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Name of Collaboratory :

 

Biomolecular Interaction Network Database (BIND)

 
 

Logo :

   
 
 

URL :

  http://www.bind.ca/  
 

Collaboratory Status :

 
In Development   Start Date : End Date : Info Last Updated : Fri, Dec 3 2010 4:01am PST
 
 

Primary Collaboratory Function :

  Community Data Systems  
 

Secondary Collaboratory Functions :

   
 

Domain(s) :

   
 

Brief Description of the Collaboratory :

 

3/4/11: 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.


*****PREVIOUSLY*****

"The Biomolecular Interaction Network Database (BIND) is a database designed to store full descriptions of interactions, molecular complexes and pathways."

Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW.

Department of Biochemistry, University of Toronto, Canada, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto M5G 1X5, Canada.

The Biomolecular Interaction Network Database (BIND; http://binddb. org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes can also be described. Everything from small molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. BIND anticipates the coming large influx of interaction information from high-throughput proteomics efforts including detailed information about post-translational modifications from mass spectrometry. Version 2.0 of the BIND data model is discussed as well as implementation, content and the open nature of the BIND project. The BIND data specification is available as ASN.1 and XML DTD.

The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature.

BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.

A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction.

Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways.

A molecular complex is a collection of two or more molecules that associate to form a function unit in a living organism. In BIND, these are represented as a molecular complex object, formed by linking two or more interaction records. Molecular complex records are supplemented with additional information such as complex topology and the number of subunits (BIND objects) involved in the interaction.

A pathways is a collection of two or more interactions that occur in a defined sequence within a living organism. In BIND, a these are represented by Pathway records that are formed by linking two or more interaction records. Pathway records are supplemented with additional information such as which stage of the cell cycle the pathway exists and whether the pathway is associated with a particular disease.

The object-oriented design of BIND has allows the database to represent a diversity of interactions in a format that is efficiently interpreted by computers and used by software engineers developing novel Bioinformatics tools. Thanks to submissions from Blueprint curators and external researchers, BIND has been growing exponentially since it inception in 1998. As BIND grows and receives submissions from researchers in different countries, researchers may use BIND to understand publicly available experimental data in a global context.

 
 

Access to Instruments :

   
 

Access to Information Resources :

  Rich resources for developers, including BIND source code at SourceForge.net; BIND/NCBI.ASN.1 Spec Browser; NCBI toolkit FTP site; Linking to BIND Records; and ASN.1 Resources (SLRI NCBI Toolkit Page; ASN.1 Information Site; The OSS ASN.1 Tools; ASN.1 homepage)  
 

Access to People as Resources :

  Curation of the BIND Database
Where do BIND records come from?
BIND curators review published literature to discover publications that describe the identification or characterization of molecular interaction. These publications are then converted into BIND records, human- and machine-readable versions of experimental evidence that supports the occurrence of an interaction, complex or pathway. Before BIND records are created, interactions are "backfilled", BIND is a public database and everyone is welcome to submit interactions through the BIND Submit/Edit page. Submissions currently come from BIND curators and from scientists wishing to include their interactions in the BIND database. To ensure that all interaction records maintain the standards described in the BIND Curation Reference Manual, each record is thoroughly scrutinized during two independent validation cycles by our group of in-house curators.


Who are the Curators?
Each BIND curator has hands-on scientific research experience in the field of molecular interactions. Their technical experties in the areas of signal transduction, enzyme kinetics and regulation of transcription and translation enables them to read the literature, extract data and enter records from an informed perspective. In addition, Principle Investigators with extensive knowledge in several areas of biochemistry oversee curators and provide an additional resource to enhance the fidelity of accurate interaction records.


Editing BIND Records
Feedback about BIND records is always welcome and can be sent to info@bind.ca. Any time we receive feedback, we will try to contact the original submitter and encourage them to edit their record. According to BIND principles, BIND curators may only edit records which were submitted by BIND curators. All other records must be edited by the scientists that originally submitted them. All edits are validated before the associated BIND records are updated.
 
 

Funding Agency or Sponsor :

   
 
 

Notes on Funding Agencies/Sponsors:
The Blueprint Initiative is a public good research program of the Samuel Lunenfeld Research Institute at Mount Sinai Hospital, affiliated with the University of Toronto. Blueprint has recently opened an affiliated node in Singapore.

 
 
 
TOTAL PARTICIPANTS:
 

Notes on Participants/Organizations:
Submitting Data to BIND
BIND contains three types of records: Interaction, Molecular Complex and Pathway. Click here for a brief description.

There are currently two methods available for BIND data submission.

1. If you are submitting 10 or fewer records, please use our submission site located at http://submit.bind.ca. Once you have registered as a BIND submitter, you will have access to create and submit interaction and complex records individually, along with their associated annotation.

2. If you are submitting greater than 10 records, you may use our batch submission service by contacting htp@blueprint.org. Send your submission in a spreadsheet file (i.e. StarOffice or MS Excel format) with the following information:


Interactions: Short labels, identifiers (e.g. GenBank accession numbers) and source information (e.g. taxonomy) for both Molecule A and Molecule B
Complexes: The Interaction accession numbers (i.e. BIND IDs) involved in this complex
Pathways: The Interaction accession numbers (i.e. BIND IDs) involved in this pathway
For all three types of submissions, clearly indicate your name, address, phone number, e-mail address and the PubMed ID for the publication. If the publication is submitted or in press, please include a pre-print.
For all three types of submissions you are encouraged to include all other relevant information, especially for the benefit of future BIND users. For example, experimental conditions, binding sites and cellular localization annotation can all be incorporated via batch submission.
Include any special requests you might have and we will do our best to accommodate you. For example, let us know if you do not wish the data to be released until a certain date.

More information pertaining to high throughput datasets may be found here.


Editing Data in BIND
You can edit any owned BIND records by using our submission site located at http://submit.bind.ca.

   
     
 
 

Communications Technology Used :

   
 

Technical Capabilities :

   
  Key Articles :    
 

Project-reported performance data :

 

****PREVIOUSLY****

Current BIND Database Statistics
Record Type Record Count
Interactions (All) 96285
Interactions (Spoke Model) 94786
Molecular Complexes 1857
Pathways 8
Organisms Represented 873
Sequences (GI's) 33966
Publications 9927
 
 
         
    
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