Fast and efficient searching of biological data resources - using EB-eye

By F. Valentin, Silvano Squizzato, Mickael Goujon, Hamish McWilliam, J. Pärn, Rodrigo Lopez. 2010

39 citations recorded by the source corpus.

Subfields: Information Systems and Management, Molecular Biology

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In Molecular Biology

Citations in the corpus

A series of PDB related databases for everyday needs (2010, methodology): “Considering the substantial size of the aforementioned databases PDB, DSSP, HSSP and PDBREPORT (summing up to 160 GB in the summer of 2010), there is a strong need for a compact summary that can be parsed, searched [e.g. by SRS (37), EBeye (38) or MRS (39)], and analyzed quickly.”
Analysis Tool Web Services from the EMBL-EBI (2013, background): “The EB-eye Web Service is limited to retrieving data from selected ﬁelds stored in its indexes, so it is complemented by the dbfetch and WSDbfetch (9) services, which provide single or batch whole entry data retrieval based on entry identiﬁers.”
The IPD and IMGT/HLA database: allele variant databases (2014, methodology): “This information is also available through integration with European Bioinformatic Institute (EBI) EB-Eye search engine (20).”
The European Nucleotide Archive (2010, methodology): “Data can be queried using the EB-Eye free text search functionality available in the header section of all EBI web pages (7).”
The IPD-IMGT/HLA Database (2022, methodology): “• Sequence Search Tools – Integration into the suite of search tools provided by the EMBL-EBI include EB-eye (46), FASTA and BLAST (47,48) search tools.”
The EMBL-EBI bioinformatics web and programmatic tools framework (2015, methodology): “Integration of other resources such as EBI Search and dbfetch expands the resources the framework can draw on and facilitates user acquisition of biological data.”
IPD-IMGT/HLA Database (2019, methodology): “This information is also available through integration with the EB-eye Search Tool (31).”
Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services (2014, methodology): “These comprise services to search, retrieve, and run analysis tools on the databases hosted at the institute and to explore the network of cross-references present in the data— e.g., EBI Search (Park, Squizzato, Buso, Gur, & Lopez, 2017; Squizzato et al., 2015; Valentin et al., 2010).”