go::parsers::go_assoc_parser(3pm) [debian man page]

GO::Parsers::go_assoc_parser(3pm)			User Contributed Perl Documentation			 GO::Parsers::go_assoc_parser(3pm)

NAME

	 GO::Parsers::go_assoc_parser	  - syntax parsing of GO gene-association flat files

SYNOPSIS

DESCRIPTION

       do not use this class directly; use GO::Parser

       This generates Stag/XML event streams from GO association files.  Examples of these files can be found at http://www.geneontology.org, an
       example of lines from an association file:

	 SGD	 S0004660	 AAC1		 GO:0005743	 SGD:12031|PMID:2167309 TAS		C	ADP/ATP translocator	YMR056C gene	taxon:4932 20010118
	 SGD	 S0004660	 AAC1		 GO:0006854	 SGD:12031|PMID:2167309 IDA		P	ADP/ATP translocator	YMR056C gene	taxon:4932 20010118

       See <http://www.geneontology.org/GO.annotation.shtml#file>

       See http://www.godatabase.org/dev/xml/dtd/go_assoc-parser-events.dtd <http://www.godatabase.org/dev/xml/dtd/go_assoc-parser-events.dtd> For
       the DTD of the event stream that is generated

       The following stag-schema describes the events that are generated in parsing an assoc file:

	 (assocs
	  (dbset+
	    (proddb "s")
	    (prod+
	      (prodacc "s")
	      (prodsymbol "s")
	      (prodtype "s")
	      (prodtaxa "i")
	      (assoc+
		(assocdate "i")
		(source_db "s")
		(termacc "s")
		(is_not "i")
		(aspect "s")
		(evidence+
		  (evcode "s")
		  (ref "s"))))))

perl v5.14.2							    2010-05-31					 GO::Parsers::go_assoc_parser(3pm)

XML::LibXML::Dtd(3pm)					User Contributed Perl Documentation				     XML::LibXML::Dtd(3pm)

NAME

       XML::LibXML::Dtd - XML::LibXML DTD Handling

SYNOPSIS

	 use XML::LibXML;

	 $dtd = XML::LibXML::Dtd->new($public_id, $system_id);
	 $dtd = XML::LibXML::Dtd->parse_string($dtd_str);
	 $publicId = $dtd->getName();
	 $publicId = $dtd->publicId();
	 $systemId = $dtd->systemId();

DESCRIPTION

       This class holds a DTD. You may parse a DTD from either a string, or from an external SYSTEM identifier.

       No support is available as yet for parsing from a filehandle.

       XML::LibXML::Dtd is a sub-class of XML::LibXML::Node, so all the methods available to nodes (particularly toString()) are available to Dtd
       objects.

METHODS

       new
	     $dtd = XML::LibXML::Dtd->new($public_id, $system_id);

	   Parse a DTD from the system identifier, and return a DTD object that you can pass to $doc->is_valid() or $doc->validate().

	     my $dtd = XML::LibXML::Dtd->new(
				   "SOME // Public / ID / 1.0",
				   "test.dtd"
					     );
	      my $doc = XML::LibXML->new->parse_file("test.xml");
	      $doc->validate($dtd);

       parse_string
	     $dtd = XML::LibXML::Dtd->parse_string($dtd_str);

	   The same as new() above, except you can parse a DTD from a string. Note that parsing from string may fail if the DTD contains external
	   parametric-entity references with relative URLs.

       getName
	     $publicId = $dtd->getName();

	   Returns the name of DTD; i.e., the name immediately following the DOCTYPE keyword.

       publicId
	     $publicId = $dtd->publicId();

	   Returns the public identifier of the external subset.

       systemId
	     $systemId = $dtd->systemId();

	   Returns the system identifier of the external subset.

AUTHORS

       Matt Sergeant, Christian Glahn, Petr Pajas

VERSION

       2.0001

COPYRIGHT

       2001-2007, AxKit.com Ltd.

       2002-2006, Christian Glahn.

       2006-2009, Petr Pajas.

perl v5.14.2							    2012-06-20						     XML::LibXML::Dtd(3pm)