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A community standard format for the representation of protein affinity reagents.

David E Gloriam 1, 2 Sandra Orchard 1 Daniela Bertinetti 3 Erik Björling 4 Erik Bongcam-Rudloff 5 Carl a K Borrebaeck 6 Julie Bourbeillon 7, 8 Andrew R M Bradbury 9 Antoine de Daruvar 7, 10 Stefan Dübel 11 Ronald Frank 12 Toby J Gibson 13 Larry Gold 14 Niall Haslam 13 Friedrich W Herberg 3 Tara Hiltke 15 Jörg D Hoheisel 16 Samuel Kerrien 1 Manfred Koegl 17 Zoltán Konthur 18 Bernhard Korn 16 Ulf Landegren 19 Luisa Montecchi-Palazzi 1 Sandrine Palcy 10, 7 Henry Rodriguez 15 Sonja Schweinsberg 3 Volker Sievert 18 Oda Stoevesandt 20 Michael J Taussig 20 Marius Ueffing 21 Mathias Uhlén 4 Silvère van Der Maarel 22 Christer Wingren 23 Peter Woollard 24 David James Sherman 7, 8 Henning Hermjakob 1 
Abstract : Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.
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David E Gloriam, Sandra Orchard, Daniela Bertinetti, Erik Björling, Erik Bongcam-Rudloff, et al.. A community standard format for the representation of protein affinity reagents.. Molecular and Cellular Proteomics, American Society for Biochemistry and Molecular Biology, 2010, 9 (1), pp.1-10. ⟨10.1074/mcp.M900185-MCP200⟩. ⟨inria-00544751⟩



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