Curated databases

JWS Online. [197] A tool for simulation of kinetic models from a curated database http //www.jjj.bio.vu.nl/... 

MetaBase is a curated database of human protein-protein and protein-DNA interactions, transcriptional factors, signaling, metabolism and bioactive molecules. MetaCore provides intuitive tools for data visualization, mapping and exchange, multiple networking algorithms and data mining. 

The Insitute for Genomic Research (TIGR) provides a collection of curated databases containing DNA and protein sequences, gene expressions, cellular roles, protein families, and taxonomic data for microbes, plants, and humans. Anonymous FTP access to sequence data is also provided. 

Databases are electronic filing cabinets that serve as a convenient and efficient means of storing vast amounts of information. An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation. Their record is the sequence as it was experimentally derived. The DNA, RNA, or protein sequences are the items to be computed on and worked with as the valuable components of the primary databases. The secondary databases contain the fruits of analyses of the sequences in the primary sources such as patterns, motifs, functional sites, and so on. Most biochemical and/or molecular biology databases in the public domains are flat-file databases. Each entry of a database is given a unique identifier (i.e., an entry name and/or accession number) so that it can be retrieved uniformly by the combination of the database name and the identifier. 

II. Product Summary Jubilant Biosys has created some content products in the bioinformatics and chemoinformatics area. These products leverage Jubilant s curation services to incorporate extensive curated databases with structured query modules and front-ends for data retrieval. The content is for the drug discovery process, specifically in the areas of target prioritization and lead identification. The databases are available in Oracle, SD format, and ISIS/Base DB formats and can be exported. The database can be queried across text, structure, substructure and sequences with built-in query modules. Some of the key parameters on which information is curated are ... 

ERGO Light Integrated Genomics Curated database of public and proprietary genomic DNA with connected similarities, functions, pathways, functional models, and clusters (http //www.ergo-light.com/)... 

Additionally the curated database that includes functions likely for particular genes is occasionally discovered to be inaccurate. These errors can propagate through the database, as a gene incorrectly identified by its initial discoverer is used as a model in data mining, and all similar sequences are classified as having a similar function. If the initial identification is incorrect so will be the subsequent classifications. 

A number of companies have developed massive, manually curated databases. Some of these companies are... 

The Signal Transduction Knowledge Environment (table 7.1) is another expert-curated database, focusing exclusively on signaling pathways. It currently contains about 40 detailed and annotated pathway descriptions, including citations and graphical connection maps. Originally a collaboration between Stanford University and the journal Science, it is now available by subscription. 

To collaborate and share information, a proposal for a users group in metabonomics was put forth [110]. Since then, the Consortium for Metabonomic Toxicology (COMET) was formed and the first report from this group was given in 2003 [111]. The final report was just published [112]. This report describes what methodologies have been assessed, the development of a curated database for metabonomic profiles, and computer-based experts systems for data analysis. 

As indicated above, the focus of this review is on curated databases containing chemical structure and biological activity taken from literature sources. We nevertheless recognise the existence of a growing number of databases that also contain such structure and activity data but which do not fall within our primary scope. Of particular relevance here are databases that contain "raw" screening data, often generated by publicly-funded research initiatives. Two prominent examples are Pubchem [4] and Chembank [5]. 

Although this chapter is about the GenBank nucleotide database, GenBank is just one member of a community of databases that includes three important protein databases SWISS-PROT, the Protein Information Resomce (PIR), and the Protein DataBank (PDB). PDB, the database of nucleic acid and protein structures, is described in Chapter 5. SWISS-PROT and PIR can be considered secondary databases, curated databases that add value to what is already present in the primary databases. Both SWISS-PROT and PIR take the majority of their protein sequences from nucleotide databases. A small proportion of SWISS-PROT sequence data is submitted directly or enters through a journal-scanning effort, in which the sequence is (quite literally) taken directly from the published literature. This process, for both SWISS-PROT and PIR, has been described in detail elsewhere (Bairoch and Apweiller, 2000 Barker et al., 2000.)... 

Conceptually, the amino and carboxyl termini of a polypeptide chain are flexible and amendable to form a peptide bond. The formation of the terminally linked peptide bond yields circular (cyclic) proteins with circular backbones. Cyclic peptides such as cyclosporin are known. These peptides tend to be less than 12 amino acids in size, contain modifled amino acids and are generally metabolic products. Whereas circular proteins are 14-70 amino acids in size, true gene products (encoded by DNA) with well-defined 3D structures. They occur in microorganisms, plants and animals, as products for an enhanced stability or involvement in host defense (Trabi and Craik, 2002). Several naturally occurring circular proteins are listed in Table 5.10. CyBase (http //research.imb.uq.edu.au/ cybase) is the curated database for cyclic proteins. 

Cheng K, Sloan A, McCorrister S, et al. Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation. BMC Res Notes. 2014 7 444. doi 10.1186/1756-0500-7-444. 

A well-curated database and a large collection of plasmids and genomic libraries that are available. 

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