B03-GenomeContent-Intermine
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The document discusses how InterMine uses RESTful web services for data integration and interoperability between biological databases, providing examples of how the InterMine API can be used to query databases and manage workflows through client libraries and sugar syntax. It also covers lessons learned in developing InterMine including using JSON for data exchange and implementing token-based authentication.
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B03-GenomeContent-Intermine
- 2. Why webservices matter to us
- 10. metabolicMine
- 11. ?? [MGI]
- 12. ?? [Wormbase]
- 13. ?
- 14. Flybase Ensembl Biogrid RedFly NCBI Wormbase OMIM Reactome anoEST PDB ArrayExpress FlyAtlas
- 15. Storage and Organisation ObjectStore DB
- 16. Storage and Organisation Heavily denormalised – read-only Rebuilt for each release Read-write – persists across releases UserProfile DB ObjectStore DB Lists refers to
- 17. Retrieval Internal API ObjectStore DB Lists SQL IQL PathQuery Template
- 18. Webapp Interface
- 19. Webapp Interface
- 21. Mine ↔ Mine
- 22. User ↔ Mine
- 27. Perl client
- 29. Python client
- 33. JSON
- 34. Biological formats (GFF3, Fasta, BED)
- 37. Easy to debug
- 38. Can do what you need
- 39. Where you need to do it (the browser)
- 41. For not much code IMBedding . loadTemplate ( { name : "Gene_Identifiers" , constraint1 : "Gene.secondaryIdentifier" , op1 : "<" , value1 : "CG1046" , }, "#placeholder" );
- 42. For not much code use Webservice::InterMine 'flymine'; my $query = Webservice::InterMine ->new_query(class => 'Gene'); $query->add_views(qw/symbol pathways.name/); $query->add_constraint('Gene.symbol', 'ONE OF', ['zen', 'h']); while (<$query>) { print @$_; }
- 44. Retrieval
- 45. Updates
- 46. Deletion
- 48. Automated Workflows List of Identifiers -> List of database records -> Homologues in X -> Their protein domains use InterMine::Webservice; my $flymine = Webservice::InterMine->get_service(' www.flymine.org/query ', 'TOKEN'); my $list = $flymine->new_list(type => 'Gene', content => “some/file.txt”); my $query = $list->to_query; $query->add_views('homologues.homologue.symbol'); $query->add_constraint('homologues.homologue.organism.shortName', '=', 'R norvegicus'); my $rat_symbols = [map {$_->{ homologues.homologue.symbol}} $query->results(''hashrefs”)]; my $ratmine = Webservice::InterMine->get_service('ratmine.mcw.edu/ratmine'); my $rat_query = $ratmine->new_query(class => 'Gene'); $rat_query->add_views(qw/symbol primaryIdentifier proteins.proteinDomains.name/); $rat_query->add_constraint('symbol', 'ONE OF', $rat_symbols); $rat_query->show;
- 49. Automated Workflows with Sugar List of Identifiers -> List of database records -> Homologues in X -> Their protein domains use InterMine::Webservice; my $flymine = Webservice::InterMine->get_service(' www.flymine.org/query ', 'TOKEN'); my $fly_results = $flymine ->new_list(type => 'Gene', content => “some/file.txt”) ->select('homologues.homologue.symbol') ->where('homologues.homologue.organism.shortName', '=', 'R norvegicus') ->results('hashrefs'); my $rat_symbols = [map {$_->{ homologues.homologue.symbol}} $fly_results]; my $ratmine = Webservice::InterMine->get_service('ratmine.mcw.edu/ratmine'); $ratmine->new_query(class => 'Gene') ->select(qw/symbol proteins.proteinDomains.name/) ->where('symbol', 'ONE OF', $rat_symbols) ->show;
- 51. Users can manage their workflows
- 53. Integration with other software projects (Perl client is BioPerl aware)
- 55. Nearly provides all the services the webapp does (see intermine.org/wiki/WebService)
- 57. But the more formats the better (within reason)
- 58. Fail loudly
- 59. REST doesn't mean you have to follow CRUD method mappings.
- 60. Every language has its quirks, especially with HTTP requests; simple is better.
- 63. NIH
- 64. Wellcome Trust Gos Micklem (PI), Richard Smith, Julie Sullivan, Sergio Contrino, Daniela Butano, Radek Stepan, Fengyuan Hu, Adrian Carr, Mike Lyne, Alex Kalderimis
Editor's Notes
- Unpack “widgets” terminology - statistical/graphical analysis of lists
- Unpack “widgets” terminology - statistical/graphical analysis of lists
- Unpack “widgets” terminology - statistical/graphical analysis of lists
- More snippets – show on on the backend: - what requests are made to perform this.
- More snippets – show on on the backend: - what requests are made to perform this.