InterMine Presentation

This Wiki page is an edited version of Gos's presentation

Background

InterMine was developed as the generic underpinnings of the FlyMine Project

• Team of 7 FTE
  • 5 developers, one sys admin,
  • 1 biologist/ bioinformatician
• Java/ postgreSQL
• SVN repository: 125,000 lines of code + 57,000 lines of tests
• Under development since 2002
• In use by others in Cambridge, Edinburgh, Vienna… + modENCODE DCC if funded
• modENCODE/ Chado

Technical Overview

• Data model --> Java classes, relational schema, mappings through automatic code generation
• Custom Java object/relational system
  • When we started, couldn’t select from multiple classes at one time using hibernate.
• Optimised for read-only performance
• Designed for big, complex queries, bulk data
• Performance optimisation
  • Transparent query re-writing
• Web application - Struts/JSP/Ajax

Loading Data

• Read-only in production environment (therefore Problems 3 and 5 skipped)
• Load data from InterMine XML
• Parsers from standard formats
  • e.g. UniProt, GFF3, PSI, FASTA
• Powerful integration system: coarse/fine grained data source priorities give load-order independence

Test problems

• Used SOFA as core data model - similar to Chado.
• Added Gene.description (absent from model), compiled, loaded data (here XML + FASTA), released webapp.

Example InterMine XML for Problem 1: load genes + annotation

<items>
   <item id="0_3" class=”” implements="http://www.flymine.org/model/genomic#Gene">
      <attribute name="identifier" value="xfile" />
      <attribute name="description" value="A test gene for GMOD meeting" />
      <reference name="organism" ref_id="0_1" />
      <collection name="transcripts">
         <reference ref_id="0_9" />
      </collection>
   </item>
   <item id="0_1" class="" implements="http://www.flymine.org/model/genomic#Organism">
      <attribute name="taxonId" value="7227" />
   </item>
   ...

Resulting webapp object page

Code for Problem 2: Print gene annotation report

public class BakeOff {
    public static void main(String[] args) throws Exception {
        // code to get the "xfile" gene
        ObjectStore os = ObjectStoreFactory.getObjectStore("os.production");
        Query q = new Query();
        QueryClass qcObj = new QueryClass(Gene.class);
        q.addFrom(qcObj);
        QueryField qf = new QueryField(qcObj, "identifier");
        q.addToSelect(qf);
        SimpleConstraint sc = new SimpleConstraint(qf, ConstraintOp.EQUALS, new QueryValue("xfile"));
        q.setConstraint(sc);
        System.err.println("query: " + q);
        Results res = os.execute(q);
 
        // a Results object is a List of Lists
        List rr = (List) res.get(0);
        Gene gene = (Gene) rr.get(0);
 
        System.err.println ("symbol: " + gene.getIdentifier());
 
        // a BioEntity in FlyMine has a collection of Synonym objects -
        // we need Synonym.value for each Synonym
        System.err.print ("synonyms: ");
        Iterator synIter = gene.getSynonyms().iterator();
        while (synIter.hasNext()) {
            Synonym syn = (Synonym) synIter.next();
            System.err.print (syn.getValue() + ' ');
        }
 
        System.err.println ("description: " + gene.getDescription());
 
        // get the class name, but we already know that the gene is a Gene
        System.err.println ("type: " + gene.getClass().getName());
 
        // make a List from a the Set of exons for this Gene
        List exons = new ArrayList(gene.getExons());
        Exon exon1 = (Exon) exons.get(0);
        Exon exon2 = (Exon) exons.get(1);
 
        // get the start and end via the Location object
        System.err.println ("exon1 start: " + exon1.getChromosomeLocation().getStart());
        System.err.println ("exon1 end: " + exon1.getChromosomeLocation().getEnd());
        System.err.println ("exon2 start: " + exon2.getChromosomeLocation().getStart());
        System.err.println ("exon2 end: " + exon2.getChromosomeLocation().getEnd());
 
        // write out the first cds
        List cdss = new ArrayList(gene.getCDSs());
        FlyMineSequence flymineSequence = FlyMineSequenceFactory.make((CDS) cdss.get(0));
 
        // use BioJava to output the sequence
        Annotation annotation = flymineSequence.getAnnotation();
        annotation.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE,
                               gene.getIdentifier() + " cds");
        SeqIOTools.writeFasta(System.err, flymineSequence);
    }
}

Quicksearch - Problem 4: find genes starting with x

Java API

  Query q = new Query();
  QueryClass qcObj = new QueryClass(Gene.class);
  q.addFrom(qcObj);
  q.addToSelect(qcObj);
 
  QueryField qf = new QueryField(qcObj, "identifier");
 
  SimpleConstraint sc = new SimpleConstraint(qf, ConstraintOp.MATCHES, new QueryValue("x-%"));
  q.setConstraint(sc);

IQL

  SELECT DISTINCT a1_.identifier AS a2_ FROM org.flymine.model.genomic.Gene AS a1_ WHERE a1_.identifier LIKE 'x-%'

Perl API

  my $genes = InterMine::Gene::Manager->get_genes(query => [
                             identifier => { like => 'x-%' },],);

Larger Query

Within FlyMine: For one or more genes report:

• Gene, Transcripts, Exons, Chromosomal Locations, Lengths

• Query joins 7 classes
  • all are on select list of query
  • many more tables than classes are joined

• Performance:
  • One gene:
    • 2 rows in ~2 seconds
  • All genes, all organisms
    • ~300,000 rows in 36 seconds (without using pre-computation to enhance performance)
    • ~300,000 rows in ~1 second (using pre-computation)

Implications of Query Optimisation

• Performance optimisation not tied to schema design
• Can adapt performance optimisation to usage of live database
• Template queries pre-computed
  • ~40 template queries run per gene details page - renders in seconds

Acknowlegements

• Richard Smith
• Kim Rutherford
• Matthew Wakeling
• Xavier Watkins
• Julie Sullivan
• Rachel Lyne
• Hilde Janssens
• François Guillier
• Philip North
• Tom Riley
• Peter Mclaren
• Mark Woodbridge
• Debashis Rana
• Wenyan Ji
• Markus Brosch
• Florian Reising
• Andrew Varley
• Gos Micklem

InterMine/FlyMine are funded by the Wellcome Trust (grant no. 067205), awarded to M. Ashburner, G. Micklem, S. Russell, K. Lilley and K. Mizuguchi.