INSTALL INSTRUCTIONS
perl Build.PL
./Build
./Build test
./Build install
If you are on a windows box you should use 'nmake' rather than 'make'.
IMPLEMENTATION NOTES
The primary module provided with this distribution,
Bio::GMOD::GenericGenePage, is an abstract perl class that provides a
render_xml method to create the 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 impmentations 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
http://gmod.org/cgi-bin/gbrowse/chado_yeast/
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:
http://sgn.cornell.edu/phenome/locus_display.pl?locus_id=1238
For more information see (GMOD WEB PAGE) or contact Scott Cain, scain@cpan.org.
PROVIDED METHODS
new
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:
render_xml
Usage: my $xml = $page->render_xml();
Desc : render the XML for this generic gene page
Args : none
Ret : string of xml
Side Effects: none
render_html NOT IMPLEMENTED!
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
ABSTRACT METHODS
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
synonyms
Usage: my @syn = $genepage->synonyms();
Desc : get a list of synonyms for this gene
Args : none
Ret : list of strings, with the canonical/official/approved gene
name first.
e.g. ( 'Pax6',
'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',
...
)
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
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
ABSTRACT METHODS
Methods below should be overridden by each GenericGenePage implementaâ€
tion.
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 accession the is used by the MOD providing the
information.
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