Biomolecular Object Network Databank: Difference between revisions

Revision as of 00:49, 29 November 2015

Latest revision as of 15:11, 19 January 2024

(12 intermediate revisions by 9 users not shown)

Line 1:

The '''Biomolecular Object Network Databank''' is a [[bioinformatics]] [[databank]] containing information on [[small molecule]] and , structures and interactions. The databank integrates a number of existing databases to provide a comprehensive overview of the information currently available for a given molecule.

==Background==

{{Infobox Softwaresoftware|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]}}

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. BOND facilitates cross-database queries and is an [[Open access (publishing)|open access]] resource which integrates interaction and sequence data.<ref name= "BOND">[http://bond.unleashedinformatics.com BOND at Unleashed Informatics] {{webarchive|url=https://web.archive.org/web/20070314195713/http://bond.unleashedinformatics.com/ |date=March 14, 2007 }}</ref>

==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]] (CDD), which interact with a query small molecule. The CDD from [[National Center for Biotechnology Information|NCBI]] amalgamates data from several different sources; [[Protein FAMilies]] (PFAM), [[Simple Modular Architecture Research Tool]] (SMART), [[Cluster of Orthologous Genes]] (COGs), and NCBI’sNCBI's own curated sequences. The data in SMID is derived from the Protein Data Bank (PDB), a database of known protein crystal structures.

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.

Line 18:

===Introduction===

The idea of a database to document all known molecular interactions was originally put forth by [[Anthony Pawson|Tony Pawson]] in the 1990s and was later developed by scientists at the [[University of Toronto]] in collaboration with the [[University of British Columbia]]. The development of the Biomolecular Interaction Network Database (BIND) has been supported by grants from the Canadian Institutes of Health Research ([[CIHR]]), Genome Canada,<ref>[https://www.genomecanada.ca/en/biomolecular-interaction-network-database-bind BIND at genomecanada.ca]</ref> the Canadian Foundation for Innovation and the Ontario Research and Development Fund. BIND was originally designed to be a constantly growing depository for information regarding biomolecular interactions, molecular complexes and pathways. As [[proteomics]] is a rapidly advancing field, there is a need to have information from scientific journals readily available to researchers. BIND facilitates the understanding of molecular interactions and pathways involved in cellular processes and will eventually give scientists a better understanding of developmental processes and disease pathogenesis

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.

Line 24:

===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 amount of information about a molecule; it provides information on its name and synonyms, where it is found (e.g. where in the cell, what species, when it is active, etc.), and its sequence or where its sequence can be found. The interaction entry also outlines the experimental conditions required to observe binding in vitro, chemical dynamics (including [[thermodynamics]] and [[chemical kinetics|kinetics]]).

# The second type of BIND entries are the molecular complexes. Molecular complexes are defined as an aggregate of molecules that are stable and have a function when bound to each other. The record may also contain some information on the role of the complex in various interactions and the molecular complex entry links data from 2 or more interaction records.

# 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 withiinwithin the database provides references/authors for the data. As BIND is a constantly growing database, all components of BIND track updates and changes.<ref name= "BIND, 2001">Bader, GD, ''et al.'' BIND- The Biomolecular Interaction Network Database. ''Nucleic Acids Research'' 29: 242-245 (2001).</ref>

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.<ref name= "BIND, 2001"/> Bader and Hogue (2000) have prepared a detailed manuscript on the ASN.1 data specification used by BIND.<ref name= "BIND, 2000">Bader, GD, Hogue, CWV. BIND- a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. ''Bioinformatics'' 16(5): 465-477 (2000).</ref>

Line 42:

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.<ref name= "2005 update"/> [[ProteoGlyphs]] are graphical representations of the structural and binding properties of proteins at the level of conserved domains. The protein is diagrammed as a straight horizontal line and glyphs are inserted to represent conserved domains. Each glyph is displayed to represent the relative position and length of its alignment in the protein sequence.

Line 55:

==References==

{{reflist}}

<references />

[[Category:BiologicalBiochemistry databases]]