go::parsers::generic_tagval_parser(3pm) [debian man page]
GO::Parsers::generic_tagval_parser(3pm) User Contributed Perl Documentation GO::Parsers::generic_tagval_parser(3pm)NAME
GO::Parsers::generic_tagval_parser - syntax parsing of GO .def flat files
SYNOPSIS
do not use this class directly; use GO::Parser
DESCRIPTION
This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for
details
Examples of these files can be found at http://www.geneontology.org
A description of the event streams generated follows; Stag or an XML handler can be used to catch these events
GO DEFINITION FILES
These have a suffix .defs or .definitions
AUTHOR perl v5.14.2 2010-05-12 GO::Parsers::generic_tagval_parser(3pm)
Check Out this Related 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)
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