Bio::GMOD::GenericGenePage - Generic GMOD gene page base class
my $page = Bio::GMOD::GenericGenePage->new( $gene_identifier ); my $xml = $page->render_xml();
Bio::GMOD::GenericGenePage is an abstract class to make it easier for Model Organism Databases (MODs) to serve up a simple XML that describes attributes of their gene models. In order to implement this, the user needs to subclass Bio::GMOD::GenericGenePage and provide the methods listed below as abstract classes. These methods are then used by the render_xml method to create XML for a given gene.
There is one example implementation included with this distribution, Bio::GMOD::GenericGenePage::Chado, which is a Chado adapter for a yeast database derived from SGD's GFF3. In order to implement this for another Chado database it should be fairly easy to modify the provided methods to create your own adaptor. For example, ParameciumDB could subclass Bio::GMOD::GenericGenePage::Chado and create Bio::GMOD::GenericGenePage::Chado::ParameciumDB and only override the data_provider and organism methods to have a working adaptor. Databases not based on Chado will only have slightly more work, in order to implement all of the abstract classes in Bio::GMOD::GenericGenePage.
Another example implementation is included, CXGN::Phenome::GenericGenePage, however this is only a partial implementation and will not work with the current release of Bio::GMOD::GenericGenePage.
none
Bio::GMOD::GenericGenePage::Chado CXGN::Phenome::GenericGenePage
Please report bugs and make support requests on the GMOD developers list, gmod-devel@lists.sourceforge.net.
Scott Cain CPAN ID: SCAIN Cold Spring Harbor Laboratory scain@cpan.org http://www.gmod.org/
and Robert Buels.
Copyright (c) 2008 Scott Cain and Robert Buels. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
The full text of the license can be found in the LICENSE file included with this module.
perl(1).
Usage: my $genepage = MyGenePage->new( -id => $gene_identifier ); Desc : create a new gene page object. should be overridden Args : not specified Ret : a new gene page object Side Effects: none as implemented here, but subclass implementations may have side effects Example:
Usage: my $xml = $page->render_xml(); Desc : render the XML for this generic gene page Args : none Ret : string of xml Side Effects: none
Usage: my $html = $page->render_html(); Desc : render HTML for this generic gene page. you may want to override this method for your implementation Args : none Ret : string of html Side Effects: none
Methods below should be overridden by each GenericGenePage implementation.
Usage: my $name = $genepage->name(); Desc : get the string name of this gene Args : none Ret : string gene name, e.g. 'Pax6' Side Effects: none
Usage: my @accessions = $genepage->accessions(); Desc : get a list of local accession values Args : none Ret : a list of local accessions Side Effects: none
Note that these are the accessions that are used by the MOD providing the information, not accessions in external databases like GenBank.
Usage: my $data_provider = $genepage->data_provider(); Desc : The name of the data providing authority (ie, WormBase, SGD, etc) Args : none Ret : string, name of the data provider Side Effects: none
Usage: my @syn = $genepage->synonyms(); Desc : get a list of synonyms for this gene Args : none Ret : list of strings, e.g. ( '1500038E17Rik', 'AEY11', 'Dey', "Dickie's small eye", 'Gsfaey11', 'Pax-6', ) Side Effects: none
Usage: my @locs = $genepage->map_locations() Desc : get a list of known map locations for this gene Args : none Ret : list of map locations, each a hashref as: { map_name => string map name, chromosome => string chromosome name, marker => (optional) associated marker name, position => numerical position on the map, units => map units, either 'cm', for centimorgans, or 'b', for bases } Side Effects: none
Usage: my @terms = $genepage->ontology_terms(); Desc : get a list of ontology terms Args : none Ret : hash-style list as: termname => human-readable description, Side Effects: none Example: my %terms = $genepage->ontology_terms() # and %terms is now ( GO:0016711 => 'F:flavonoid 3'-monooxygenase activity', ... )
Note that the value in that has is the the concatenation of F:, B: or C: for molecular_function, biological_process, or cellular_component GO terms respectively. If the term does not belong to GO, there is no prepended identifier.
Usage: my @dbxrefs = $genepage->dbxrefs(); Desc : get a list of database cross-references for info related to this gene Args : none Ret : list of strings, like type:id e.g. ('PFAM:00012') Side Effects: none
Usage: my @comments = $genepage->comments(); Desc : get a list of comments with types Args : none Ret : a hash of comment=>type, where type is optional (empty string) Side Effects: none
Usage: my @refs = $genepage->lit_refs(); Desc : get a list of literature references for this gene Args : none Ret : list of literature reference identifers, as type:id, like ('PMID:0023423',...) Side Effects: none
Usage: my $summary = $page->summary_text(); Desc : get a text string of plain-English summary text for this gene Args : none Ret : string of summary text Side Effects: none
Usage: my $species_info = $genepage->organism Desc : get a handful of species-related information Args : none Ret : hashref as: { ncbi_taxon_id => ncbi taxon id, (e.g. 3702), binomial => e.g. 'Arabidopsis thaliana', common => e.g. 'Mouse-ear cress', } Side Effects: none
To install Bio::GMOD::GenericGenePage, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::GMOD::GenericGenePage
CPAN shell
perl -MCPAN -e shell install Bio::GMOD::GenericGenePage
For more information on module installation, please visit the detailed CPAN module installation guide.