Entrez: molecular biology database and retrieval system.

By G. Schuler, Jonathan A. Epstein, H. Ohkawa, J. Kans. 1996

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Citations in the corpus

PubChem Substance and Compound databases (2015, methodology): “E-Utilities, used for programmatic access to information contained in the Entrez system (31,32), are suited for accessing text or numeric-fielded data, but cannot deal with more complex types of data specific to PubChem, such as chemical structures and tabular bioactivity data.”
Database resources of the National Center for Biotechnology Information (2020, background): “Entrez (2) is an integrated database retrieval system that provides access to a diverse set of 34 databases that together contain 3.”
BIND: the Biomolecular Interaction Network Database (2003, methodology): “SeqHound is our in-house integrated database (18), similar in scope to the Entrez system (12), which contains extensive C, Cþþ and Perl programming APIs.”
Text-mining and information-retrieval services for molecular biology (2005, methodology): “Currently, biologists and bioinformaticians take advantage of those tools, not only when searching generic documents such as news articles using search engines such as Alta Vista [1] and Google [2], but especially when querying publications specific to biomedicine, for example those stored in PubMed”
NCBI GEO: mining millions of expression profiles—database and tools (2004, methodology): “The NCBI Entrez (5) database system is used as grounds for the query engine and retrieval system; two databases are deﬁned: (i) GEO DataSets stores all experimental metadata, providing an ‘experiment-centric’ perspective of GEO data.”
PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem (2015, methodology): “NCBI’s Entrez Utilities (also called E-Utilities or E-Utils) are used for programmatic access to information contained in the Entrez system (5,6).”
The NCBI Taxonomy database (2011, background): “Entrez (3) was the first system to link nucleotide sequences and protein sequences (from all of these sources) together with relevant abstracts from the scientific literature in a single unified resource.”
State of the nation in data integration for bioinformatics (2008, unknown): “Systems such as SRS [19], Entrez [20] and Integr8 [21] are portals and keyword indexing systems that maintain the interresource link network.”
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels (2006, background): “Cross-referenced links to external database are also provided, including Entrez Gene (14), TIGR’s Comprehensive Microbial Resource (CMR) (15), MIPS (16), EcoCyc (17) and PubMed.”
Database resources of the National Center for Biotechnology Information. (2019, background): “Entrez (1) is an integrated database retrieval system that provides access to a diverse set of 35 databases that together contain 2.”
NCBI GEO: mining tens of millions of expression profiles—database and tools update (2006, background): “Gene annotation is derived from querying sequence identifiers (e.g. GenBank accessions, clone IDs) with the latest Entrez Gene and UniGene databases, an important point given the dynamic nature of gene annotation.”
Database resources of the National Center for Biotechnology Information (2009, background): “Entrez (11) is an integrated database retrieval system that provides access to a diverse set of 38 databases that together contain over 400 million records (Table 1).”
Intermediate sequences increase the detection of homology between sequences. (1997, background): “Indeed information on intermediate sequences is available from the Entrez database (Schuler et al., 1996).”
Database resources of the National Center for Biotechnology Information (2010, background): “Entrez (6) is an integrated database retrieval system that provides access to a diverse set of 38 databases that together contain over 450 million records (Table 1).”
Database resources of the National Center for Biotechnology (2003, methodology): “Entrez (2) is an integrated database retrieval system for DNA and protein sequences derived from several sources (1,3–6), the NCBI taxonomy, genome maps, population sets, gene expression data, protein structures from the Molecular Modeling Database (MMDB) (7), 3D and alignment-based protein domains,”
What is Bioinformatics? A Proposed Definition and Overview of the Field (2001, background): “Another is the Entrez facility [42], which provides similar gateways to DNA and protein sequences, genome mapping data, 3D macromolecular structures and the PubMed bibliographic database [43].”
BLAST: improvements for better sequence analysis (2006, background): “These include highlighting mismatches between similar sequences, showing where the query was masked for low-complexity sequence and integrating information from the NCBI Entrez system (5) into the BLAST display.”
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins (2004, methodology): “NCBI makes RefSeq publicly available, at no cost, over the internet via FTP, Entrez query (1), Basic Local Alignment Search Tool (BLAST) (2,3) programs, and incorporation in a wide range of NCBI resources.”