The document discusses using XML and object-oriented APIs to improve interoperability between databases and applications. It proposes a specification called XORT to map XML to the relational model in a generic way. This allows applications to communicate with databases via XML in a language-independent manner. It also describes using PostgreSQL functions and ChadoXML services to encapsulate domain logic in a reusable way across different applications.

1. Chado and interoperability Chris Mungall, BDGP Pinglei Zhou, FlyBase-Harvard

2. Databases and applications SQL ? How do we get databases and applications speaking to one another? Application Application Java Perl Chado seq cv rad genetic phylo pub

3. Databases and applications posgresql driver posgresql driver Application Application SQL Java Perl Generic database interfaces only solve part of the problem JDBC DBI They let us embed SQL inside application code Chado seq cv rad genetic phylo pub method calls row objects method calls perl arrays

5. Language mismatch String sql = " SELECT srcfeature_id, fmax, fmin “+ “ FROM featureloc "+ " WHERE feature_id =" + featId; try { Statement s = conn.createStatement(); ResultSet rs = s.executeQuery(sql); rs.next(); sourceFeatureId = rs.getInt(" srcfeature_id "); fmin = rs.getInt(" fmin "); fmax = rs.getInt(" fmax "); } catch (SQLException sqle) { System.err.println(this.getClass() + ": SQLException retrieving feature loc" + " for feature_id = " + featId); sqle.printStackTrace(System.err); }

9. A solution:Object Oriented APIs biosql adapter chado adapter Application Perl Different perl applications share the same API API Different schemas can be added by writing adapters chado method calls domain objects Perl driver DBI biosql driver DBI Application Perl domain objects

13. XML middleware impl Application Perl Database XML as lingua franca interface chado query params chado xml Perl driver DBI Application query params chado xml Java any Generic SQL to XML mapper OO APIs can be implemented on top of XML layer

14. XML middleware impl Application Perl interface Implementation can be any language chado query params chado xml Java driver JDBC Application query params chado xml Java any

20. Object Reference By Global Accession <feature> <uniquename>CG3123</uniquename> <type_id>gene</type_id> <feature_relationship> <subject_id> Gadfly:CG3123-RA:1 </subject_id> <type_id>producedby</type_id> <feature_relationship> …… </feature> </feature>

21. Object Reference By Local ID <cv id=“ SO ”> <name>Sequence Ontology</name> </cv> <cvterm id=“ exon ”> <cv_id> SO </cv_id> <name>exon</name> </cvterm> <feature> <type_id> exon </type_id>

22. Object Reference By key Value (s) <feature> <type_id> <cvterm> <cv_id> <cv> <name>Sequence Ontology</name> </cv> </cv_id> <name>exon</name> </cvterm> </type_id> … .

23. ChadoXML Example <cv id=“ SO ”> <name>Sequence Ontology</name> </cv> <feature op =“lookup” id =“CG3312”> <uniquename>CG3312</uniquename> <type_id> <cvterm> <name>gene</name> <cv_id> SO </cv_id> </cvterm> <type_id> <organism_id> <feature_relationship> <subject_id> Gadfly:CG3312-RA </subject_id> <type_id> producedby </type_id> </feature_relationship> </feature>

26. <feature dump=&quot;all&quot;> <uniquename test=&quot;yes&quot;>CG3312</uniquename> <!-- get all mRNAs of this gene --> <feature_relationship dump=&quot;all&quot;> <subject_id test=&quot;yes&quot;> <feature> <type_id><cvterm> <name>mRNA</name> </cvterm> </type_id> </feature> </subject_id> <subject_id> <feature dump=&quot;all&quot;> <!-- get all exons of those mRNAs --> <feature_relationship dump=&quot;all&quot;> <subject_id test=&quot;yes&quot;> <feature> <type_id> ><cvterm><name>exon</name> </cvterm> </type_id> </feature> </subject_id> <subject_id> <feature dump=&quot;all“/> </subject_id> </feature_relationship> </feature> DumpSpec Sample

27. Use Case 1 Chado <-> Apollo Interaction XML Dumper XML Loader + validator GameBridge Chado GAME XML Chado XML GAME XML Chado XML GameBridge DumpSpec1 DDL XML Schema By_product Apollo

28. Use Case 2 Gene Page Dataflow Chado XML Dumper Chado XML DumpSpec2 acode FlyBase

32. ChadoXML Services XML:: XORT Application XORT interface chado query params chado xml driver DBI ChadoXML services interface Format converters, dumpers chado xml query params chado xml other xml XSLT sequence domain logic C Perl Ontology services Java XQuery Lisp Prolog companalysis logic Java Perl

33. ChadoXML Services Application ChadoXML services interface Format converters, dumpers chado xml query params chado xml other xml XSLT sequence domain logic C Perl Ontology services Java XQuery Lisp Prolog Can be independent of DB companalysis logic Java Perl

34. PL/PgSQL Function Impl DB Functions API Application Implementation inside database Chado db function calls sql result objects DB Functions API posgresql driver JDBC/ DBI sequence library C

37. Putting it together: storing ontologies in chado Chado XML XML::XORT or DBIx::DBStag oboxml_to_ chadoxml.xsl obo-edit Obo XML cv fill_cvtermpath() owl_to_ oboxml.xsl protege OWL