2005-01-31 - [cjm] Inititation of Changes file
2005-01-31 - [cjm] changed dependencies in Makefile.PL
Data::Stag 0.07 is the only dependency
(and as of 0.08, no dependencies for Data::Stag)
- [cjm] XML::LibXML now used in place of xsltproc hack
- [cjm] Added acc2name_h to base_parser - index
can be used for fast ID checking during parsing
- [cjm] fixed litemode to report namespace
(map2slim no longer complains)
- [cjm] fixed prob with go_ont_parser
files with '*' as a type code
2005-02-01 - [cjm] map2slim now uses no_duplicates option
2005-02-08 - [cjm] new scripts:
go-dag-summary.pl
go-filter-subset.pl
go-show-paths-to-root.pl
2005-03-14 - [cjm] new parser/handler: obj_storable
added caching to parser
new script option: -use_cache
2005-03-28 - [cjm] added go-apply-xslt to go-perl/scripts
2005-04-02 - [cjm] obo_text output date is now oboedit compatible
2005-04-16 - [cjm] fixed subtle obo_text_parser bug
is_root was not being set if the root term
was immediately followed by a Typedef stanza
2005-05-20 - [cjm] allowed unsetting of $term->synonym_list
- [cjm] new scripts
go-show-assocs-by-node.pl
go-apply-xslt
2005-05-25 - [cjm] xslt processing: behaviour unchanged for when
GO_ROOT is set; if GO_ROOT is not set, then
the install directory (eg %INC{GO/..}) is checked
for the xsl directory. This makes things easier
for users who wish to use go-perl and the xslts
without downloading and installing all of go-dev
This affects:
go-apply-xslt
GO::Parsers::base_parser
2005-06-29 - [cjm] now accepts obo1.2 format synonyms
accepts obo1.2 xref tag (maps to xref_analog in xml)
VERSION 0.04
============
2005-08-18 - [cjm] made no_duplicates(1) default in exporting
an ontology to deprecated go_ont format
(this was causing problems with cycles)
2005-09-06 - [cjm] incorporate changes to xsl for chadoxml
when converting to chadoxml, only use
relationship as cv.name if no namespace specified
2005-10-05 - [cjm] obo_text_parser - no longer warns of missing
namespace, if it is a header-only
obo file
owl2obo fixed
VERSION 0.05
============
2005-12-01 - [cjm] more docs for map2slim. made -b option safe'
new convenience methods in Graph and GeneProduct
added create_handler to Parser
improved POD docs
new test t140
2006-02-12 - [cjm] added methods for new obo Typedef tag
is_transitive, transitive_over etc
2006-03-29 - [cjm] added GO::Model::LogicalDefinition
2006-04-19 - [cjm] added new test for chadoxml
2006-07-14 - [cjm] support for idspace tag
2006-07-24 - [cjm] support for synonymtypedef tag
[cjm] more synonym info from ncbi_taxonomy_parser
2006-08-25 - [cjm] added checks to dbxref parsing
2006-09-11 - [cjm] exports subsetdefs in obo format
fixed definition dbxref parsing (was only getting 1 dbxref)
2006-10-18 - [cjm] finalised code for GO::Model::LogicalDefinition
added Relationship->complete
- [cjm] removed some cruft
VERSION 0.06
============
No code changes in this release; the 0.05 CPAN release erroneously
contained out of date copies of the XSL files