and Genomics Laboratory, Jean Mayer-United States Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| | - Penelope M. Perkins-Veazie
- Department of Horticulture, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
| | - Amnon Levi
- United States Department of Agriculture (USDA), Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Laurence D. Parnell
- United States Department of Agriculture (USDA), Agricultural Research Service, Nutrition and Genomics Laboratory, Jean Mayer-United States Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
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21
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Abstract
The amount of data available on chemical structures and their properties has increased steadily over the past decades. In particular, articles published before the mid-1990 are available only in printed or scanned form. The extraction and storage of data from those articles in a publicly accessible database are desirable, but doing this manually is a slow and error-prone process. In order to extract chemical structure depictions and convert them into a computer-readable format, Optical Chemical Structure Recognition (OCSR) tools were developed where the best performing OCSR tools are mostly rule-based. The DECIMER (Deep lEarning for Chemical ImagE Recognition) project was launched to address the OCSR problem with the latest computational intelligence methods to provide an automated open-source software solution. Various current deep learning approaches were explored to seek a best-fitting solution to the problem. In a preliminary communication, we outlined the prospect of being able to predict SMILES encodings of chemical structure depictions with about 90% accuracy using a dataset of 50-100 million molecules. In this article, the new DECIMER model is presented, a transformer-based network, which can predict SMILES with above 96% accuracy from depictions of chemical structures without stereochemical information and above 89% accuracy for depictions with stereochemical information.
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Affiliation(s)
- Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
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22
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Yirik MA, Sorokina M, Steinbeck C. MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle. J Cheminform 2021; 13:48. [PMID: 34217353 PMCID: PMC8254276 DOI: 10.1186/s13321-021-00529-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022] Open
Abstract
The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering. Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN's architecture and algorithm are outlined and the software is benchmarked in single-threaded mode against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution PMG. Based on the benchmarking, MAYGEN is on average 47 times faster than PMG and on average three times slower than MOLGEN in performance.
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Affiliation(s)
- Mehmet Aziz Yirik
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743 Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743 Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743 Jena, Germany
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23
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Abstract
Chemical compounds can be identified through a graphical depiction, a suitable string representation, or a chemical name. A universally accepted naming scheme for chemistry was established by the International Union of Pure and Applied Chemistry (IUPAC) based on a set of rules. Due to the complexity of this ruleset a correct chemical name assignment remains challenging for human beings and there are only a few rule-based cheminformatics toolkits available that support this task in an automated manner. Here we present STOUT (SMILES-TO-IUPAC-name translator), a deep-learning neural machine translation approach to generate the IUPAC name for a given molecule from its SMILES string as well as the reverse translation, i.e. predicting the SMILES string from the IUPAC name. In both cases, the system is able to predict with an average BLEU score of about 90% and a Tanimoto similarity index of more than 0.9. Also incorrect predictions show a remarkable similarity between true and predicted compounds.
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Affiliation(s)
- Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
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24
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Rajan K, Brinkhaus HO, Sorokina M, Zielesny A, Steinbeck C. DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature. J Cheminform 2021; 13:20. [PMID: 33685498 PMCID: PMC7941967 DOI: 10.1186/s13321-021-00496-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Chemistry looks back at many decades of publications on chemical compounds, their structures and properties, in scientific articles. Liberating this knowledge (semi-)automatically and making it available to the world in open-access databases is a current challenge. Apart from mining textual information, Optical Chemical Structure Recognition (OCSR), the translation of an image of a chemical structure into a machine-readable representation, is part of this workflow. As the OCSR process requires an image containing a chemical structure, there is a need for a publicly available tool that automatically recognizes and segments chemical structure depictions from scientific publications. This is especially important for older documents which are only available as scanned pages. Here, we present DECIMER (Deep lEarning for Chemical IMagE Recognition) Segmentation, the first open-source, deep learning-based tool for automated recognition and segmentation of chemical structures from the scientific literature. The workflow is divided into two main stages. During the detection step, a deep learning model recognizes chemical structure depictions and creates masks which define their positions on the input page. Subsequently, potentially incomplete masks are expanded in a post-processing workflow. The performance of DECIMER Segmentation has been manually evaluated on three sets of publications from different publishers. The approach operates on bitmap images of journal pages to be applicable also to older articles before the introduction of vector images in PDFs. By making the source code and the trained model publicly available, we hope to contribute to the development of comprehensive chemical data extraction workflows. In order to facilitate access to DECIMER Segmentation, we also developed a web application. The web application, available at https://decimer.ai, lets the user upload a pdf file and retrieve the segmented structure depictions.![]()
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Affiliation(s)
- Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
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25
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Sorokina M, Merseburger P, Rajan K, Yirik MA, Steinbeck C. COCONUT online: Collection of Open Natural Products database. J Cheminform 2021; 13:2. [PMID: 33423696 PMCID: PMC7798278 DOI: 10.1186/s13321-020-00478-9] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net .
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Affiliation(s)
- Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Peter Merseburger
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Mehmet Aziz Yirik
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
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26
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Abstract
Chemical graph generators are software packages to generate computer representations of chemical structures adhering to certain boundary conditions. Their development is a research topic of cheminformatics. Chemical graph generators are used in areas such as virtual library generation in drug design, in molecular design with specified properties, called inverse QSAR/QSPR, as well as in organic synthesis design, retrosynthesis or in systems for computer-assisted structure elucidation (CASE). CASE systems again have regained interest for the structure elucidation of unknowns in computational metabolomics, a current area of computational biology.
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Affiliation(s)
- Mehmet Aziz Yirik
- Friedrich Schiller Universität Jena, Institute for Inorganic and Analytical Chemistry, Jena, Germany
| | - Christoph Steinbeck
- Friedrich Schiller Universität Jena, Institute for Inorganic and Analytical Chemistry, Jena, Germany
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27
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Ashrafian H, Sounderajah V, Glen R, Ebbels T, Blaise BJ, Kalra D, Kultima K, Spjuth O, Tenori L, Salek RM, Kale N, Haug K, Schober D, Rocca-Serra P, O'Donovan C, Steinbeck C, Cano I, de Atauri P, Cascante M. Metabolomics: The Stethoscope for the Twenty-First Century. Med Princ Pract 2020; 30:301-310. [PMID: 33271569 PMCID: PMC8436726 DOI: 10.1159/000513545] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/29/2020] [Indexed: 11/19/2022] Open
Abstract
Metabolomics encompasses the systematic identification and quantification of all metabolic products in the human body. This field could provide clinicians with novel sets of diagnostic biomarkers for disease states in addition to quantifying treatment response to medications at an individualized level. This literature review aims to highlight the technology underpinning metabolic profiling, identify potential applications of metabolomics in clinical practice, and discuss the translational challenges that the field faces. We searched PubMed, MEDLINE, and EMBASE for primary and secondary research articles regarding clinical applications of metabolomics. Metabolic profiling can be performed using mass spectrometry and nuclear magnetic resonance-based techniques using a variety of biological samples. This is carried out in vivo or in vitro following careful sample collection, preparation, and analysis. The potential clinical applications constitute disruptive innovations in their respective specialities, particularly oncology and metabolic medicine. Outstanding issues currently preventing widespread clinical use are scalability of data interpretation, standardization of sample handling practice, and e-infrastructure. Routine utilization of metabolomics at a patient and population level will constitute an integral part of future healthcare provision.
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Affiliation(s)
- Hutan Ashrafian
- Institute of Global Health Innovation and Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Viknesh Sounderajah
- Institute of Global Health Innovation and Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Robert Glen
- Institute of Global Health Innovation and Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timothy Ebbels
- Institute of Global Health Innovation and Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Benjamin J. Blaise
- Institute of Global Health Innovation and Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Dipak Kalra
- Department of Medical Informatics and Statistics, University of Ghent, Ghent, Belgium
| | - Kim Kultima
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Reza M. Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Daniel Schober
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Philippe Rocca-Serra
- Department of Engineering Science, Oxford e-Research Centre, University of Oxford, Oxford, United Kingdom
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany
| | - Isaac Cano
- Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and CIBERHD (CIBER de Enfermedades hepáticas y digestivas), Barcelona, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and CIBERHD (CIBER de Enfermedades hepáticas y digestivas), Barcelona, Spain
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28
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Schaub J, Zielesny A, Steinbeck C, Sorokina M. Too sweet: cheminformatics for deglycosylation in natural products. J Cheminform 2020; 12:67. [PMID: 33292501 PMCID: PMC7641802 DOI: 10.1186/s13321-020-00467-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022] Open
Abstract
Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove the sugars before a theoretical or experimental study of a molecule. Deglycogenases, enzymes that specialized in sugar removal from small molecules, are often used in laboratories to perform this task. However, there is no standardized computational procedure to perform this task in silico. In this work, we present a systematic approach for in silico removal of ring and linear sugars from molecular structures. Particular attention is given to molecules of biological origin and to their structural specificities. This approach is made available in two forms, through a free and open web application and as standalone open-source software.
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Affiliation(s)
- Jonas Schaub
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743, Jena, Germany.
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743, Jena, Germany.
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29
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Abstract
The automatic recognition of chemical structure diagrams from the literature is an indispensable component of workflows to re-discover information about chemicals and to make it available in open-access databases. Here we report preliminary findings in our development of Deep lEarning for Chemical ImagE Recognition (DECIMER), a deep learning method based on existing show-and-tell deep neural networks, which makes very few assumptions about the structure of the underlying problem. It translates a bitmap image of a molecule, as found in publications, into a SMILES. The training state reported here does not yet rival the performance of existing traditional approaches, but we present evidence that our method will reach a comparable detection power with sufficient training time. Training success of DECIMER depends on the input data representation: DeepSMILES are superior over SMILES and we have a preliminary indication that the recently reported SELFIES outperform DeepSMILES. An extrapolation of our results towards larger training data sizes suggests that we might be able to achieve near-accurate prediction with 50 to 100 million training structures. This work is entirely based on open-source software and open data and is available to the general public for any purpose.
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Affiliation(s)
- Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
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30
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Steinbeck C, Koepler O, Bach F, Herres-Pawlis S, Jung N, Liermann J, Neumann S, Razum M, Baldauf C, Biedermann F, Bocklitz T, Boehm F, Broda F, Czodrowski P, Engel T, Hicks M, Kast S, Kettner C, Koch W, Lanza G, Link A, Mata R, Nagel W, Porzel A, Schlörer N, Schulze T, Weinig HG, Wenzel W, Wessjohann L, Wulle S. NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany. RIO 2020. [DOI: 10.3897/rio.6.e55852] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The vision of NFDI4Chem is the digitalisation of all key steps in chemical research to support scientists in their efforts to collect, store, process, analyse, disclose and re-use research data. Measures to promote Open Science and Research Data Management (RDM) in agreement with the FAIR data principles are fundamental aims of NFDI4Chem to serve the chemistry community with a holistic concept for access to research data. To this end, the overarching objective is the development and maintenance of a national research data infrastructure for the research domain of chemistry in Germany, and to enable innovative and easy to use services and novel scientific approaches based on re-use of research data. NFDI4Chem intends to represent all disciplines of chemistry in academia. We aim to collaborate closely with thematically related consortia. In the initial phase, NFDI4Chem focuses on data related to molecules and reactions including data for their experimental and theoretical characterisation.
This overarching goal is achieved by working towards a number of key objectives:
Key Objective 1: Establish a virtual environment of federated repositories for storing, disclosing, searching and re-using research data across distributed data sources. Connect existing data repositories and, based on a requirements analysis, establish domain-specific research data repositories for the national research community, and link them to international repositories.
Key Objective 2: Initiate international community processes to establish minimum information (MI) standards for data and machine-readable metadata as well as open data standards in key areas of chemistry. Identify and recommend open data standards in key areas of chemistry, in order to support the FAIR principles for research data. Finally, develop standards, if there is a lack.
Key Objective 3: Foster cultural and digital change towards Smart Laboratory Environments by promoting the use of digital tools in all stages of research and promote subsequent Research Data Management (RDM) at all levels of academia, beginning in undergraduate studies curricula.
Key Objective 4: Engage with the chemistry community in Germany through a wide range of measures to create awareness for and foster the adoption of FAIR data management. Initiate processes to integrate RDM and data science into curricula. Offer a wide range of training opportunities for researchers.
Key Objective 5: Explore synergies with other consortia and promote cross-cutting development within the NFDI.
Key Objective 6: Provide a legally reliable framework of policies and guidelines for FAIR and open RDM.
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31
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Abstract
Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.
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Affiliation(s)
- Maria Sorokina
- University Friedrich-Schiller, Lessing Strasse 8, 07743, Jena, Germany.
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32
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Guo H, Schwitalla JW, Benndorf R, Baunach M, Steinbeck C, Görls H, de Beer ZW, Regestein L, Beemelmanns C. Gene Cluster Activation in a Bacterial Symbiont Leads to Halogenated Angucyclic Maduralactomycins and Spirocyclic Actinospirols. Org Lett 2020; 22:2634-2638. [PMID: 32193935 DOI: 10.1021/acs.orglett.0c00601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Growth from spores activated a biosynthetic gene cluster in Actinomadura sp. RB29, resulting in the identification of two novel groups of halogenated polyketide natural products, named maduralactomycins and actinospirols. The unique tetracyclic and spirocyclic structures were assigned based on a combination of NMR analysis, chemoinformatic calculations, X-ray crystallography, and 13C labeling studies. On the basis of HRMS2 data, genome mining, and gene expression studies, we propose an underlying noncanonical angucycline biosynthesis and extensive post-polyketide synthase (PKS) oxidative modifications.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jan W Schwitalla
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - René Benndorf
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Martin Baunach
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743 Jena, Germany
| | - Helmar Görls
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743 Jena, Germany
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0002 Pretoria, South Africa
| | - Lars Regestein
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
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33
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Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinformatics 2019; 35:3752-3760. [PMID: 30851093 PMCID: PMC6761976 DOI: 10.1093/bioinformatics/btz160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator. RESULTS We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science. AVAILABILITY AND IMPLEMENTATION The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Payam Emami Khoonsari
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joachim Burman
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Marco Capuccini
- Department of Information Technology, Uppsala University, Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Matteo Carone
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Metabolomics Node at INB-Bioinfarmatics Platform, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Metabolomics Node at INB-Bioinfarmatics Platform, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Metabolomics Node at INB-Bioinfarmatics Platform, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | | | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Sijin He
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Stephanie Herman
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Anders Larsson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Kristian Peters
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Luca Pireddu
- CRS4: Center for Advanced Studies, Research and Development in Sardinia, Distributed Computing Group, Pula, Italy
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, MetaboHUB, Gif-sur-Yvette, France
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ruttkies
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Noureddin Sadawi
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Reza M Salek
- International Agency for Research on Cancer, 69372 Lyon CEDEX 08, France
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Daniel Schober
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biomedicine, and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Metabolomics Node at INB-Bioinfarmatics Platform, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, MetaboHUB, Gif-sur-Yvette, France
| | - Michael van Vliet
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Gianluigi Zanetti
- CRS4: Center for Advanced Studies, Research and Development in Sardinia, Distributed Computing Group, Pula, Italy
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Abstract
Natural products (NPs), often also referred to as secondary metabolites, are small molecules synthesised by living organisms. Natural products are of interest due to their bioactivity and in this context as starting points for the development of drugs and other bioactive synthetic products. In order to select compounds from virtual libraries, Ertl et al. developed a natural product likeness score which was later published as an open data, open source implementation. Here we present NaPLeS, an easily portable, containerised, open source web application based on open data to compute natural product likeness scores for chemical libraries.
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Affiliation(s)
- Maria Sorokina
- University Friedrich-Schiller, Lessingstrasse 8, 07743, Jena, Germany.
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35
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Abstract
"The formation of a National Research Data Infrastructure for Chemistry (NFDI4Chem), integrated into a National Research Data Infrastructure for all scientific disciplines, is a great opportunity for our discipline. Proper research data management is the basis for good scientific practice and opens up new fields of research …" Read more in the Guest Editorial by S. Herres-Pawlis et al.
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Affiliation(s)
| | - Oliver Koepler
- Leibniz Information Centre of Science and Technology (TIB), Germany
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36
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Affiliation(s)
| | - Oliver Koepler
- Leibniz Information Centre of Science and Technology (TIB) Deutschland
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37
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Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Automated structure prediction of trans-acyltransferase polyketide synthase products. Nat Chem Biol 2019; 15:813-821. [PMID: 31308532 PMCID: PMC6642696 DOI: 10.1038/s41589-019-0313-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/23/2019] [Indexed: 12/01/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex known enzymes from secondary metabolism and are responsible for the biosynthesis of highly diverse bioactive polyketides. However, most of these metabolites remain uncharacterized, since trans-AT PKSs frequently occur in poorly studied microbes and feature a remarkable array of non-canonical biosynthetic components with poorly understood functions. As a consequence, genome-guided natural product identification has been challenging. To enable de novo structural predictions for trans-AT PKS-derived polyketides, we developed the trans-AT PKS polyketide predictor (TransATor). TransATor is a versatile bio- and chemoinformatics web application that suggests informative chemical structures for even highly aberrant trans-AT PKS biosynthetic gene clusters, thus permitting hypothesis-based, targeted biotechnological discovery and biosynthetic studies. We demonstrate the applicative scope in several examples, including the characterization of new variants of bioactive natural products as well as structurally new polyketides from unusual bacterial sources.
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Affiliation(s)
- Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Alon Dolev
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Gianmaria Califano
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - Pablo Moreno
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.
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38
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Fritsch S, Neumann S, Schaub J, Steinbeck C, Zielesny A. ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK). J Cheminform 2019; 11:37. [PMID: 31165338 PMCID: PMC6549326 DOI: 10.1186/s13321-019-0361-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/28/2019] [Indexed: 11/29/2022] Open
Abstract
The Ertl algorithm for automated functional groups (FG) detection and extraction of organic molecules is implemented on the basis of the Chemistry Development Kit (CDK). A distinct impact of the chosen CDK aromaticity model is demonstrated by an FG analysis of the ChEMBL database compounds. The average performance of less than a millisecond for a single-molecule FG extraction allows for fast processing of even large compound databases.
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Affiliation(s)
- Sebastian Fritsch
- GNWI - Gesellschaft für naturwissenschaftliche Informatik, Oer-Erkenschwick, Germany
| | - Stefan Neumann
- GNWI - Gesellschaft für naturwissenschaftliche Informatik, Oer-Erkenschwick, Germany
| | - Jonas Schaub
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany.
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39
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Ritter M, Neupane S, Seidel RA, Steinbeck C, Pohnert G. In vivo and in vitro identification of Z-BOX C - a new bilirubin oxidation end product. Org Biomol Chem 2019. [PMID: 29532847 DOI: 10.1039/c8ob00164b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A new bilirubin oxidation end product (BOX) was isolated and characterized. The formation of the so-called Z-BOX C proceeds from bilirubin via propentdyopents as intermediates. This BOX was detected in pathological human bile samples using liquid chromatography/mass spectrometry and has potential relevance for liver dysfunction and cerebral vasospasms.
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Affiliation(s)
- Marcel Ritter
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, D-07743 Jena, Germany.
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40
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Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. PhenoMeNal: processing and analysis of metabolomics data in the cloud. Gigascience 2019; 8:giy149. [PMID: 30535405 PMCID: PMC6377398 DOI: 10.1093/gigascience/giy149] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/19/2018] [Accepted: 11/20/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. FINDINGS PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. CONCLUSIONS PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - James Bradbury
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marco Capuccini
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Timothy M D Ebbels
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Robert Glen
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, United Kingdom
| | - Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Ulrich L Günther
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Evangelos Handakas
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stephanie Herman
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | | | - Massimiliano Izzo
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Daniel Jacob
- INRA, University of Bordeaux, Plateforme Métabolome Bordeaux-MetaboHUB, 33140 Villenave d'Ornon, France
| | - David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
- Department of Informatics and Media, Uppsala University, Box 513, 751 20 Uppsala, Sweden
| | - Fabien Jourdan
- INRA - French National Institute for Agricultural Research, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ibrahim Karaman
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom
| | - Bita Khalili
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Payam Emami Khonsari
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | - Samuel Lampa
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Anders Larsson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Christian Ludwig
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jon Ander Novella
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jake T M Pearce
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Alina Peluso
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | | | | | - Michelle A C Reed
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence and CIRMMP, 50019 Sesto Fiorentino, Florence, Italy
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Noureddin Sadawi
- Department of Computer Science, College of Engineering, Design and Physical Sciences, Brunel University, London, UK
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Daniel Schober
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Mattia Tomasoni
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Merlijn van Rijswijk
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands
| | - Michael van Vliet
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | | | - Christoph Steinbeck
- Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
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McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Nat Prod Rep 2019; 36:35-107. [PMID: 30003207 PMCID: PMC6350634 DOI: 10.1039/c7np00064b] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/20/2022]
Abstract
Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.
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Affiliation(s)
- James B McAlpine
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Andrei Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Giovanni Appendino
- Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, Universita` del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | | | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Maique W Biavatti
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Stefan Bluml
- University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Young H Choi
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Michael T Crimmins
- Kenan and Caudill Laboratories of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie Csete
- University of Southern California, Huntington Medical Research Institutes, 99 N. El Molino Ave., Pasadena, CA 91101, USA
| | - Pradeep Dewapriya
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Joseph M Egan
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Mary J Garson
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Grégory Genta-Jouve
- C-TAC, UMR 8638 CNRS, Faculté de Pharmacie de Paris, Paris-Descartes University, Sorbonne, Paris Cité, 4, Aveue de l'Observatoire, 75006 Paris, France
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Eberhard Karls University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Precilia Hermanto
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - James M Hook
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luke Hunter
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Damien Jeannerat
- University of Geneva, Department of Organic Chemistry, 30 quai E. Ansermet, CH 1211 Geneva 4, Switzerland
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China
| | - Tyler A Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hiroyuki Koshino
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Guy Lewin
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Tadeusz F Molinski
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joo-Won Nam
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ram P Neupane
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Matthias Niemitz
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jean-Marc Nuzillard
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Nicholas H Oberlies
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | | | - Guohui Pan
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jean-Hugues Renault
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - José Rivera-Chávez
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Wolfgang Robien
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Carla M Saunders
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Thomas J Schmidt
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Seger
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ben Shen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Steinbeck
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Hermann Stuppner
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Sonja Sturm
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Orazio Taglialatela-Scafati
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Dean J Tantillo
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Robert Verpoorte
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bin-Gui Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China and Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Craig M Williams
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Philip G Williams
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Julien Wist
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jian-Min Yue
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Chen Zhang
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Zhengren Xu
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Charlotte Simmler
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - David C Lankin
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Jonathan Bisson
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Guido F Pauli
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
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McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Nat Prod Rep 2018; 36:248-249. [PMID: 30468235 DOI: 10.1039/c8np90041h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .
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Affiliation(s)
- James B McAlpine
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA.
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA.
| | - Andrei Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Giovanni Appendino
- Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | | | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Maique W Biavatti
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Stefan Bluml
- University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Young H Choi
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Michael T Crimmins
- Kenan and Caudill Laboratories of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie Csete
- University of Southern California, Huntington Medical Research Institutes, 99 N. El Molino Ave., Pasadena, CA 91101, USA
| | - Pradeep Dewapriya
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Joseph M Egan
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Mary J Garson
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Grégory Genta-Jouve
- C-TAC, UMR 8638 CNRS, Faculté de Pharmacie de Paris, Paris-Descartes University, Sorbonne, Paris Cité, 4, Aveue de l'Observatoire, 75006 Paris, France
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Eberhard Karls University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Precilia Hermanto
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - James M Hook
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luke Hunter
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Damien Jeannerat
- University of Geneva, Department of Organic Chemistry, 30 quai E. Ansermet, CH 1211 Geneva 4, Switzerland
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China
| | - Tyler A Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hiroyuki Koshino
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Guy Lewin
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Tadeusz F Molinski
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joo-Won Nam
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Ram P Neupane
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Matthias Niemitz
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Jean-Marc Nuzillard
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Nicholas H Oberlies
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | | | - Guohui Pan
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jean-Hugues Renault
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - José Rivera-Chávez
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Wolfgang Robien
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Carla M Saunders
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Thomas J Schmidt
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Christoph Seger
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Ben Shen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Christoph Steinbeck
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Hermann Stuppner
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Sonja Sturm
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Orazio Taglialatela-Scafati
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Dean J Tantillo
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Robert Verpoorte
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bin-Gui Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China and Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Craig M Williams
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Philip G Williams
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Julien Wist
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Jian-Min Yue
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Chen Zhang
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Zhengren Xu
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. and
| | - Charlotte Simmler
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA.
| | - David C Lankin
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA.
| | - Jonathan Bisson
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA.
| | - Guido F Pauli
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA.
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Guo H, Benndorf R, König S, Leichnitz D, Weigel C, Peschel G, Berthel P, Kaiser M, Steinbeck C, Werz O, Poulsen M, Beemelmanns C. Frontispiece: Expanding the Rubterolone Family: Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans. Chemistry 2018. [DOI: 10.1002/chem.201884465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - René Benndorf
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Stefanie König
- Institute of Pharmacy; Friedrich-Schiller-University Jena; Philosophenweg 14 07743 Jena Germany
| | - Daniel Leichnitz
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Gundela Peschel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Patrick Berthel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy; Socinstraße 57 4002 Basel Switzerland
- University of Basel; Petersplatz 1 4003 Basel Switzerland
| | - Christoph Steinbeck
- Institute for Analytical Chemistry; Friedrich-Schiller-University Jena; Lessingstr. 8 07743 Jena Germany
| | - Oliver Werz
- Institute of Pharmacy; Friedrich-Schiller-University Jena; Philosophenweg 14 07743 Jena Germany
| | - Michael Poulsen
- Centre for Social Evolution; University of Copenhagen; 2100 Copenhagen East Denmark
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
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Pupier M, Nuzillard JM, Wist J, Schlörer NE, Kuhn S, Erdelyi M, Steinbeck C, Williams AJ, Butts C, Claridge TD, Mikhova B, Robien W, Dashti H, Eghbalnia HR, Farès C, Adam C, Kessler P, Moriaud F, Elyashberg M, Argyropoulos D, Pérez M, Giraudeau P, Gil RR, Trevorrow P, Jeannerat D. NMReDATA, a standard to report the NMR assignment and parameters of organic compounds. Magn Reson Chem 2018; 56:703-715. [PMID: 29656574 PMCID: PMC6226248 DOI: 10.1002/mrc.4737] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/22/2018] [Accepted: 03/25/2018] [Indexed: 05/29/2023]
Abstract
Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases.
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Affiliation(s)
- Marion Pupier
- Department of Organic Chemistry, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, BP 1039, 51687, Reims Cedex 2, France
| | - Julien Wist
- Chemistry Department, Universidad del Valle, 76001 Cali, Colombia
| | - Nils E. Schlörer
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939 Köln, Germany
| | - Stefan Kuhn
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939 Köln, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743 Jena, Germany
| | - Antony J. Williams
- National Center for Computational Toxicology, Environmental Protection Agency, 109 T.W. Alexander Drive, Room D131I, Mail Drop D143-02, Research Triangle Park, NC 27711, USA
| | - Craig Butts
- School of Chemistry, Bristol University, BS8 1TS Bristol, UK
| | - Tim D.W. Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Bozhana Mikhova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Akad. G. Bonchev Str. Bl.9, Sofia 1113, Bulgaria
| | - Wolfgang Robien
- University of Vienna, Department of Organic Chemistry, Währingerstr. 38, 1090 Vienna, Austria
| | - Hesam Dashti
- Department of Biochemistry, National Magnetic Resonance Facility at Madison (NMRFAM), 433 Babcock Drive, Madison, WI, USA
| | - Hamid R. Eghbalnia
- Department of Biochemistry, National Magnetic Resonance Facility at Madison (NMRFAM), 433 Babcock Drive, Madison, WI, USA
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Abteilung NMR, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christian Adam
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Pavel Kessler
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten, Germany
| | - Fabrice Moriaud
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Mikhail Elyashberg
- Moscow Department, Advanced Chemistry Development, 6 Akademik Bakulev Street, Moscow 117513, Russian Federation
| | - Dimitris Argyropoulos
- Advanced Chemistry Development, Inc. (ACD/Labs), Venture House, Arlington Square, Downshire Way, Bracknell, Berkshire RG12 1WA, UK
| | - Manuel Pérez
- Mestrelab Research, S.L., Feliciano Barrera 9B - Bajo, ES-15706 Santiago de Compostela, Spain
| | - Patrick Giraudeau
- EBSI Team, Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM) CNRS, UMR 6230, Université de Nantes, 92208, 2 rue de la Houssinière, BP 44322 Nantes, France
- Institut Universitaire de France, 1 rue Descartes, 75005 Paris Cedex 05, France
| | - Roberto R. Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | | | - Damien Jeannerat
- Department of Organic Chemistry, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
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Guo H, Benndorf R, König S, Leichnitz D, Weigel C, Peschel G, Berthel P, Kaiser M, Steinbeck C, Werz O, Poulsen M, Beemelmanns C. Expanding the Rubterolone Family: Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans. Chemistry 2018; 24:11319-11324. [PMID: 29846024 DOI: 10.1002/chem.201802066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/26/2018] [Indexed: 12/20/2022]
Abstract
We characterized two key biosynthetic intermediates of the intriguing rubterolone family (tropolone alkaloids) that contain a highly reactive pyran moiety (in equilibrium with the hydrolyzed 1,5-dione form) and undergo spontaneous pyridine formation in the presence of primary amines. We exploited the intrinsic reactivity of the pyran moiety and isolated several new rubterolone derivatives, two of which contain a unique thiazolidine moiety. Three rubterolone derivatives were chemically modified with fluorescence and biotin tags using peptide coupling and click reaction. Overall, eight derivatives were fully characterized by HRMS/MS and 1D and 2D NMR spectroscopy and their antimicrobial, cytotoxic, anti-inflammatory and antiparasitic activities evaluated.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - René Benndorf
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Stefanie König
- Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Daniel Leichnitz
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Gundela Peschel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Patrick Berthel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, Socinstraße 57, 4002, Basel, Switzerland.,University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Christoph Steinbeck
- Institute for Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Oliver Werz
- Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Michael Poulsen
- Centre for Social Evolution, University of Copenhagen, 2100, Copenhagen East, Denmark
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
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Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. Current Challenges in Plant Eco-Metabolomics. Int J Mol Sci 2018; 19:E1385. [PMID: 29734799 PMCID: PMC5983679 DOI: 10.3390/ijms19051385] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
- UFZ-Helmholtz-Centre for Environmental Research, Department Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
| | - Oliver Alka
- Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
| | - Gerd Balcke
- Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany.
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany.
| | - Onno W Calf
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Sophie Dietz
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Kai Dührkop
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany.
| | - Uwe Heinig
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Marlen Kücklich
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Mirka Macel
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany.
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Christian Ristok
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Victor Manuel Rodríguez
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Meredith Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany.
| | - Rabea Schweiger
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Nir Shahaf
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Christoph Steinbeck
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Maria Tortosa
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Brigitte M Weiß
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Anja Widdig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
- Research Group of Primate Kin Selection, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
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Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C. Automated assembly of species metabolomes through data submission into a public repository. Gigascience 2018; 6:1-4. [PMID: 28830114 PMCID: PMC5737527 DOI: 10.1093/gigascience/gix062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 07/09/2017] [Indexed: 11/14/2022] Open
Abstract
Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.
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Affiliation(s)
- Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pablo Conesa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Keeva Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kalai Vanii Jayaseelan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Ramon Macias
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Venkata Chandrasekhar Nainala
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert D Hall
- Wageningen University and Research, Wageningen Plant Research - Bioscience, P.O. Box 16, 6700AA, Wageningen, the Netherlands
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, P.O. Box 870344, Tuscaloosa, AL 35487, USA
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743 Jena, Germany
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48
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Abstract
INTRODUCTION Data sharing is being increasingly required by journals and has been heralded as a solution to the 'replication crisis'. OBJECTIVES (i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals' policies to those that publish the most metabolomics papers. METHODS A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications. RESULTS Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data. CONCLUSION Further efforts are required to improve data sharing in metabolomics.
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Affiliation(s)
- Rachel A Spicer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany.
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49
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Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. Anal Chem 2017; 90:649-656. [PMID: 29035042 DOI: 10.1021/acs.analchem.7b02795] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.
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Affiliation(s)
- Daniel Schober
- Leibniz Institute of Plant Biochemistry , Department of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany
| | - Daniel Jacob
- INRA, Univ. Bordeaux , UMR1332 Fruit Biology and Pathology, Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, F-33140 Villenave d'Ornon, France
| | - Michael Wilson
- Departments of Computing Sciences and Biological Sciences, University of Alberta , Edmonton, Canada T6G 2E8
| | - Joseph A Cruz
- Departments of Computing Sciences and Biological Sciences, University of Alberta , Edmonton, Canada T6G 2E8
| | - Ana Marcu
- Departments of Computing Sciences and Biological Sciences, University of Alberta , Edmonton, Canada T6G 2E8
| | - Jason R Grant
- Departments of Computing Sciences and Biological Sciences, University of Alberta , Edmonton, Canada T6G 2E8
| | - Annick Moing
- INRA, Univ. Bordeaux , UMR1332 Fruit Biology and Pathology, Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, F-33140 Villenave d'Ornon, France
| | - Catherine Deborde
- INRA, Univ. Bordeaux , UMR1332 Fruit Biology and Pathology, Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, F-33140 Villenave d'Ornon, France
| | - Luis F de Figueiredo
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Kenneth Haug
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | | | - John Easton
- School of Engineering, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Timothy M D Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , London, SW7 2AZ, U.K
| | - Jie Hao
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , London, SW7 2AZ, U.K
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Ulrich L Günther
- Institute of Cancer and Genomic Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence , 50019 Sesto Fiorentino, Florence, Italy
| | - Matthias S Klein
- Department of Biological Sciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence , 50019 Sesto Fiorentino, Florence, Italy
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool , Bioscience Building, Crown Street, Liverpool L69 7ZB, U.K
| | - Arturas Grauslys
- Institute of Integrative Biology, University of Liverpool , Bioscience Building, Crown Street, Liverpool L69 7ZB, U.K
| | - Martin Larralde
- Ecole Normale Supérieure Paris-Saclay , 61 Avenue du Président Wilson, 94230 Cachan, France
| | - Masashi Yokochi
- Institute for Protein Research (IPR), Osaka University , 3-2 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research (IPR), Osaka University , 3-2 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan
| | - Andrea Porzel
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry , 06120 Halle (Saale), Germany
| | - Julian L Griffin
- Department of Biochemistry, University of Cambridge , Downing Site, Cambridge CB2 1QW, U.K
| | - Mark R Viant
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - David S Wishart
- Departments of Computing Sciences and Biological Sciences, University of Alberta , Edmonton, Canada T6G 2E8
| | - Christoph Steinbeck
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Reza M Salek
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry , Department of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany
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50
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Spicer RA, Salek R, Steinbeck C. Compliance with minimum information guidelines in public metabolomics repositories. Sci Data 2017; 4:170137. [PMID: 28949328 PMCID: PMC5613734 DOI: 10.1038/sdata.2017.137] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards.
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Affiliation(s)
- Rachel A. Spicer
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, UK
| | - Reza Salek
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, UK
| | - Christoph Steinbeck
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, UK
- Friedrich-Schiller-University, Fürstengraben 1, 07743 Jena, Germany
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