Retrieval biology

Jelier, R., Jenster, G., Dorssers, L.C.J., van der Eijk, C.C., van Mulligen, E.M., Mons, B., Kors, J.A. 2005. Co-occurrence based meta-analysis of scientific texts retrieving biological relationships between genes. Bioinformatics. 21(9) 2049-2058... 

In 1983 we undertook a major overhaul of our existing system and, for reasons which I shall briefly discuss, we put early emphasis on the module for storing and retrieving biological test data. The new system, which we called ABACUS (Advanced Biological And Chemical Unified System) has been operational for about 18 months although it is still evolving. 

The previously retrieved biological data sub-file would be used to query the inventory file. Once matching records (i.e. records with the seune sample numt>er) were found they would be checked for an amount on hand equal to or greater than 500 mg and no shipment to test system MM. If these criteria are met, the matching inventory records are used to create a new SUBSET file. The search may then continue to obtain additional information from the chemistry files. The Report Generator would then process all appropriate SUBSET files according to criteria specified by the user to generate the final report. 

The factor A has been measured for a variety of samples, indicating that the approximation can be applied up to quasi-atomic resolution. In the case of biological specimens typical values of are of the order of 5-7%, as detemiined from images with a resolution of better than 10 A [37,38]- For an easy interpretation of image contrast and a retrieval of the object infomiation from the contrast, such a combination of phase and amplitude hifomiation is necessary. 

Biological indicators for steam sterilization utilize bacillus stearothermophilus. In monitoring industrial cycles, a sufficient number of preparations each having a known degree of resistance are added to the load and retrieved after exposure, and cultured. 

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

Krallinger M, Valencia A. Text-mining and information-retrieval services for molecular biology. Genome Biol 2005 6 224. 

All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Methods in Molecular Biology is a trademark of The Humana Press Inc. 

The advent of new techniques to collect undisturbed sediment cores, with well preserved sediment - water interface has brought into sharper focus the various deep sea sedimentary processes, their rates and their effects on the preserved records. As mentioned earlier, recent studies have shown that the record contained in sediments is not a direct reflection of the delivery pattern of a substance to the ocean floor as has so far been assumed the record is modified as a result of several complex physical, chemical and biological processes. Therefore, information on the temporal variations in the tracer input to oceans, if sought, has to be deciphered from the sediment-residuum. In the following we consider one specific example of retrieval of information from the sediment pile the application of deep sea sediments to obtain historical records of cosmic ray intensity variations. 

PC-Based Information Products Floppy Disk Based. We currently have ready access to a rapidly growing variety of relevant information resources. From a current awareness perspective, an excellent source of weekly information is the floppy disk-based product called Current Contents on Diskette (CCOD). Several versions are available however, the Life Sciences version is most appropriate for this review because of its coverage, on a weekly basis, of over 1200 journals describing work in the biological sciences. One will note that the product has several useful features, including very quick retrieval of article citations as well as several output options (including either hard copy or electronic storage of references as well as reprint requests). 

The assembly of large screening libraries for HTS requires the development of archival and retrieval systems that can handle solid compounds and compound solutions in microtubes or in plates in either the 96 or the 384 format. Barcodes are used to identify each sample vial, tube, or plate. Databases record which samples are available, what type of sample it is, and how much is available. All solid samples are prepared first as stock (master) solutions ( around 5 mg/mL in DMSO) in 2-D bar-coded tubes that are then aliquotted to plates and processed as described earlier. The tubes and plates are usually made of polypropylene for compatibility with DMSO. DMSO is the industry standard solvent for screening libraries because many of the archived compounds are not soluble in water at 5 mg/mL. DMSO, an organic solvent, also has a favorable combination of biological... 

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