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The '''Biomolecular Object Network Databank'''
==Background==
{{Infobox
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 (Toronto)|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==
BOND 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, [[Gene Ontology]] descriptions, [[Online Mendelian Inheritance in Man]] identifiers, [[conserved domains]], data base cross-references, LocusLink Identifiers and complete genomes are also available.
==Small Molecule Interaction Database (SMID)==
The [[Small Molecule]] Interaction Database is a database containing protein ___domain-small molecule interactions. It uses a ___domain-based approach to identify ___domain families, found in the [[Conserved Domain Database]] (
SMID can be queried by entering a protein GI, ___domain identifier, PDB ID or SMID ID. The results of a search provide small molecule, protein, and ___domain information for each interaction identified in the database. Interactions with non-biological contacts are normally screened out by default.
SMID-BLAST is a tool developed to annotate known small-molecule binding sites as well as to predict binding sites in proteins whose [[crystal structures]] have not yet been determined. The prediction is based on extrapolation of known interactions, found in the PDB, to interactions between an uncrystallized protein with a small molecule of interest. SMID-BLAST was validated against a test set of known small molecule interactions from the PDB. It was shown to be an accurate predictor of protein-small molecule interactions; 60% of predicted interactions identically matched the PDB annotated binding site, and of these 73% had greater than 80% of the binding residues of the protein correctly identified. Hogue, C et al. estimated that 45% of predictions that were not observed in the PDB data do in fact represent true positives.
==Biomolecular Interaction Network Database (BIND)==
===Introduction===
The idea of a database to document all known molecular interactions was originally put forth by [[Anthony Pawson|Tony Pawson]] in the
The major goals of the BIND project are: to create a public proteomics resource that is available to all; to create a platform to enable [[datamining]] from other sources (PreBIND); to create a platform capable of presenting visualizations of complex molecular interactions. From the beginning, BIND has been [[Open access (publishing)|open access]] and software can be freely distributed and modified. Currently, BIND includes a data specification, a database and associated data mining and visualization tools. Eventually, it is hoped that BIND will be a collection of all the interactions occurring in each of the major model organisms.
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===Database structure===
BIND contains information on three types of data: interactions, molecular complexes and pathways.
# Interactions are the basic component of BIND and describe how 2 or more objects (A and B) interact with each other. The objects can be a variety of things: [[DNA]], [[RNA]], [[genes]], [[proteins]], [[ligands]], or [[photons]]. The interaction entry contains the most
# The second type of BIND entries are the molecular complexes. Molecular complexes are defined as an aggregate of molecules that are stable
# The third component of BIND is the pathway record section. A pathway consists of a network of interactions that are involved in the regulation of cellular processes. This section may also contain information on phenotypes and diseases related to the pathway.
<br />The minimum amount of information needed to create an entry in BIND is a [[PubMed]] publication reference and an entry in another database (e.g. [[GenBank]]). Each entry
BIND is based on a data specification written using Abstract Syntax Notation 1 ([[ASN.1]]) language. ASN.1 is used also by [[National Center for Biotechnology Information|NCBI]] when storing data for their [[Entrez]] system and because of this BIND uses the same standards as NCBI for data representation. The ASN.1 language is preferred because it can be easily translated into other data specification languages (e.g. [[XML]]), can easily handle complex data and can be applied to all biological interactions – not just proteins.
===Data submission and curation===
User submission to the database is encouraged. To contribute to the database, one must submit: contact info, [[PubMed]] identifier and the two molecules that interact. The person who submits a record is the owner of it. All records are validated before being made public and BIND is curated for quality assurance. BIND curation has two tracks: high-throughput (HTP) and low-throughput (LTP). HTP records are from papers which have reported more than 40 interaction results from one experimental methodology. HTP curators typically have a [[bioinformatics]] backgrounds. The HTP curators are responsible for the collection of storage of experimental data and they also create scripts to update BIND based on new publications. LTP records are curated by individuals with either an MSc or PhD and laboratory experience in interaction research. LTP curators are given further training through the [[Canadian Bioinformatics Workshops]]. Information on [[small molecule]] chemistry is curated separately by chemists to ensure the curator is knowledgeable about the subject. The priority for BIND curation is to focus on LTP to collect information as it is published. Although, HTP studies provide more information at once, there are more LTP studies being reported and similar numbers of interactions are being reported by both tracks. In 2004, BIND collected data from 110 journals.<ref name= "2005 update">Alfarano, C, ''et al.'' The Biomolecular Interaction Network Database and related tools 2005 update. ''Nucleic Acids Research'' 33: D418-D424 (2005).
===Database growth===
BIND has grown significantly since its conception; in fact, the database saw a 10 fold increase in entries between 2003 and 2004. By September 2004, there were over 100,000 interaction records by 2004 (including 58,266 protein-protein, 4,225 genetic, 874 protein-small molecule, 25,857 protein-DNA, and 19,348 biopolymer interactions). The database also contains sequence information for 31,972 proteins, 4560 DNA samples and 759 RNA samples. These entries have been collected from 11,649 publications; therefore, the database represents an important amalgamation of data. The organisms with entries in the database include: ''[[Saccharomyces cerevisiae]]'', ''[[Drosophila melanogaster]]'', ''[[Homo sapiens]]'', ''[[Mus musculus]]'', ''[[Caenorhabditis elegans]]'', ''[[Helicobacter pylori]]'', ''[[Bos taurus]]'', [[HIV-1]], ''[[Gallus gallus]]'', ''[[Arabidopsis thaliana]]'', as well as others. In total, 901 [[taxa]] were included by September 2004 and BIND has been split up into BIND-Metazoa, BIND-Fungi, and BIND-Taxroot.<ref name= "2005 update"/>
Not only is the information contained within the database continually updated, the software itself has gone through several revisions. Version 1.0 of BIND was released in 1999 and based on user feedback it was modified to include additional detail on experimental conditions required for binding and a hierarchical description of cellular ___location of the interaction. Version 2.0 was released in 2001 and included the capability to link to information available in other databases.<ref name= "BIND, 2001"/> Version 3.0 (2002) expanded the database from physical/biochemical interactions to also include genetic interactions.<ref name= "BIND, 2003">Bader, GD, ''et al.''. BIND: the Biomolecular Interaction Network Database. ''Nucleic Acids Research'' 31: 248-250 (2003).</ref> Version 3.5 (2004) included a refined user-interface that aimed to simplify information retrieval.<ref name= "2005 update"/> In 2006, BIND was incorporated into the Biomolecular Object Network Database (BOND) where it continues to be updated and improved.
===Special features===
BIND was the first database of its kind to contain info on biomolecular interactions, reactions and pathways in one schema. It is also the first to base its [[ontology]] on chemistry which allows 3D representation of molecular interactions. The underlying chemistry allows molecular interactions to be described down to the atomic level of resolution.<ref name= "2005 update"/>
PreBIND an associated system for data mining to locate biomolecular interaction information in the scientific literature. The name or [[Accession number (bioinformatics)|accession number]] of a protein can be entered and PreBIND will scan the literature and return a list of potentially interacting proteins. BIND [[BLAST (biotechnology)|BLAST]] is also available to find interactions with proteins that are similar to the one specified in the query.<ref name= "2005 update"/>
BIND offers several “features” that many other proteomics databases do not include. The authors of this program have created an extension to traditional [[IUPAC]] nomenclature to help describe [[post-translational modifications]] that occur to amino acids. These modifications include: [[acetylation]], [[formylation]], [[methylation]], [[palmitoylation]], etc. the extension of the traditional IUPAC codes allows these amino acids to be represented in sequence form as well. BIND also utilizes a unique visualization tool known as [[OntoGlyphs]]. The OntoGlyphs were developed based on [[Gene Ontology]] (GO) and provide a link back to the original GO information. A number of GO terms have been grouped into categories, each one representing a specific function, binding specificity, or localization in the cell. There are 83 OntoGlyph characters in total. There are 34 functional OntoGlyphs which contain information about the role of the molecule (e.g. cell physiology, ion transport, signaling). There are 25 binding OntoGlyphs which describe what the molecule binds (e.g. ligands, DNA, ions). The other 24 OntoGlyphs provide information about the ___location of the molecule within a cell (e.g. nucleus, cytoskeleton). The OntoGlyphs can be selected and manipulated to include or exclude certain characteristics from search results. The visual nature of the OntoGlyphs also facilitates pattern recognition when looking at search results.
===Accessing the database===
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==User statistics==
The number of Unleashed Registrants has increased 10 fold since the integration of BIND. As of December 2006 registration fell just short of 10,000. Subscribers to the commercial versions of BOND fall into six general categories; [[agriculture]] and [[food]], [[biotechnology]], [[pharmaceuticals]], [[Information technology|informatics]], [[Biomaterial|materials]] and other. The biotechnology sector is the largest of these groups, holding 28% of subscriptions. Pharmaceuticals and informatics follow with 22% and 18% respectively. The [[United States]] holds the bulk of these subscriptions, 69%. Other countries with access to the commercial versions of BOND include [[Canada]], the [[United Kingdom]], [[Japan]], [[China]], [[Korea]], [[Germany]], [[France]], [[India]] and [[Australia]]. All of these countries fall below 6% in user share.<ref name= "BOND"/>
==References==
{{reflist}}
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