Modware

Modware: An Object-oriented Perl Interface to the Chado Schema Eric Just Senior Bioinformatics Scientist dictyBase: http://dictybase.org Northwestern University Generic Model Organism Database Project (GMOD)

Agenda

What?

What is Chado?

What is Modware?

Why?

How?

Example: a protein coding gene

Storing in Chado

Writing a Web Page with Modware

Try

Getting Modware

What is Chado?

Standardized genomics database schema

Developed by FlyBase

Adopted and distributed by GMOD project

Extremely flexible and compact

Heavy ontology usage

Entity-Attribute-Value tables

Modularized for different areas of bioinformatics

See Talk on Chado at ISMB (Paper 65)

What is Modware

Open-source tool for programmers who write software to QUERY AND UPDATE Chado

Object-oriented API with semantically sensible classes and methods

Developed at dictyBase

Working with GMOD

Agenda

What?

What is Chado?

What is Modware?

Why?

How?

Storing in database

Try

Getting Modware

Why Modware Exists

Chado has many business rules

Modware encapsulates many Chado business rules

Faster, more efficient development time

More readable code

UI changes, logic does not

Leverage GMOD/Chado/Open Source community

Agenda

What?

What is Chado?

What is Modware?

Why?

How?

Storing in database

Try

Getting Modware

A Simple Gene Example A gene is a region on a chromosome that encloses one or more transcript objects. An mRNA is a protein-coding transcript is composed of one or more exons which have coordinates on a chromosome. Chromosome 3

Storing mlcE in Chado CV (controlled vocabulary) Feature Featureloc Feature_relationship CVterm 1 68706 68256 104 100 1 67982 67979 103 100 1 68706 67979 102 100 1 68706 67979 101 100 strand fmax fmin feature_id srcfeature name Feat_type Feat_id _DDB0214813_exon_2 253 104 _DDB0214813_exon_1 253 103 DDB0214813 252 102 mlcE 251 101 Chr 3 250 100 Sequence Ontology 1 cv cv_id 1 mRNA 252 1 exon 253 1 gene 251 1 chromosome 250 cv cvterm cvterm_id Located on part of part of Sequence Ontology 1 Relationsip Ontology 2 cv cv_id 1 exon 253 1 mRNA 252 2 part_of 301 1 gene 251 1 chromosome 250 cv cvterm cvterm_id 102 301 104 102 301 103 101 301 102 object_id type_id subject_id

A Simple Gene Page

#!/usr/bin/perl use Modware::Feature; use CGI; my $id = CGI::param(‘primary_id'); my $count = 1; # Get all data from database my $feature = new Modware::Feature( -primary_id => $id ); my $chromosome = $feature->reference_feature()->name(); my $gene = $feature->gene()->name(); my @exons = $feature->bioperl()->exons(); my $sequence = $feature->sequence( -type => ’protein', -format => 'fasta' ); # print the report print CGI->header; print "<pre>"; print $id." is on chromosome $chromosome"; print " and is the gene $gene "; # print the number and position of each exon foreach my $exon (@exons) { print "Exon $count. start=".$exon->start(). " end=".$exon->end()." "; $count++; } print $sequence; print "</pre>";

Modware::Features

Modware Feature Classes

Gene

mRNA

ncRNA

Contig

Chromosome

EST

Generic (catch-all)

Modware can manage

the following annotations

Sequence

Location

Name

Synonyms

Description

Public identifiers

External identifiers

(dbxrefs)

Modware::Search

These classes retrieve groups (iterators) of features

Modware::Search::Gene->Search_by_name_and_synonym(‘*kinase*’); Modware::Search::Feature->Search_overlapping_feats_by_range( ‘ Chr3’, 100000, 500000, ‘mRNA’ );

Location searches

Find all protein-coding genes on Chromosome 3 between bases 100,000 and 500,000

Text searches

Retrieve all kinase genes

Updating a Gene Name, add Synonym

# get gene

my ($gene) = new Modware::Search::Gene->Search_by_name(‘mlcA' );

# change the name

$gene->name( ‘newname' );

# add a synonym

$gene->add_synonym( ‘mlcA' );

# write changes to database

$gene->update();

Modware Goals

Future releases will include:

Literature annotations

GO annotations

Phenotype annotations

Incorporate feedback from users

Agenda

What?

What is Chado?

What is Modware?

Why?

How?

Storing in database

Try

Getting Modware

Getting Modware

http://gmod-ware.sourceforge.net

Download the NEW Virtual Machine

Modware is preinstalled and ready for you!

See me if you have any questions or want a demo

Visit Poster N41 at ISMB

Online Documentation http://gmod-ware.sourceforge.net/doc/

Dankes

The organizers of BOSC 2007

O|B|F

dictyBase

PIs

Rex Chisholm, PhD

Warren Kibbe, PhD

Programmer

Sohel Merchant

Curators

Petra Fey

Pascale Gaudet, PhD

Other Groups

Funding

NIH (NIGMS and NHGRI)

GMOD

Scott Cain

Brian O’Connor

Chado developers

Bioperl developers

# USE CASE: Add a description, dbxref, and an exon my $transcript = new Modware::Feature( -primary_id => 'DDB0233595' ); $transcript->description( 'Gene model derived from AU12345' ); $transcript->add_external_id( -source => 'GenBank Accession Number', -id => 'AU12345' ); # call the bioperl method to retrieve bioperl representation of object # need this to view/edit exon structure $bioperl = $transcript->bioperl(); # here, we are manipulating a Bio::SeqFeature::Gene object # shift the last exon back a little bit (to lose stop codon) [$bioperl->exons()]->[2]->start( 281050 ); # create a new exon and add it to the feature my $exon = Bio::SeqFeature::Gene::Exon->new( -start => 280921, -end => 280959, -strand => -1 ); $exon->is_coding(1); $bioperl->add_exon($exon); # update writes everything to the database $transcript->update();

Modware::Feature Modware::Feature::GENE Modware::Feature::MRNA Bio::SeqFeature::Gene::Transcript Bio::Seq Modware::Feature::CHROMOSOME Bio::SeqFeature::Gene::Exon

Feature ncRNA mRNA Contig Chromosome getOverlappingFeatures() getOverlappingAlignments() Bio::SeqFeature::Gene::Transcript Bio::SeqFeature::Generic Bio::SeqFeature::Generic Bio::Seq