1. Interactions and Ontologies
First & Last Name
February X, 2003
Interactions and Ontologies
CBW Bioinformatics Workshop
February 24th 2004, Vancouver
Christopher Hogue
Blueprint Initiative
Lab 10.4
(c) 2003 CGDN

2. In the lab Predicting Interactions with
First & Last Name
February X, 2003
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 10.4
(c) 2003 CGDN

3. Predicting Interactions
How to make reasonable-quality integrative interaction predictions?
STRING
Pre-BIND
BIND-BLAST
Beware of GiGo.
Lab 10.4

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9. Lab 10.4

10. 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”
Lab 10.4

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14. BIND-BLAST
Lab 10.4

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19. Co-localization filtering!
Lab 10.4

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21. BIND Divisions and Searching
Lab 10.4

22. From BIND Stats to Sets
Lab 10.4

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24. Lab 10.4

25. 41 Identifier Searches Supported
Lab 10.4

26. BIND Divisions Blueprint Databases Partner 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
Lab 10.4

27. Division Controls
Lab 10.4

28. Displays Interactions in Cn3D, and generates experimental
MMDBBIND
Displays Interactions in Cn3D, and
generates experimental
annotation from PDB
comments
Lab 10.4

29. MMDBBIND is a large fraction of BIND – most of the records are oligomers.
Lab 10.4

30. Ribosomal protein contacts
Lab 10.4

31. A ribosome interaction record
Ribosomal protein L5AB
Lab 10.4

32. Lab 10.4

33. Individual contacts between L5AB and rRNA are highlighted in yellow

34. BIND Searching, Filtering, Reporting, Exporting
Lab 10.4

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47. OntoGlyphs A graphical language Derived from Gene Ontology annotation
The most-used terms/categories
A means of compressing molecular function concepts into tiny spaces…
Lab 10.4

48. Lab 10.4

49. Annotation Links
Links to Domain DBs
Links to AmiGO
Lab 10.4

50. All GO sources are listed with Evidence Codes
Lab 10.4

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52. Lab 10.4

53. HIV Integrase Interaction Network Red – DNA binding Blue – Protein Transport
Lab 10.4

54. DNA Binding/Transcription
Proteasome
Chaperones
Nuclear Transport
DNA Binding/Transcription
Lab 10.4

55. BIND Viewer Tool – atp14
Many hits
From yeast-two-hybrid data
Lab 10.4

56. Lab 10.4

57. Too many…
Which molecules
are co-localized
With the atp14?
Lab 10.4

58. Select
Lab 10.4

59. Invert
Lab 10.4

60. Hide Selected
Lab 10.4

61. Voila
Only
co-localized
Proteins!
Lab 10.4

62. Ontoglyps - complete details on blueprint.org
Lab 10.4

63. Blueprint’s FTP Site and the BIND Index
First & Last Name
February X, 2003
Blueprint’s FTP Site and the BIND Index
Lab 10.4
(c) 2003 CGDN

64. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

65. FTP Site Browser
Lab 10.4

66. First & Last Name
February X, 2003
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.
Lab 10.4
(c) 2003 CGDN

67. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

68. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

69. SeqHound
Lab 10.4

70. Application Programing Interface
What is SeqHound?
GenBank
MMDB
MedLine
BIND
Taxonomy, GO,
LocusLink, CDD
SeqHound
SeqHound Module
Database Interface
Application Programing Interface
Local Programmer
Web Interface
Remote Interface
Lab 10.4
Web user
Remote Programmer

71. First & Last Name
February X, 2003
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.
Lab 10.4
(c) 2003 CGDN

72. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

73. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

74. 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 "SHoundFindAcc ";
$aa = SHoundFindAcc("CAA28783");
print "SHoundFini ";
$aa = SHoundFini();
Lab 10.4

75. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

76. Lab 10.4