BP_QUERY_ENTREZ_TAXA(1p) User Contributed Perl Documentation BP_QUERY_ENTREZ_TAXA(1p)NAME
query_entrez_taxa - query Entrez taxonomy database and print out information
USAGE
query_entrez_taxa "Homo sapiens" "Saccharomyces cerevisiae" Rhizopus Metazoa query_entrez_taxa -gi 28800981 -gi 54301680 -db nucleotide
query_entrez_taxa -gi 71836523 -db protein
Provide the genus and species name in quotes, you can also query for
a non-species node like Family or Order
Command-line options:
-v or --verbose : print verbose debugging info
-gi : one or many GI numbers to lookup taxon id for
-db : the sequence db (nucleotide or protein) the GI is for
other arguments are assumed to be species names to lookup in taxonomy db
AUTHOR
Jason Stajich jason-at-bioperl-dot-org
perl v5.14.2 2012-03-02 BP_QUERY_ENTREZ_TAXA(1p)
Check Out this Related Man Page
HTML::Microformats::Format::species(3pm) User Contributed Perl Documentation HTML::Microformats::Format::species(3pm)NAME
HTML::Microformats::Format::species - the species microformat
SYNOPSIS
use HTML::Microformats::DocumentContext;
use HTML::Microformats::Format::hCard;
my $context = HTML::Microformats::DocumentContext->new($dom, $uri);
my @objects = HTML::Microformats::Format::species->extract_all(
$dom->documentElement, $context);
foreach my $species (@objects)
{
print $species->get_binomial . "
";
}
DESCRIPTION
HTML::Microformats::Format::species inherits from HTML::Microformats::Format. See the base class definition for a description of property
getter/setter methods, constructors, etc.
MICROFORMAT
The species documentation at <http://microformats.org/wiki/species> is very sketchy. This module aims to be roughly compatible with the
implementation of species in the Operator extension for Firefox, and data published by the BBC and Wikipedia. Here are some brief notes on
how is has been impemented:
o The root class name is 'biota'.
o Important properties are 'vernacular' (alias 'common-name', 'cname' or 'fn'), 'binomial', 'trinomial', 'authority'.
o Also recognised are 'class', 'division', 'family', 'genus', 'kingdom', 'order', 'phylum', 'species' and various other ranks.
o Because some of these property names are fairly generic, you can alternatively use them in a prefixed form: 'taxo-class',
'taxo-division', etc.
o If an element with class 'biota' has no recognised properties within it, the entire contents of the element are taken to be a binomial
name. This allows for very simple markup:
<i class="biota">Homo sapiens</i>
o The meaning of some terminology differs when used by botanists and zoologists. You can add the class 'botany' or 'zoology' to the root
element to clarify your usage. e.g.
<i class="biota zoology">Homo sapiens</i>
An example:
<span class="biota zoology">
<i class="binomial">
<span class="genus">Homo</span>
<span class="species">sapiens</span>
<span class="subspecies">sapiens</span>
</i>
(<span class="authority">Linnaeus, 1758</span>)
a.k.a. <span class="vernacular">Humans</span>
</span>
RDF OUTPUT
RDF output uses the Biological Taxonomy Vocabulary 0.2 (<http://purl.org/NET/biol/ns#>).
BUGS
Please report any bugs to <http://rt.cpan.org/>.
SEE ALSO
HTML::Microformats::Format, HTML::Microformats.
AUTHOR
Toby Inkster <tobyink@cpan.org>.
COPYRIGHT
Copyright 2008-2011 Toby Inkster
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
DISCLAIMER OF WARRANTIES
THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
perl v5.14.2 2011-12-06 HTML::Microformats::Format::species(3pm)