Publications

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results.
AR Jones, M Eisenacher, G Mayer, O Kohlbacher, J Siepen, SJ Hubbard, JN Selley, BC Searle, J Shofstahl, SL Seymour, R Julian, PA Binz, EW Deutsch, H Hermjakob, F Reisinger, J Griss, JA Vizcaíno, M Chambers, A Pizarro, D Creasy
Molecular and Cellular Proteomics, Vol. 11 (July 2012), M111.014381

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
S Orchard, S Kerrien, S Abbani, B Aranda, J Bhate, S Bidwell, A Bridge, L Briganti, FS Brinkman, G Cesareni, A Chatr-aryamontri, E Chautard, C Chen, M Dumousseau, J Goll, RE Hancock, LI Hannick, I Jurisica, J Khadake, DJ Lynn, U Mahadevan, L Perfetto, A Raghunath, S Ricard-Blum, B Roechert, L Salwinski, V Stümpflen, M Tyers, P Uetz, I Xenarios, H Hermjakob
Nature Methods, Vol. 9 (April 2012), pp. 345-350

PRIDE Inspector: a tool to visualize and validate MS proteomics data.
R Wang, A Fabregat, D Ríos, D Ovelleiro, JM Foster, RG Côté, J Griss, A Csordas, Y Perez-Riverol, F Reisinger, H Hermjakob, L Martens, JA Vizcaíno
Nature Biotechnology, Vol. 30 (February 2012), pp. 135-137, doi:10.1038/nbt.2112

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.
S Orchard, JP Albar, EW Deutsch, M Eisenacher, PA Binz, S Martinez-Bartolomé, JA Vizcaíno, H Hermjakob
Proteomics, Vol. 12 (February 2012), pp. 351-355, doi:10.1002/pmic.201290016

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
F Reisinger, R Krishna, F Ghali, D Ríos, H Hermjakob, JA Vizcaíno, AR Jones
Proteomics, Vol. 12 (March 2012), pp. 790-794, doi:10.1002/pmic.201100577

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
J Griss, F Reisinger, H Hermjakob, JA Vizcaíno
Proteomics, Vol. 12 (March 2012), pp. 795-798, doi:10.1002/pmic.201100578

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.
Andreas Römpp, Thorsten Schramm, Alfons Hester, Ivo Klinkert, Jean-Pierre Both, Ron Heeren, Markus Stöckli, Bernhard Spengler
Methods in molecular biology (Clifton, N.J.), Vol. 696 (2011), pp. 205-224, doi:10.1007/978-1-60761-987-1_12

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.
S Orchard, JP Albar, EW Deutsch, M Eisenacher, JA Vizcaíno, H Hermjakob
Proteomics, Vol. 11 (November 2011), pp. 4284-4290, doi:10.1002/pmic.201190117

Minimum information about a bioactive entity (MIABE).
Sandra Orchard, Bissan Al-Lazikani, Steve Bryant, Dominic Clark, Elizabeth Calder, Ian Dix, Ola Engkvist, Mark Forster, Anna Gaulton, Michael Gilson, Robert Glen, Martin Grigorov, Kim Hammond-Kosack, Lee Harland, Andrew Hopkins, Christopher Larminie, Nick Lynch, Romeena Mann, Peter Murray-Rust, Elena Lo, Piparo Christopher Southan, Christoph Steinbeck, David Wishart, Henning Hermjakob, John Overington, Janet Thornton
Nature reviews. Drug discovery, Vol. 10, No. 9. (31 September 2011), pp. 661-669, doi:10.1038/nrd3503

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Bruno Aranda, Hagen Blankenburg, Samuel Kerrien, Fiona Brinkman, Arnaud Ceol, Emilie Chautard, Jose Dana, Javier De, Las Rivas, Marine Dumousseau, Eugenia Galeota, Anna Gaulton, Johannes Goll, Robert Hancock, Ruth Isserlin, Rafael Jimenez, Jules Kerssemakers, Jyoti Khadake, David Lynn, Magali Michaut, Gavin O'Kelly, Keiichiro Ono, Sandra Orchard, Carlos Prieto, Sabry Razick, Olga Rigina, Lukasz Salwinski, Milan Simonovic, Sameer Velankar, Andrew Winter, Guanming Wu, Gary Bader, Gianni Cesareni, Ian Donaldson, David Eisenberg, Gerard Kleywegt, John Overington, Sylvie Ricard-Blum, Mike Tyers, Mario Albrecht, Henning Hermjakob
Nature methods, Vol. 8, No. 7. (29 July 2011), pp. 528-529, doi:10.1038/nmeth.1637

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