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Akune Y, Arpinar S, Silva LM, Palma AS, Tajadura-Ortega V, Aoki-Kinoshita KF, Ranzinger R, Liu Y, Feizi T. OUP accepted manuscript. Glycobiology 2022; 32:552-555. [PMID: 35352122 PMCID: PMC9191619 DOI: 10.1093/glycob/cwac018] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022] Open
Abstract
Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
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Affiliation(s)
- Yukie Akune
- Corresponding author: The Glycosciences Laboratory, Burlington Danes Building Room 509, Du Cane Road, London W12 0NN, United Kingdom.
| | - Sena Arpinar
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Lisete M Silva
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Angelina S Palma
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Lisbon, 2819-516 Caparica, Portugal
| | - Virginia Tajadura-Ortega
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
| | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Yan Liu
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
| | - Ten Feizi
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
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Aoki K, Kumagai T, Ranzinger R, Bergmann C, Camus A, Tiemeyer M. Serum N-Glycome Diversity in Teleost and Chondrostrean Fishes. Front Mol Biosci 2021; 8:778383. [PMID: 34859056 PMCID: PMC8631502 DOI: 10.3389/fmolb.2021.778383] [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: 09/16/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in carbohydrate chemistry, chemical biology, and mass spectrometric techniques have opened the door to rapid progress in uncovering the function and diversity of glycan structures associated with human health and disease. These strategies can be equally well applied to advance non-human health care research. To date, the glycomes of only a handful of non-human, non-domesticated vertebrates have been analyzed in depth due to the logistic complications associated with obtaining or handling wild-caught or farm-raised specimens. In contrast, the last 2 decades have seen advances in proteomics, glycoproteomics, and glycomics that have significantly advanced efforts to identify human serum/plasma biomarkers for various diseases. In this study, we investigated N-glycan structural diversity in serum harvested from five cultured fish species. This biofluid is a useful starting point for glycomic analysis because it is rich in glycoproteins, can be acquired in a sustainable fashion, and its contents reflect dynamic physiologic changes in the organism. Sera acquired from two chondrostrean fish species, the Atlantic sturgeon and shortnose sturgeon, and three teleost fish species, the Atlantic salmon, Arctic char, and channel catfish, were delipidated by organic extraction and the resulting protein-rich preparations sequentially treated with trypsin and PNGaseF to generate released N-glycans for structural analysis. Released N-glycans were analyzed as their native or permethylated forms by nanospray ionization mass spectrometry in negative or positive mode. While the basic biosynthetic pathway that initiates the production of glycoprotein glycan core structures is well-conserved across the teleost fish species examined in this study, species-specific structural differences were detected across the five organisms in terms of their monosaccharide composition, sialylation pattern, fucosylation, and degree of O-acetylation. Our methods and results provide new contributions to a growing library of datasets describing fish N-glycomes that can eventually establish species-normative baselines for assessing N-glycosylation dynamics associated with pathogen invasion, environmental stress, and fish immunologic responses.
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Affiliation(s)
- Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Tadahiro Kumagai
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States.,Procter & Gamble, Takasaki, Japan
| | - René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Carl Bergmann
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Alvin Camus
- College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
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Tiemeyer M, Aoki K, Paulson J, Cummings RD, York WS, Karlsson NG, Lisacek F, Packer NH, Campbell MP, Aoki NP, Fujita A, Matsubara M, Shinmachi D, Tsuchiya S, Yamada I, Pierce M, Ranzinger R, Narimatsu H, Aoki-Kinoshita KF. GlyTouCan: an accessible glycan structure repository. Glycobiology 2017; 27:915-919. [PMID: 28922742 PMCID: PMC5881658 DOI: 10.1093/glycob/cwx066] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 11/12/2022] Open
Abstract
Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.
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Affiliation(s)
- Michael Tiemeyer
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - James Paulson
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Richard D Cummings
- Harvard Medical School, 330 Brookline Ave, Room SL-0408, Boston, MA 02115, USA
| | - William S York
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | | | - Frederique Lisacek
- Swiss Institute of Bioinformatics, CUI - 7, route de Drize, CH-1211 Geneva, Switzerland
| | - Nicolle H Packer
- Institute for Glycomics, Gold Coast Campus, Griffith University, Parklands Drive, Gold Coast, QLD 4222, Australia
- Macquarie University, Balaclava Road, North Ryde, NSW 2109, Australia
| | - Matthew P Campbell
- Institute for Glycomics, Gold Coast Campus, Griffith University, Parklands Drive, Gold Coast, QLD 4222, Australia
| | - Nobuyuki P Aoki
- Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Akihiro Fujita
- Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Masaaki Matsubara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | | | | | - Issaku Yamada
- The Noguchi Institute, 1-9-7, Kaga, Itabashi-ku, Tokyo 173-0003, Japan
| | - Michael Pierce
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - René Ranzinger
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - Hisashi Narimatsu
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-0046, Japan
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Aoki-Kinoshita K, Agravat S, Aoki NP, Arpinar S, Cummings RD, Fujita A, Fujita N, Hart GM, Haslam SM, Kawasaki T, Matsubara M, Moreman KW, Okuda S, Pierce M, Ranzinger R, Shikanai T, Shinmachi D, Solovieva E, Suzuki Y, Tsuchiya S, Yamada I, York WS, Zaia J, Narimatsu H. GlyTouCan 1.0--The international glycan structure repository. Nucleic Acids Res 2016; 44:D1237-42. [PMID: 26476458 PMCID: PMC4702779 DOI: 10.1093/nar/gkv1041] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [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: 08/10/2015] [Revised: 09/15/2015] [Accepted: 09/30/2015] [Indexed: 11/14/2022] Open
Abstract
Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the 'face' of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused many duplicated efforts when integration is attempted between different databases, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary. As such, an international team of developers and glycobiologists have collaborated to develop this repository, called GlyTouCan and is available at http://glytoucan.org/, to provide a centralized resource for depositing glycan structures, compositions and topologies, and to retrieve accession numbers for each of these registered entries. This will thus enable researchers to reference glycan structures simply by accession number, as opposed to by chemical structure, which has been a burden to integrate glycomics databases in the past.
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Affiliation(s)
- Kiyoko Aoki-Kinoshita
- Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Japan Glycoscience and Glycotechnology Research Group, AIST, Ibaraki 305-8568, Japan
| | - Sanjay Agravat
- Department of Mathematics and Computer Science, Emory University, Atlanta, GA, 30322, USA
| | - Nobuyuki P Aoki
- Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Japan
| | - Sena Arpinar
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115,USA
| | - Akihiro Fujita
- Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Japan
| | - Noriaki Fujita
- Glycoscience and Glycotechnology Research Group, AIST, Ibaraki 305-8568, Japan
| | - Gerald M Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Stuart M Haslam
- Department of Life Sciences, Faculty of National Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Toshisuke Kawasaki
- Research Center for Glycobiotechnology, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | | | - Kelley W Moreman
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Michael Pierce
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Toshihide Shikanai
- Glycoscience and Glycotechnology Research Group, AIST, Ibaraki 305-8568, Japan
| | - Daisuke Shinmachi
- Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Japan
| | - Elena Solovieva
- Glycoscience and Glycotechnology Research Group, AIST, Ibaraki 305-8568, Japan
| | - Yoshinori Suzuki
- Glycoscience and Glycotechnology Research Group, AIST, Ibaraki 305-8568, Japan
| | | | | | - William S York
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Dept. of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hisashi Narimatsu
- Glycoscience and Glycotechnology Research Group, AIST, Ibaraki 305-8568, Japan
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Abstract
Over the last two decades, several carbohydrate structure databases have been developed and made publicly available by different research groups around the world. This led to the fragmentation of information about carbohydrate structures into different resources that have no or only weak interaction with each other. GlycomeDB was developed to integrate the carbohydrate structures from different resources by generating a single-indexed catalog of these structures that associates each structure with its reference in the original resources. GlycomeDB facilitates searching for carbohydrate structures in all the integrated resources by eliminating the need to use several different search interfaces and manually integrating the results. References provided by GlycomeDB make it possible to retrieve information that is beyond the scope of GlycomeDB but present in the integrated databases. This chapter illustrates the use of the GlycomeDB search interfaces and web services by way of three example cases.
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Affiliation(s)
- René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602-4712, USA,
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Damerell D, Ceroni A, Maass K, Ranzinger R, Dell A, Haslam SM. Annotation of glycomics MS and MS/MS spectra using the GlycoWorkbench software tool. Methods Mol Biol 2015; 1273:3-15. [PMID: 25753699 DOI: 10.1007/978-1-4939-2343-4_1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The GlycoWorkbench software tool allows users to semiautomatically annotate glycomics MS and MS/MS spectra and MS glycoproteomics spectra. The GlycanBuilder software tool is embedded within GlycoWorkbench allowing users to draw glycan structures and export images of the drawn structures. This chapter demonstrates to users how to draw glycan structures within GlycoWorkbench using the GlycanBuilder software tool. This chapter also demonstrates how to use GlycoWorkbench to import MS and MS/MS glycomics spectra and use the cascading annotation feature to annotate both the MS and MS/MS spectra with a single command.
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Affiliation(s)
- David Damerell
- Department of Life Sciences, Faculty of Natural Sciences, Sir Ernst Chain Building, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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7
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Abstract
Most currently available glycan structure databases use their own proprietary structure representation schema and contain numerous annotation errors. These cause problems when glycan databases are used for the annotation or mining of data generated in the laboratory. Due to the complexity of glycan structures, curating these databases is often a tedious and labor-intensive process. However, rigorously validating glycan structures can be made easier with a curation workflow that incorporates a structure-matching algorithm that compares candidate glycans to a canonical tree that embodies structural features consistent with established mechanisms for the biosynthesis of a particular class of glycans. To this end, we have implemented Qrator, a web-based application that uses a combination of external literature and database references, user annotations and canonical trees to assist and guide researchers in making informed decisions while curating glycans. Using this application, we have started the curation of large numbers of N-glycans, O-glycans and glycosphingolipids. Our curation workflow allows creating and extending canonical trees for these classes of glycans, which have subsequently been used to improve the curation workflow.
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Affiliation(s)
| | | | | | - René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-7404, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-7404, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-7404, USA
| | - William S York
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-7404, USA
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Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F. Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics 2014; 15 Suppl 1:S9. [PMID: 24564482 PMCID: PMC4016020 DOI: 10.1186/1471-2105-15-s1-s9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.
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Aoki-Kinoshita KF, Sawaki H, An HJ, Campbell M, Cao Q, Cummings R, Hsu DK, Kato M, Kawasaki T, Khoo KH, Kim J, Kolarich D, Li X, Liu M, Matsubara M, Okuda S, Packer NH, Ranzinger R, Shen H, Shikanai T, Shinmachi D, Toukach P, Yamada I, Yamaguchi Y, Yang P, Ying W, Yoo JS, Zhang Y, Zhang Y, Narimatsu H. The Fifth ACGG-DB Meeting Report: Towards an International Glycan Structure Repository. Glycobiology 2013. [DOI: 10.1093/glycob/cwt084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Aoki-Kinoshita KF, Sawaki H, An HJ, Cho JW, Hsu D, Kato M, Kawano S, Kawasaki T, Khoo KH, Kim J, Kim JD, Li X, Lütteke T, Okuda S, Packer NH, Paulson JC, Raman R, Ranzinger R, Shen H, Shikanai T, Yamada I, Yang P, Yamaguchi Y, Ying W, Yoo JS, Zhang Y, Narimatsu H. The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics. Glycobiology 2013; 23:144-6. [PMID: 23271684 DOI: 10.1093/glycob/cws167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM. EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology 2011; 21:493-502. [PMID: 21106561 PMCID: PMC3055595 DOI: 10.1093/glycob/cwq188] [Citation(s) in RCA: 104] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/03/2010] [Accepted: 11/03/2010] [Indexed: 01/03/2023] Open
Abstract
The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.
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Affiliation(s)
| | - Ana Ardá Freire
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Dennis Blank
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | - Matthew P Campbell
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Alessio Ceroni
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - David R Damerell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Anne Dell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Raymond A Dwek
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Beat Ernst
- Department of Pharmaceutical Science, University of Basel, BaselSwitzerland
| | - Rasmus Fogh
- European Bioinformatics Institute, Hinxton, UK
| | - Martin Frank
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Hildegard Geyer
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | - Rudolf Geyer
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | | | - Kim Henrick
- European Bioinformatics Institute, Hinxton, UK
| | - Stefan Herget
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - William E Hull
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | | | - Hiren J Joshi
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
- European Bioinformatics Institute, Hinxton, UK
| | - Johannis P Kamerling
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Bas R Leeflang
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Thomas Lütteke
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | | | - Kai Maass
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | | | - René Ranzinger
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Jimmy Rosen
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Louise Royle
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Pauline M Rudd
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Siegfried Schloissnig
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Roland Stenutz
- Organic Chemistry, Stockholm University, Stockholm, Sweden
| | | | - Göran Widmalm
- Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Stuart M Haslam
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Abstract
GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank, which renders the database currently the most comprehensive and unified resource for carbohydrate structures worldwide. GlycomeDB retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases. The complete database can be downloaded freely or accessed through a Web-interface (www.glycome-db.org) that provides flexible and powerful search functionalities.
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Affiliation(s)
- René Ranzinger
- German Cancer Research Center, DKFZ, Core Facility, Molecular Structure Analysis, W160, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics 2010; 1:8. [PMID: 20727200 PMCID: PMC2939597 DOI: 10.1186/2041-1480-1-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 08/21/2010] [Indexed: 11/30/2022] Open
Abstract
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.
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Affiliation(s)
- Toshiaki Katayama
- Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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Ranzinger R, Frank M, von der Lieth CW, Herget S. Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. Glycobiology 2009; 19:1563-7. [PMID: 19759275 DOI: 10.1093/glycob/cwp137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite ongoing harmonization efforts, the major carbohydrate sequence databases following the first initiative in this field, CarbBank, are still isolated islands, with mechanisms for automatic structure exchange and comparison largely missing. This unfavorable situation has been overcome with a systematic data integration effort, resulting in the GlycomeDB, a meta-database for public carbohydrate sequences. It contains at present 35,056 unique structures in GlycoCT encoding, referencing more than 100,000 external records from 1845 different taxonomic sources. We have created a user-friendly, web-based graphical interface which allows taxonomic and structural data to be entered and searched for. The structural search possibilities include substructure search, similarity search, and maximum common substructure. A novel search refinement mechanism allows the assembly of complex queries. With GlycomeDB (www.glycome-db.org), it is now possible to use a single portal to access all digitally encoded, public structural data in glycomics and to perform complex queries with the help of a web-based user interface.
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Affiliation(s)
- René Ranzinger
- German Cancer Research Center, Molecular Structure Analysis (W160), Molecular Modeling Group, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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Ranzinger R, Herget S, Wetter T, von der Lieth CW. GlycomeDB - integration of open-access carbohydrate structure databases. BMC Bioinformatics 2008; 9:384. [PMID: 18803830 PMCID: PMC2567997 DOI: 10.1186/1471-2105-9-384] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [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: 04/04/2008] [Accepted: 09/19/2008] [Indexed: 11/19/2022] Open
Abstract
Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.
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Affiliation(s)
- René Ranzinger
- German Cancer Research Center DKFZ, Core Facility Molecular Structural Analysis, Im Neuenheimer Feld 280, Heidelberg, Germany.
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Herget S, Toukach PV, Ranzinger R, Hull WE, Knirel YA, von der Lieth CW. Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. BMC Struct Biol 2008; 8:35. [PMID: 18694500 PMCID: PMC2543016 DOI: 10.1186/1472-6807-8-35] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 08/11/2008] [Indexed: 11/24/2022]
Abstract
Background There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are typically displayed at the cell surface, they can interact with the environment and, therefore, have significant biomedical importance. Results The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties. Conclusion For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.
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Affiliation(s)
- Stephan Herget
- Core Facility: Molecular Structure Analysis (W160), German Cancer Research Center, Heidelberg, Germany.
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Maass K, Ranzinger R, Geyer H, von der Lieth CW, Geyer R. “Glyco-peakfinder” -
de novo
composition analysis of glycoconjugates. Proteomics 2007; 7:4435-44. [DOI: 10.1002/pmic.200700253] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Werz DB, Ranzinger R, Herget S, Adibekian A, von der Lieth CW, Seeberger PH. Exploring the structural diversity of mammalian carbohydrates ("glycospace") by statistical databank analysis. ACS Chem Biol 2007; 2:685-91. [PMID: 18041818 DOI: 10.1021/cb700178s] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The diversity of three major classes of mammalian carbohydrates, mainly glycolipids and O- and N-linked glycans, deposited in the databank GLYCOSCIENCES.de was subjected to statistical analyses. Size, chain length, and branching complexity were accessed and revealed that the average oligosaccharide is composed of about eight monosaccharide units. About a quarter of all oligosaccharides are strictly linear, and the remainder are branched at least once. Glucosamine, galactose, and mannose are dominating and comprise ~75% of the monosaccharides within mammalian oligosaccharide frameworks. alpha-Linked sialic acid, alpha-linked fucose, and beta-linked galactose decorate the majority of reducing termini. Glucose as the most abundant carbohydrate in mammals plays only a very minor role within these structures. Particular emphasis was placed on analyzing the way the monosaccharide units are linked within the oligomeric framework. Just 11 monosaccharide connections account for >75% of all linkages. Thus, the number of structural combinations found in nature, the part of the occupied mammalian glycospace, is much smaller than expected. As a result, a potential set of building blocks for oligosaccharide assembly is presented. This potential building block set was correlated with the accessible 3299 mammalian carbohydrate structures in the GLYCOSCIENCES.de databank. Only 36 building blocks are required to construct 75% of the 3299 mammalian oligosaccharides.
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Affiliation(s)
- Daniel B. Werz
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology (ETH) Zürich, HCI F 315, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
- Present address: Institute for Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany
| | - René Ranzinger
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Stephan Herget
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Alexander Adibekian
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology (ETH) Zürich, HCI F 315, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | | | - Peter H. Seeberger
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology (ETH) Zürich, HCI F 315, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
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Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth CW. Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. Nucleic Acids Res 2007; 35:D280-6. [PMID: 17202164 PMCID: PMC1899093 DOI: 10.1093/nar/gkl883] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at and the GLYCOSCIENCES.de portal at
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Affiliation(s)
| | - Hiren J Joshi
- German Cancer Research Center, Spectroscopic Department (B090)Molecular Modeling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - René Ranzinger
- German Cancer Research Center, Spectroscopic Department (B090)Molecular Modeling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | | | - Claus-W. von der Lieth
- German Cancer Research Center, Spectroscopic Department (B090)Molecular Modeling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 424541; Fax: +49 6221 42454;
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Abstract
Using a web browser without additional software and generating interactive high quality and high resolution images of bio-molecules is no longer a problem. Interactive visualization of 3D molecule structures by Internet browsers normally is not possible without additional software and the disadvantage of browser-based structure images (e.g. by a Java applet) is their low resolution. Scientists who want to generate 3D molecular images with high quality and high resolution (e.g. for publications or to render a molecule for a poster) therefore require separately installed software that is often not easy to use. The alternative concept is an interactive server-side rendering application that can be interfaced with any web browser. Thus it combines the advantage of the web application with the high-end rendering of a raytracer. This article addresses users who want to generate high quality images from molecular structures and do not have software installed locally for structure visualization. Often people do not have a structure viewer, such as RasMol or Chime (or even Java) installed locally but want to visualize a molecule structure interactively. AISMIG (An Interactive Server-side Molecule Image Generator) is a web service that provides a visualization of molecule structures in such cases. AISMIG-URL: .
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Affiliation(s)
| | - Wolf-Dieter Groch
- University of Applied Sciences, Department of Computer ScienceSchöfferstr. 8b, D-64295 Darmstadt, Germany
| | - René Ranzinger
- To whom correspondence should be addressed. Tel: +49 6221 42 4670; Fax: +49 6221 42 2995;
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