Modern high-throughput structural biology laboratories produce vast amounts of raw experimental data. The traditional method of data reduction is very simple—results are summarized in peer-reviewed publications, which are hopefully published in high-impact journals. By their nature, publications include only the most important results derived from experiments that may have been performed over the course of many years. The main content of the published paper is a concise compilation of these data, an interpretation of the experimental results, and a comparison of these results with those obtained by other scientists.
Due to an avalanche of structural biology manuscripts submitted to scientific journals, in many recent cases descriptions of experimental methodology (and sometimes even experimental results) are pushed to supplementary materials that are only published online and sometimes may not be reviewed as thoroughly as the main body of a manuscript. Trouble may arise when experimental results are contradicting the results obtained by other scientists, which requires (in the best case) the reexamination of the original raw data or independent repetition of the experiment according to the published description of the experiment. There are reports that a significant fraction of experiments obtained in academic laboratories cannot be repeated in an industrial environment (Begley CG & Ellis LM, Nature 483(7391):531–3, 2012). This is not an indication of scientific fraud but rather reflects the inadequate description of experiments performed on different equipment and on biological samples that were produced with disparate methods. For that reason the goal of a modern data management system is not only the simple replacement of the laboratory notebook by an electronic one but also the creation of a sophisticated, internally consistent, scalable data management system that will combine data obtained by a variety of experiments performed by various individuals on diverse equipment. All data should be stored in a core database that can be used by custom applications to prepare internal reports, statistics, and perform other functions that are specific to the research that is pursued in a particular laboratory.
This chapter presents a general overview of the methods of data management and analysis used by structural genomics (SG) programs. In addition to a review of the existing literature on the subject, also presented is experience in the development of two SG data management systems, UniTrack and LabDB. The description is targeted to a general audience, as some technical details have been (or will be) published elsewhere. The focus is on “data management,” meaning the process of gathering, organizing, and storing data, but also briefly discussed is “data mining,” the process of analysis ideally leading to an understanding of the data. In other words, data mining is the conversion of data into information. Clearly, effective data management is a precondition for any useful data mining. If done properly, gathering details on millions of experiments on thousands of proteins and making them publicly available for analysis—even after the projects themselves have ended—may turn out to be one of the most important benefits of SG programs.
Databases Data management Structural biology LIMS PSI CSGID
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The authors would like to thank Alex Wlodawer, Tom Terwilliger, Heidi Imker, Steve Almo, Wayne Anderson, Andrzej Joachimiak, Rachel Vigour, and Zbyszek Dauter for valuable comments on the manuscript. This work was supported by PSI:Biology grants U54 GM094585 and U54 GM094662 as well as grants R01 GM053163 and U54 GM093342. This work was also supported with federal funds from the NIAID, NIH, Department of Health and Human Services, under Contract Nos. HHSN272200700058C and HHSN272201200026C.
Begley CG, Ellis LM (2012) Drug development: Raise standards for preclinical cancer research. Nature 483(7391):531–533Google Scholar
Minor W et al (2006) HKL-3000: the integration of data reduction and structure solution—from diffraction images to an initial model in minutes. Acta Crystallogr D Biol Crystallogr 62(Pt 8):859–866PubMedCrossRefGoogle Scholar
Peat TS, Christopher JA, Newman J (2005) Tapping the Protein Data Bank for crystallization information. Acta Crystallogr D Biol Crystallogr 61(Pt 12):1662–1669PubMedCrossRefGoogle Scholar
Wlodawer A et al (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275(1):1–21PubMedCrossRefGoogle Scholar
Gabanyi MJ et al (2011) The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics 12(2):45–54PubMedCentralPubMedCrossRefGoogle Scholar
Chen L et al (2004) TargetDB: a target registration database for structural genomics projects. Bioinformatics 20(16):2860–2862PubMedCrossRefGoogle Scholar
O’Toole N et al (2004) The structural genomics experimental pipeline: insights from global target lists. Proteins 56(2):201–210PubMedCrossRefGoogle Scholar
Goh CS et al (2004) Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol 336(1):115–130PubMedCrossRefGoogle Scholar
Pajon A et al (2005) Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins 58(2):278–284PubMedCrossRefGoogle Scholar
Prilusky J et al (2005) HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Crystallogr D Biol Crystallogr 61(Pt 6):671–678PubMedCrossRefGoogle Scholar
Morris C et al (2011) The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory. Acta Crystallogr D Biol Crystallogr 67(Pt 4):249–260PubMedCentralPubMedCrossRefGoogle Scholar
Bucher MH, Evdokimov AG, Waugh DS (2002) Differential effects of short affinity tags on the crystallization of Pyrococcus furiosus maltodextrin-binding protein. Acta Crystallogr D Biol Crystallogr 58(Pt 3):392–397PubMedCrossRefGoogle Scholar
Koth CM et al (2003) Use of limited proteolysis to identify protein domains suitable for structural analysis. Methods Enzymol 368:77–84PubMedCrossRefGoogle Scholar
Cormier CY et al (2010) Protein structure initiative material repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res 38(Database issue):D743–D749PubMedCentralPubMedCrossRefGoogle Scholar
Page R et al (2003) Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome. Acta Crystallogr D Biol Crystallogr 59(Pt 6):1028–1037PubMedCrossRefGoogle Scholar
Kimber MS et al (2003) Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens. Proteins 51(4):562–568PubMedCrossRefGoogle Scholar
Newman J et al (2005) Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy. Acta Crystallogr D Biol Crystallogr 61(Pt 10):1426–1431PubMedCrossRefGoogle Scholar