Biomolecular Object Network Databank: Difference between revisions

Revision as of 11:14, 15 March 2007

Revision as of 11:19, 15 March 2007

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The '''Biomolecular Object Network Databank''' ('''BOND''') is a database of of molecule interactions, which integrates a number of existing databses and provides additional functionality.

==Background==

{{Infobox Software|name=BOND|developer=Christopher Hogue et al., Samuel Lunenfeld Research Institute, Mount Sinai. Commercial rights: Unleashed Informatics|latest_release_version=BIND 4.0, SMIDsuite|genre=Bioinformatics tool|license=Open Access|website=[http://bond.unleashedinformatics.com/index.jsp?pg=0]}}

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The [[Blueprint Initiative]] started as a research program in the lab of [[Dr. Christopher Hogue]] at the [[Samuel Lunenfeld Research Institute]] at [[Mount Sinai Hospital in Toronto]]. On [[December 14]] [[2005]] [[Unleashed Informatics Limited]] acquired the commercial rights to The Blueprint Initiative [[intellectual property]]. This included rights to the protein interaction database BIND, the small molecule interaction database SMID, as well as the data warehouse SeqHound. Unleashed Informatics is a data management service provider and is overseeing the management and curation of The Blueprint Initiative under the guidance of Dr. Hogue.<ref>[http://www.blueprint.org Blueprint.org]</ref>

==Construction==

==Biomolecular Object Network Databank (BOND)==

The Biomolecular Object Network Databank, whichBOND integrates the original Blueprint Initiative databases as well as other databases, such as [[Genbank]], combined with many tools required to analyze these data. Annotation links for sequences, including [[taxon identifiers]], [[redundant sequences]], [[Genome Ontology descriptions]], [[Online Mendelian Inheritance in Man]] identifiers, [[conserved domains]], data base cross-references, [[LocusLink Identifiers]] and complete genomes are also available. Bond facilitates cross-database queries and is an [[open access]] resource which integrates interaction and sequence data[2].

==Small Molecule Interaction Database (SMID)==

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[[Image:Copy of BIND Screen.JPG|thumb|Figure 1: Screen shot of sequence results obtained using BOND ]]

The database user interface is web-based and can be queried using text or accession numbers/identifiers. Since its integration with the other components of BOND, sequences have been added to interactions, molecular complexes and pathways in the results. Records include information on: BIND ID, description of the interaction/complex/pathway, publications, update records, organism, OntoGlyphs, ProteoGlyphs, and links to other databases where additional information can be found. BIND records include various viewing formats (e.g. [[HTML]], [[ASN.1]], [[XML]], [[FASTA]]), various formats for exporting results (e.g. [[ASN.1]], [[XML]], [[GI list]], [[PDF]]), and visualizations (e.g. [[Cytoscape]]). The exact viewing and exporting options vary depending on what type of data has been retrieved.

==User statistics==