The "4D Biology Workshop for Health and Disease", held on 16-17th ofMarch 2010 in Brussels, aimed at finding the best organising principlesfor large-scale proteomics, interactomics and structural... Show moreThe "4D Biology Workshop for Health and Disease", held on 16-17th ofMarch 2010 in Brussels, aimed at finding the best organising principlesfor large-scale proteomics, interactomics and structural genomics/biology initiatives, and setting the vision for future high-throughputresearch and large-scale data gathering in biological and medical science.Major conclusions of the workshop include the following. (i)Development of new technologies and approaches to data analysis iscrucial. Biophysical methods should be developed that span a broadrange of time/spatial resolution and characterise structures andkinetics of interactions. Mathematics, physics, computational andengineering tools need to be used more in biology and new tools needto be developed. (ii) Database efforts need to focus on improveddefinitions of ontologies and standards so that system-scale data andassociated metadata can be understood and shared efficiently. (iii)Research infrastructures should play a key role in fosteringmultidisciplinary research, maximising knowledge exchange betweendisciplines and facilitating access to diverse technologies. (iv)Understanding disease on a molecular level is crucial. Systemapproaches may represent a new paradigm in the search for biomarkersand new targets in human disease. (v) Appropriate education andtraining should be provided to help efficient exchange of knowledgebetween theoreticians, experimental biologists and clinicians. Theseconclusions provide a strong basis for creating major possibilities inadvancing research and clinical applications towards personalisedmedicine. Show less
Bourbeillon, J.; Orchard, S.; Benhar, I.; Borrebaeck, C.; Daruvar, A. de; Dubel, S.; ... ; Sherman, D. 2010
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... Show moreProtein 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 online 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. Molecular & Cellular Proteomics 9: 1-10, 2010. Show less
