The document discusses Modware, an object-oriented Perl interface for querying and updating the Chado database schema. It provides semantically sensible classes and methods that encapsulate Chado's business rules for easier and more efficient development. An example demonstrates storing a gene with exons in Chado using Modware and generating a web page to display the gene details.

1. 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)

8. 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

9. 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

10. A Simple Gene Page

11. #!/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 &quot;<pre>&quot;; print $id.&quot; is on chromosome $chromosome&quot;; print &quot; and is the gene $gene&quot;; # print the number and position of each exon foreach my $exon (@exons) { print &quot;Exon $count. start=&quot;.$exon->start(). &quot; end=&quot;.$exon->end().&quot;&quot;; $count++; } print $sequence; print &quot;</pre>&quot;;

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

20. # 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();

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

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