Standardisation and Guidelines

The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

  1. Frank Gibson1,
  2. Christine Hoogland2,
  3. Salvador Martinez-Bartolomé3,
  4. J. Alberto Medina-Aunon3,
  5. Juan Pablo Albar3,
  6. Gyorgy Babnigg4,
  7. Anil Wipat1,
  8. Henning Hermjakob5,
  9. Jonas S. Almeida6,
  10. Romesh Stanislaus6,
  11. Norman W. Paton7,
  12. Andrew R. Jones8,*

Article first published online: 19 JUL 2010

DOI: 10.1002/pmic.201000120

Issue

PROTEOMICS

PROTEOMICS

Volume 10, Issue 17, pages 3073–3081, No. 17 September 2010

Additional Information

How to Cite

Gibson, F., Hoogland, C., Martinez-Bartolomé, S., Medina-Aunon, J. A., Albar, J. P., Babnigg, G., Wipat, A., Hermjakob, H., Almeida, J. S., Stanislaus, R., Paton, N. W. and Jones, A. R. (2010), The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative. Proteomics, 10: 3073–3081. doi: 10.1002/pmic.201000120

Author Information

  1. 1

    School of Computing Science, Newcastle University, Newcastle, UK

  2. 2

    Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland

  3. 3

    ProteoRed, Proteomics Facility, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain

  4. 4

    Biosciences Division, Argonne National Laboratory, Argonne, IL, USA

  5. 5

    European Molecular Biology Laboratory (EMBL) – European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK

  6. 6

    Department of Bioinformatics and Computational Biology, The University of Texas MDAnderson Cancer Center, Houston, TX, USA

  7. 7

    School of Computer Science, University of Manchester, Manchester, UK

  8. 8

    Department of Comparative Molecular Medicine, School of Veterinary Science, University of Liverpool, Liverpool, UK

*Department of Comparative Molecular Medicine, School of Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, UK Fax: +44-151-7944243

Publication History

  1. Issue published online: 25 AUG 2010
  2. Article first published online: 19 JUL 2010
  3. Manuscript Accepted: 9 JUN 2010
  4. Manuscript Revised: 19 MAY 2010
  5. Manuscript Received: 26 FEB 2010

Funded by

  • BBSRC. Grant Number: BB/G010781/1
  • NIH/CTSA. Grant Number: 1UL1RR024148
  • University of Tuebingen

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article with Supporting Information (HTML) Get PDF (331K)

Keywords:

  • Bioinformatics;
  • Database;
  • Data standard;
  • Gel electrophoresis;
  • Ontology

Abstract

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

View Full Article with Supporting Information (HTML) Get PDF (331K)