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Webservice::InterMine::Cookbook::Recipe4 - Other Query Features
# Get all genes involved in biosynthetic processes, and any # publications on them use Webservice::InterMine ('www.flymine.org/query'); my $query = Webservice::InterMine->new_query(class => 'Gene'); $query->select(qw/primaryIdentifier symbol publications.year publications.firstAuthor publications.title/) ->where('ontologyAnnotations.ontologyTerm.name' => '*biosynthetic process*') ->outerjoin('publications') ->show(); # Use path descriptions for printing TSV tables: $query->add_view('ontologyAnnotations.ontologyTerm.name'); $query->add_pathdescription('ontologyAnnotations.ontologyTerm' => 'Ontology Term'); $query->add_pathdescription('publications' => 'Pub.'); $query-print_results(columnheaders => 1);
Merely including a path in a query, even in the view, by default exerts a constraining force - ie. it demands that the record you are searching for have information in the field the path describes. Sometimes, that is not what you want.
In the example above, the purpose of the query is to get a list of all genes with a particular GO annotation - whether or not they have publications is by the by: we still want to know about them. If they do have publications, then by all means let us know, but we want the full list of genes.
To specify this behaviour we describe the link from Gene -> Publication as being an 'Outer' join. Normally joins between two objects are 'Inner' joins, which requires records to have both objects, which here would mean missing genes that meet out criteria with no publications.
Because 'Inner' joins are the default, you do not need to declare them as such (although you can, just to remind yourself that you have chosen to throw away partially matching records), but 'Outer' joins always need to be declared. As we only ever need to declare outer joins, there is a more concise way to do this. The following are equivalent:
$query->outerjoin('publications'); $query->add_join('Gene.publications'); $query->add_join('Gene.publications' => 'OUTER'); $query->add_join(path => 'Gene.publications', style => 'OUTER');
If you plan to automatically upload queries or to use them to make templates, or you simply want to get more concise column headers, then you can use path descriptions:
$query->add_pathdescription( path => 'Gene.downstreamIntergenicRegion.overlappingFeatures', description => 'Overlapping Features', );
This allows you to alias long paths, and if you use the
columnheaders feature to get results with them, it can make for more legible result tables.
Joins and path descriptions are two features which help you tell the server, and remind yourself, what you meant by the query you composed, and help document what kind of results you expect to get back from it, and why they will be useful. In the next recipe we look at how to deal with these results.
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