Two-dimensional databases

Wattiez R et al. Human bronchoalveolar lavage fluid protein two-dimensional database study of interstitial lung diseases. Electrophoresis 2000 21 2703-2712. Yanagida M et al. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry analysis of proteins detected by anti-phosphotyrosine antibody on two-dimensional-gels of fibrolast cell lysates after tumor necrosis factor-alpha stimulation. Electrophoresis 2000 21 1890-1898. 

Fountoulakis M et al. Two-dimensional database of mouse liver proteins changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol. Electrophoresis 2000 21 2148-2161. 

Wattiez R et al. Human bronchoalveolar lavage fluid protein two-dimensional database study of interstitial lung diseases. Electrophoresis 2000 21 2703-2712. 

Fountoulakis, M., Bemdt, R, Boelsterli, U.S., Crameri, F., Winter, M., Albertini, S., and Suter, L., Two-dimensional database of mouse liver proteins changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol, Electrophoresis 21, 2148-2161, 2000. 

Poirier, F., Pontet, M., Labas, V., Le Caer, J.P., Sghiouar-lmam, N., Raphael, M., Caron, M., and Jouhert-Caron, R., 2001c, Two-dimensional database of a Burkitt l)unphoma cell line (DG 75) proteins Protein pattern changes following treatment with 5 -azyc)hidine. 

Diagnostic studies on oligoclonal IgG, however, are better carried out by two-dimensional analysis. Characteristic changes in CSF proteins derived from the CNS have been associated with CNS disorders such as amytrophic lateral sclerosis and Fluntingdon s chorea. Increased ai-haptoglobin levels are associated with Alzheimer s disease and schizophrenia and an increase in apolipoprotein E with low back pain. The establishment of two-dimensional databases of CSF proteins will be of considerable... 

Different problems for substructure searching on chiral compounds arise in two-dimensional structure databases compared with three-dimensional databases. The two-dimensional case is the worse of the two, because two-dimensional databases... 

The characteristic of a relational database model is the organization of data in different tables that have relationships with each other. A table is a two-dimensional consti uction of rows and columns. All the entries in one column have an equivalent meaning (c.g., name, molecular weight, etc. and represent a particular attribute of the objects (records) of the table (file) (Figure 5-9). The sequence of rows and columns in the tabic is irrelevant. Different tables (e.g., different objects with different attributes) in the same database can be related through at least one common attribute. Thus, it is possible to relate objects within tables indirectly by using a key. The range of values of an attribute is called the domain, which is defined by constraints. Schemas define and store the metadata of the database and the tables. 

The National Chemical Laboratory for Industry (NCLl), Japan, has developed an integrated Spectral Database System (SDBS) which is available to users in Japan. AU spectra were deterrnined at NCLl under controUed conditions and are available on a PC/CD-ROM or magnetic tape. The system has both H-nmr (6000 compounds) and C-nmr spectra (5700 compounds), along with searching software. NCLl has also developed an integrated C— H-nmr system that can be used for two-dimensional data elucidation (70,71). 

Other Individual Country Databases and Auxiliary Files. The USPatents files on ORBIT, supphed by Derwent, are similar ia their contents to the CLAIMS-Bibliographic files, including all the front page information and the full claims language. These files do not iaclude the two-dimensional stmctures provided by IFI, nor do they have IFI s standardization of assignee names. Citation searching is available at a cost considerably less than that for the portion of the CLAIMS-Citation file that covers the same period. 

Henzel, W. J., Billeci, T. M., Stults, J. T., and Wong, S. C. (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90, 5011-5015. 

If sample patterns in a large database are each defined by just two values, a two-dimensional plot may reveal clustering that can be detected by the eye (Figure 3.1). However, in science our data often have many more than two dimensions. An analytical database might contain information on the chemical composition of samples of crude oil extracted from different oilfields. Oils are complex mixtures containing hundreds of chemicals at detectable levels thus, tire composition of an oil could not be represented by a point in a space of two dimensions. Instead, a space of several hundred dimensions would be needed. To determine how closely oils in the database resembled one another, we could plot the composition of every oil in this high-dimensional space, and then measure the distance between the points that represent two oils the distance would be a measure of the difference in composition. Similar oils would be "close together" in space,... 

Fabian and Kalman [5] retrieved 50 structures from the Cambridge Structural Database, including the polymorphs of 22 compounds, in order to evaluate the frequency of isostructurality among polymorphs. It was found that one-, two-, or three-dimensional isostructurality was exhibited by approximately one-half of the compounds studied. Three-dimensional isostructurality was connected to the gradual ordering of crystal structures, while one- and two-dimensional isostructurality could be related to specific packing interactions. Interestingly, conformational polymorphs were not found to exhibit isostructurality. 

Journet A et al. Towards a human repertoire of monocytic lysosomal proteins. Electrophoresis 2000 21 3411-3419. Soskic V et al. Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor. Biochemistry 1999 38 1757-1764. Thiede B et al. A two dimensional electrophoresis database of a human Jurkat T-cell line. Electrophoresis 2000 21 2713-2720. 

Scharfe C et al. MITOP, the mitochondrial proteome database 2000 update. Nucleic Acids Res 2000 28 155-158. Molloy MP et al. Establishment of the human reflex tear two-dimensional polyacrylamide gel electrophoresis reference map new proteins of potential diagnostic value. Electrophoresis 1997 18 2811-2815. 

Anderson NL et al. An updated two-dimensional gel database of rat liver proteins useful in gene regulation and drug effect studies. Electrophoresis 1995 16 1977-1981. 

W. J. Henzel, et al., Identifying Proteins from Two-Dimensional Gels by Molecular Mass Searching of Peptide Fragments in Protein Sequence Databases. Proc. Natl. Acad. Sci. U.S.A., 90, no. 11 (1993) 5011-5015. 

In this way, the vectors at nodes in different regions in the two-dimensional map gradually evolve to represent different classes of sample (Figure 13). If, by way of example, the database contained information on a large numbers of solvents, with data on their ability to dissolve a variety of common solids, once training was complete, those solvents that were effective... 

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