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

2. Lab 10.12 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

3. Lab 10.13 Predicting Interactions How to make reasonable-quality integrative interaction predictions? –STRING –Pre-BIND –BIND-BLAST Beware of GiGo.

4. Lab 10.14 http://string.embl.de/

5. Lab 10.15

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8. 8 Feb 2006

9. Lab 10.19

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11. Lab 10.111 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”

12. Lab 10.112 Cytoscape: Various plug-ins do tasks Data retrieval Text Mining Microarray Network Analysis Modules

13. Lab 10.113

14. Lab 10.114 Default is to scan 10 abstracts…

15. Lab 10.115

16. Lab 10.116 BIND-BLAST

17. Lab 10.117

18. Lab 10.118

19. Lab 10.119

20. Lab 10.120 Querying BIND

21. Lab 10.121 41 Identifier Searches Supported

22. Lab 10.122 Viewing BIND results

23. Lab 10.123

24. Lab 10.124

25. Lab 10.125 Exporting Records

26. Lab 10.126 Small Molecule Annotation

27. Lab 10.127 BIND Interaction Viewer – p53

28. Lab 10.128 3DBP & 3DSM Division Interactions from 3D Structures

29. Lab 10.129 A ribosome interaction record Ribosomal protein L5AB

30. Lab 10.130

31. Lab 10.131 Individual contacts between L5AB and rRNA are highlighted in yellow

32. Lab 10.132 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. 182778 “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!

33. Lab 10.133 Viral Network Visualization HIV Integrase Proteasome Chaperones DNA Binding/Transcription Nuclear Transport

34. Lab 10.134 From BIND Stats to Sets

35. Lab 10.135

36. Lab 10.136

37. Lab 10.137 BIND to Cytoscape

38. Lab 10.138

39. Lab 10.139

40. Lab 10.140

41. Lab 10.141 An Interaction Viewer (BIV + Cytoscape) is used by only about 1/10 users Released (PIM Rider=522 downlads since 03)

43. Lab 10.143

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45. Lab 10.145

46. Lab 10.146

47. Lab 10.147

48. Lab 10.148 FTP Site Browser

49. Lab 10.149 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.