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NAMEBio::Phylo::Parsers::Dwca - Parser used by Bio::Phylo::IO, no serviceable parts inside DESCRIPTIONThis module parses standard Darwin Core Archive files as produced by GBIF (see: <http://www.gbif.org/resource/80639>). The end result is a Bio::Phylo::Taxa object that has as many taxon objects in it as there are distinct "dwc:scientificName"s in the archive. For example, if the archive is for a single species there will thus be only one taxon object in the produced result. Each taxon object is annotated with as many "dwc:Occurrence" records, instantiated as Bio::Phylo::NeXML::Meta annotations, as there are occurrences for that species in the archive. In turn, nested in each of these annotations are the predicates and objects for that record. Using this module, the contents of a Darwin Core Archive can be easily accessed and, for example, prepared as input for MAXENT. Here is an example to show how this is done: use Bio::Phylo::IO 'parse'; use Bio::Phylo::Util::CONSTANT ':objecttypes'; # a set of fossil occurrences of th feral horse, Equus ferus Boddaert, 1785 # this corresponds with data set doi:10.15468/dl.yyyhyn my $url = 'http://api.gbif.org/v1/occurrence/download/request/0074675-160910150852091.zip'; # like every Bio::Phylo::IO module, we can parse directly from a web location my $proj = parse( '-format' => 'dwca', '-url' => $url, '-as_project' => 1, ); # write a CSV file with MAXENT header print "Species,Latitude,Longitude\n"; for my $t ( @{ $proj->get_items(_TAXON_) } ) { my $name = $t->get_name; for my $m ( @{ $t->get_meta } ) { my $lat = $m->get_meta_object('dwc:decimalLatitude'); my $lon = $m->get_meta_object('dwc:decimalLongitude'); print "\"$name\",$lat,$lon\n"; } } SEE ALSOThere is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.
CITATIONIf you use Bio::Phylo in published research, please cite it: Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. <http://dx.doi.org/10.1186/1471-2105-12-63>
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