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

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

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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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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BIND-BLAST Lab 10.4

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Co-localization filtering! Lab 10.4

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BIND Divisions and Searching Lab 10.4

From BIND Stats to Sets Lab 10.4

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41 Identifier Searches Supported Lab 10.4

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

Division Controls Lab 10.4

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

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

Ribosomal protein contacts Lab 10.4

A ribosome interaction record Ribosomal protein L5AB Lab 10.4

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Individual contacts between L5AB and rRNA are highlighted in yellow

BIND Searching, Filtering, Reporting, Exporting Lab 10.4

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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… Lab 10.4

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Annotation Links Links to Domain DBs Links to AmiGO Lab 10.4

All GO sources are listed with Evidence Codes Lab 10.4

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

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

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

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

Select Lab 10.4

Invert Lab 10.4

Hide Selected Lab 10.4

Voila Only co-localized Proteins! Lab 10.4

Ontoglyps - complete details on blueprint.org Lab 10.4

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

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

FTP Site Browser Lab 10.4

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

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

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

SeqHound Lab 10.4

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

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

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

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

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

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

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