Bio GMOD GenericGenePage
Bio::GMOD::GenericGenePage is an abstract Perl class that provides a render_xml method to crete Common Gene Page XML, but does not fetch the data. In order to effectively use this module, you need to subclass it and implement all of the methods that are listed under ABSTRACT CLASSES below for your database. These abstract methods are responsible for providing Bio::GMOD::GenericGenePage with the data to create the XML.
There are two example implementations included with this module. Bio::GMOD::GenericGenePage::Chado is a simple implementation for a Chado database populated with S. cerevisiae data obtained from SGD as GFF3. Currently, the output of this implementation can be seen at
and by clicking on any of the genes (red arrows).
The other implementation, CXGN::Phenome::GenericGenePage, is from SGN, the Sol Genomics Network. The XML they provide can be seen by clicking on the "Download GMOD XML" link on any of there locus pages; for example, this one:
For more information see http://gmod.org/wiki/Bio_GMOD_GenericGenePage or contact Scott Cain, scain@cpan.org.
While there is no example CGI included in this distribution that show how this module can be used, that could be included in future distribution if there is interest in it.
FlyBase implementation
http://flybase.org/genome/Drosophila_melanogaster/current/genepage/FBgn0000490
EcoliWiki implementation
The EcoliWiki implementation is written as a REST-like service in PHP.
http://ecoliwiki.net/rest/gmod_gene.php/gene_symbol/pfkA
See the discussion page for issues arising.
Abstract Classes
Methods below should be overridden by each GenericGenePage implementation.
name
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
accessions
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.
data_provider
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
synonyms
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
map_locations
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
ontology_terms
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.
dbxrefs
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
comments
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
literature_references
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
summary_text
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
organism
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
