Entrez retrieval system

All the data are from the Genome Division of the Entrez retrieval system (http // www.ncbi.nlm.nih.gov/Entrez/Genome/org.html). 

Entrez (http //www.ncbi.nih.gov/entrez), information retrieval system, integrating NCBI databases of protein and nucleotide sequences, genomes, macromolecular stmctures, and MEDLINE literature database. 

Searching through Databases Applications of network BLAST server, 266, 131 Entrez molecular biology database and retrieval system, 266, 141 applying motif and profile searches,... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

Retrieve one sequence (either DNA or protein) each from three major database retrieval systems—Entrez, SRS of EBI, and DBGet—and compare their outputs. 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

Schuler, G. D., Epstein, J. A., Ohkawa, H., and Kans, J. A. (1996). Entrez Molecular biology database and retrieval system. Methods Enzymol. 266, 141-162. 

NCBI s Molecular Modeling Database (MMDB Hogue et al., 1996) is an integral part of NCBTs Entrez information retrieval system (cf. Chapter 7). It is a compilation of all the Brookhaven Protein Data Bank (Bernstein et al., 1977) three-dimensional... 

Figure 7.1. Overview of the relationships in the Entrez integrated information retrieval system. Each square represents one of the elements that can be accessed through Entrez, and the lines represent how each element connects to the other elements. Entrez is under continuous evolution, with both new components being added and the interrelationships between the elements changing dynamically.

Two comprehensive integrated retrieval systems for nucleic acids and proteins, Entrez of NCBI, and SRS of EBI will be described briefly. The molecular biology database and retrieval system, Entrez (Schuler et al 1996) was developed at and maintained by NCBI of NIH to allow retrieval of biochemical data and bibliographic citation from its integrated databases. Entrez typically provides access to ... 

Figure 14.13 Comprehensive bioinformatic retrieval system of Entrez...

MEDLINE (Medical Literature Analysis and Retrieval System Online) A bibliographic database administered by the US National Library of Medicine (NLM) that contains over 16 million references to journal articles in life sciences and medicine. Cover e extends to more than 5000 journals, with particular emphasis on US journals, and over half a million new records are added annually. The articles are indexed using the NLM s Medical Subject Heading (MeSH) thesaurus, which permits searching using both alphabetical and hierarchical approaches. MEDLINE is the major component of the NLM s PubMed database and can be accessed via Entrez. 

PubMed The US NLM at the NIH maintains PubMed as part of the Entrez information retrieval system. It is a free search engine for searching citations in MEDLINE. PubMed also provides access and hnks to the other Entrez molecular biology resources. PubMed also provides links to other sites providing full-text articles. 

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