Lab 10.11 Interactions and Ontologies LAB CBW Bioinformatics Workshop February 23 th 2006, Toronto Christopher Hogue Blueprint Initiative.

Slides:

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Presentation transcript:

Lab Interactions and Ontologies LAB CBW Bioinformatics Workshop February 23 th 2006, Toronto Christopher Hogue Blueprint Initiative

Lab 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

Lab Predicting Interactions How to make reasonable-quality integrative interaction predictions? –STRING –Pre-BIND –BIND-BLAST Beware of GiGo.

Lab

Lab 10.15

6

7

8 Feb 2006

Lab 10.19

10

Lab Agilent Literature Search Cytoscape Plug-in Organism Constrained Vocabulary –Different model organism communities use different names for genes, these are best kept separate 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”

Lab Cytoscape: Various plug-ins do tasks Data retrieval Text Mining Microarray Network Analysis Modules

Lab

Lab Default is to scan 10 abstracts…

Lab

Lab BIND-BLAST

Lab

Lab

Lab

Lab Querying BIND

Lab Identifier Searches Supported

Lab Viewing BIND results

Lab

Lab

Lab Exporting Records

Lab Small Molecule Annotation

Lab BIND Interaction Viewer – p53

Lab DBP & 3DSM Division Interactions from 3D Structures

Lab A ribosome interaction record Ribosomal protein L5AB

Lab

Lab Individual contacts between L5AB and rRNA are highlighted in yellow

Lab StatusProjectBIND recordsCollaborators CompletedHuntingtin's Disease240University of British Columbia Dengue Virus279Novartis Institute for Tropical Medicine In progressHIV-12011NIAIDS & The Southern Research Institute Directed Curation Projects 4793 “dengue” papers in PubMed – 64 papers “HIV” papers in PubMed. 22,650 are REVIEW articles! How can a scientist manage to understand the underlying molecular mechanism of disease from publications? The VALUE of BIND is in reducing the time to find the papers with experimentally-derived mechanistic data and to rapidly view those mechanisms. Scientists can focus on cures and on experiments that provide new knowledge, rather than on swimming in papers!

Lab Viral Network Visualization HIV Integrase Proteasome Chaperones DNA Binding/Transcription Nuclear Transport

Lab From BIND Stats to Sets

Lab

Lab

Lab BIND to Cytoscape

Lab

Lab

Lab

Lab An Interaction Viewer (BIV + Cytoscape) is used by only about 1/10 users Released (PIM Rider=522 downlads since 03)

Lab

Lab

Lab

Lab

Lab

Lab FTP Site Browser

Lab The BIND Index contains selected fields for BIND records in plain- text, tab-delimited format. ftp://ftp.blueprint.org/pub/BIND/current/bindflatfiles/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.