BIND: the Biomolecular Interaction Network Database

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BIND the Biomolecular Interaction Network
Database

• Gary D. Bader, Doron Betel and Christopher W. V.
  Houge

Seminar in Bioinformatics Elinor Heller
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Abstract

• What is Bind?
• Why do we need a tool like Bind?
• How does Bind work?

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What is Bind?

• Bind is a Database archive that hold information
  about
• Biomolecular interactions
• Reactions
• Complexes
• Pathways
• http//www.bind.ca

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Why do we need Protein Interaction Info?
Motivation
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Why do we need Protein Interaction Info? - cont

• Learning protein functions
• If two proteins interact, there is a very high
  possibility
• that their functions are related as well.
• Cellular operations are largely endured by
  interactions among proteins.
• From protein pathways to understanding cells,
  tissues, to life and evolution

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Protein interaction -example
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Why do we need Bind?

• Until 2001
• This type of data was stored in journal
  publications, where it is difficult to mine.

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Why do we need Bind?-cont

• The genome era has taught us that it is important
  to use effective tools for storing and managing
  data before they become too large.
• Preparing for the future A concerted effort by
  the biological community is required now to
  prepare for the interaction information of the
  near future .

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BIND -Goals

• Goals
• Provide a standard, comprehensive and integrated
  interaction resource to the scientific community
• Define protein function and mechanisms
• Recover and integrate biomolecular interaction
  knowledge
• Discover new knowledge through data mining

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BIND data specification

• The problem
• Storing different interactions, with different
  data structure in a generic way.
• Solution
• Using ASN.1
• Main concept
• ASN.1 is a formal notation used for describing
  data transmitted by telecommunications protocols,
  regardless of language implementation and
  physical representation of these data, whatever
  the application, whether complex or very simple.

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What is ASN1?

• ASN.1 Abstract Syntax Notation 1
• Internationally standardized data specification
  language used to build complex data types in a
  hierarchical manner - origins are Xerox
• Used in telephone systems, air traffic, building
  and machine control, toll highways, smart cards,
  security and more
• Used by NCBI to store GenBank, PubMed, MMDB and
  more
• For more info - http//www.oss.com/

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What kind of information does bind store?

• BIND stores information about interactions,
  molecular complexes and pathways.
• (These are the high level data types).

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Interactions

• interaction record stores a description of the
  binding event between two objects, A and B, which
  are generally molecules .

A
B
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Molecular complex

• a generally stable aggregate of molecules that
  have a function when linked together and are
  usually described as having sub-units.
• example
• the ribosome

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Pathways

• A pathway is defined as a group of molecules that
  are generally free from each other, but form a
  network of interactions usually to mediate some
  cellular function.

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Bind Objects

• An object in BIND is basically a molecule.
• It can be
• DNA RNA Protein Photon
• or a small/complex molecule.

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Bind Objects-cont

• The object record holds
• its name a list of name synonyms
• its origin - whether natural or not
• where it occurs in the cell
• the cell stages in which it occurs
• a sequence database reference to or a full
  instantiation of biological sequence and 3D
  structure.

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Bind Objects-cont

• Most of the biological information in BIND is
  stored in an interaction record .
• An interaction also stores

text description
cellular place of interaction
experimental conditions used to observe binding
binding sites on A and B and how they are connected
chemical action including kinetic and thermodynamic data and chemical state of the molecules
a comment on evolutionarily conserved biological sequence
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DATA SUBMISSION

• Data is entered into BIND either by manual or
  automatic methods.
• Who enters the data?
• Expert on the BIND team are entering high quality
  records on a continuing basis.
• Users are encouraged to enter records into the
  database by the web-based system, or to contact
  the BIND staff if they have large data sets they
  want to process.

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DATA SUBMISSION-cont

• How is a record submitted?
• First stage entering contact information.
• Second stage enter the PubMed identifier and two
  interacting molecules.
• Every record that is entered in this way will be
  validated by BIND indexers and by at least one
  other expert before it is made available in any
  public data release.

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DATA SUBMISSION-cont

• Submitters cannot limit the intended use of
  submitted BIND data
• Submitters have the right to edit/alter their
  records over time
• Suggestions made by a third party will be
  forwarded by us to the submitters to seek
  approval for any changes or corrections

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How Much Data ?
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BIND growth

• The fist version of BIND (June 1999)
• Contained over 1000 interaction records
• Pathways 6
• Complexes 40
• The last version of BIND
• Interactions 178004
• Pathways 8
• Complexes 3388

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Browsing BIND
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Visually Navigating BIND
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FAST parallel RPS BLAST
Used to spot domain similarities in a protein
interaction cluster Server-generated scalable
FLASHgraphics zoomable, printable. Followed-
up by zoom in on FASTA formatted sequences to see
domain superposition and links to SMART/PFAM
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Nucleic Acids Res. 2003 Jan 131(1)248-50
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More usages for BIND-1

• Helping direct future interaction studies
• example
• The human and mouse variants of the protein
  tyrosine kinase Fyn
• each have 9 recorded interactions in BIND
• Share 6 similar interactions
• The mouse variants is known to interact with a
  protein tyrosime kinase Vav.
• The human variant has no record of interaction
  with the Vav homologue.

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Example - continue
Using Bind in combination with other tools, it
has been lately discovered that Human
homologues with similar domain architecture to
mouse Fyn interactions can be identified.
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More usages for BIND-2

• Comparing between creatures with a different
  number of genes.
• Example
• Drosophila VS. C.elegans

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Example - continue

• Who has a higher Gene number?
• Who has larger Protein Interaction complexity ?

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References

• BIND the Biomolecular Interaction Network
  DatabaseGary D. Bader, Doron Betel, and
  Christopher W. V. Hogue. Nucleic Acids Res. 2003
  January 1 31(1) 248250.
• Bader G.D., Donaldson,I., Wolting,C.,
  Ouellette,B.F., Pawson,T. and Hogue,C.W. (2001)
  BINDthe biomolecular interaction network
  database. Nucleic Acids Res., 29, 242245.
• Bader G.D. and Hogue,C.W. (2000) BINDa data
  specification for storing and describing
  biomolecular interactions, molecular complexes a
  pathways. Bioinformatics, 16, 465477.
• The BIND and related tools 2005 update.
  D418-D422 Nucleic Acids Res, 2005 ,vol33. Doron
  Betel, and Christopher W. V. Hogue at el.
• http//www.bind.ca
• http//www.ncbi.nlm.nih.gov/
• http//www.oss.com/

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• THE END