Database Taxonomy

EMBL (European Molecular Biology Laboratory) [33] is a nucleotide sequence database provided from the online host EBl. Release 73 (December, 2002) consists of over 20 million nucleotide sequences with more than 28 billion nucleotides. The information includes sequence name, species, sequence length, promoter, taxonomy, and nucleic acid sequence. 

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

This chapter has only scratched the surface of the multitude of databases and data reviews that are now available. For instance, more than 100 materials databases of many kinds are listed by Wawrousek et al. (1989), in an article published by one of the major repositories of such databases. More and more of them are accessible via the internet. The most comprehensive recent overview of Electronic access to factual materials information the state of the art is by Westbrook et al. (1995), This highly informative essay includes a taxonomy of materials information , focusing on the many different property considerations and property types which an investigator can be concerned with. Special attention is paid to mechanical properties. The authors focus also on the quality and relutbility of data, quality of source, reproducibility, evaluation status, etc., all come into this, and alarmingly. 

Biichen-Osmond, Cornelia. ICTVdB The Universal Virus Database of the International Committee on Taxonomy of Viruses, http //www.ncbi.nlm.nih.gov/ICTVdb/index.htm. 2006. 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

Ehmayer, G., Kappel, G., and Reich, S., Connecting databases to the Web a taxonomy of gateways, Database and Expert Systems Applications 8th International Conference Proceedings, 1997. 

Specifying the taxonomy as closely as possible reduces the number of database entries that need to be considered in the search. This reduces search times, but more importantly, reduces the threshold score for significant matches, increasing the confidence of any protein identification. 

The NCBI s Entrez is apowerful database search engine. This integrated search engine provides a menu (http //www.ncbi.nih.gov/Entrez/index.html) offering the user selections to search biomedical literature (PubMed), databases on OMIM, nucleotide sequence, protein sequence, whole genome sequences, 3D macromolecular structures, taxonomy (organisms in GenBank), SNP,... 

The term flavour will be used in its broadest sense to incorporate aroma, taste, and mouth-feel. Yeast taxonomy is according to Kurtzman and Fell (1998), with the exception of the former species Saccharomyces uvarum, for which species status is still unresolved (Nguyen and Gaillardin 2005), and will therefore be recorded as Saccharomyces species bayanus/uvarum Yeast gene and enzyme notations are according to the Saccharomyces Genome Database (http //yeastgenome.org). 

The proteins separated by SDS-PAGE with MWs ranging from 10,000 Da to 100,000 Da were identified as adenoviral proteins from the SwissProt database when searched against all taxonomy. The results were summarized in Table 19-7. 

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

Taxonomy [19] is a database which contains the names of all organisms that are represented in the GENBANK with at least one nucleotide or protein sequence. The taxonomy database is organised as a tree, so the link from species to subspecies can be followed. Although taxonomy contains about 30 000 species represented in GENBANK, there is no comprehensive databank with all approximately 2 million known species. Other species data are available from projects such as Biodiversity and Species 2000. 

SeqHound is the basis for many of Blueprint s applications. The BIND Interaction Viewer 3.0 queries SeqHound to recover sequence annotation and interaction information. SeqHound has been used as a back end to replace all previous calls to the NCBI for retrieval of data such as GenBank records, taxonomy traversal, DNA and protein sequence by taxonomy ID or organism, 3D neighbors, and GO traversal. Recently the SeqHound API has been incorporated into Tavema [15], which allows biologists to assemble Web services into a pipeline. The current Web interface allows access only to the sequence aspects of the database, as the primary aim of SeqHound was to be a resource for programmers. However, a more fully featured interface is under development, which will make most of the API s functionality available to nonprogrammers. 

GenBank GenBank is the National Institute of Health database of all known nucleotide and protein sequences. Entries in the database include a description of the sequence, scientific name, and taxonomy of the source organism. Collaboration with the EMBL Data Library and the DNA Database of Japan enables shared data collection and sequence information. 

Database search parameters for the TOF/TOF data using the Mascot search engine Homo sapiens for taxonomy, NCBIr for database, no enzyme, no modifications, mass tolerance of the precursor ion at 0.2 kDa and the fragment ions at ... 

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