Interactions and Ontologies

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Interactions and Ontologies

CBW Bioinformatics Workshop February 24th 2004,
Vancouver Christopher Hogue Blueprint Initiative
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In the lab

• Predicting Interactions with
• STRING
• PreBIND
• BIND BLAST
• BIND Stats, Divisions, MMDBBIND
• BIND Searching, Filtering, Reporting, Exporting
• Exporting Data to Excel Cytoscape
• OntoGlyphs BIND Interaction Viewer
• BIND Index
• SeqHound SeqHound API

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Predicting Interactions

• How to make reasonable-quality integrative
  interaction predictions?
• STRING
• Pre-BIND
• BIND-BLAST
• Beware of GiGo.

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PreBIND

• Organism Constrained Vocabulary
• Hybrid Text-Mining Approach
• Score abstracts that have pairs of gene/protein
  names
• Score these for matches to patterns of words
  found in interaction abstracts
• Score them again for interaction sentences

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BIND-BLAST
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Co-localization filtering!
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BIND Divisions and Searching
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From BIND Stats to Sets
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41 Identifier Searches Supported
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BIND Divisions

• Blueprint Databases
• BIND Taxroot
• BIND Fungi
• BIND Metazoa
• RefBIND Taxroot
• BIND 3DBP
• BIND 3DSM (SMID)

• Partner Databases
• HIV-HPID
• MIPS
• FlyBASE
• MGI
• SGD
• IMEX Partners
• MINT
• IntACT
• DIP (?)
• Pathway Partners

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Division Controls
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MMDBBIND Displays Interactions in Cn3D,
and generates experimental annotation from
PDB comments
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MMDBBIND is a large fraction of BIND most of
the records are oligomers.
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Ribosomal protein contacts
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A ribosome interaction record
Ribosomal protein L5AB
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Individual contacts between L5AB and rRNA are
highlighted in yellow
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BIND Searching, Filtering, Reporting, Exporting
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OntoGlyphs

• A graphical language
• Derived from Gene Ontology annotation
• The most-used terms/categories
• A means of compressing molecular function
  concepts into tiny spaces

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Annotation Links
Links to Domain DBs
Links to AmiGO
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All GO sources are listed with Evidence Codes
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HIV Integrase Interaction Network Red DNA
binding Blue Protein Transport
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Proteasome
Chaperones
Nuclear Transport
DNA Binding/Transcription
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BIND Viewer Tool atp14
Many hits From yeast-two-hybrid data
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Too many Which molecules are co-localized With
the atp14?
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Select
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Invert
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Hide Selected
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Voila Only co-localized Proteins!
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Ontoglyps - complete details on blueprint.org
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Blueprints FTP Site and the BIND Index
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FTP Site Browser
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The BIND Index contains selected fields for BIND
records in plain-text, tab-delimited format.
ftp//ftp.blueprint.org/pub/BIND/current/bindflat
files/bindindex/ These files may be used to
locate BIND records that describe a given
biomolecule. BIND records contain many other
fields than those listed in these indices.
Complete BIND records are available in XML or
ASN.1 format from ftp//ftp.bind.ca/pub/BIND/data.

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SeqHound
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What is SeqHound?
GenBank
MedLine
BIND
MMDB
Taxonomy, GO, LocusLink, CDD
SeqHound
SeqHound Module
Database Interface
Application Programing Interface
Local Programmer
Remote Interface
Web Interface
Web user
Remote Programmer
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SeqHound is a bioinformatics application
programming platform. A remote application
programming interface (API) in C, C, PERL or
Java is available.This API will give you access
to a database of biological sequences and
structures. Seqhound also stores additional
information related to each of these sequences.
This includes links to Genome Ontology
descriptions, Medline abstracts, taxon
descriptions, associated structures, redundant
sequences, sequence neighbours, conserved
domains, database cross-references, Online
Mendelian Inheritance in Man identifiers,
LocusLink identifiers and complete genomes.
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A sample SeqHound program using the Perl API
!/usr/bin/perl -w use strict use
SeqHound print "Starting Program\n" print
"SHoundInit " my aa SHoundInit("TRUE",
"myapp") print "aa\n" print "SHoundIsInited
" aa SHoundIsInited() print "aa\n" print
"SHoundFindAcc " aa SHoundFindAcc("CAA28783")
print "aa\n" print "SHoundFini " aa
SHoundFini() print "aa\n"
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