File: Changes

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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

VERSION 0.07
============

2006-11-28      - [cjm] fixed obo export to properly escape {}s

2006-12-06      - [cjm] fixed boolean tags in obo format export
                        ncbi_taxonomy_parser - has_rank is now metadata property

2006-12-12      - [cjm] handles unquoted trailing modifier correctly in obof1.2

2006-12-12      - [cjm] added GO::Model::DB

2007-03-02      - [cjm] Fixed GO::Parsers::go_xref_parser - now handles >1 xref per line

2007-05-13      - [cjm] object model now handles consider and replaced_by tags
                - [cjm] disjointness and union_of support in object model
                - [cjm] fixed definition xref parsing with escape characters

2007-07-05      - [cjm] parses secondary taxon IDs (multi-species terms)

2007-07-10      - [cjm] GO::Parsers::obo_text_parser - handles term expresssions (obof1.3)
2007-07-10      - [cjm] GO::Parsers::go_assoc_parser - handles new properties column(16)

2007-08-02      - [cjm] object parser now catches species & assocdate

2007-09-09      - [cjm] GO::Parsers::obo_text_parser - synonymtypedef now uses ID and NAME as sub-elements

VERSION 0.08
============

2007-01-06      - [cjm] includes modified xslt xref handling for OBO_REL xrefs
2007-01-06      - [cjm] added test for handling of xrefs in OBO_REL 
2007-01-17      - [cjm] support for instances
2007-01-22      - [cjm] fixed bug in exporting synonymtypedefs - was not quoting description/name

VERSION 0.09
============

2007-02-14      - [cjm] add test for disjoint_from
2007-03-14      - [cjm] imports tag followed
2007-06-10      - [cjm] chadoxml only: xref handling of OBO_REL : relationship namespace is used
2007-06-10      - [cjm] shownames option in map2slim

VERSION 0.10
============


VERSION 0.11
============

2010-05-18	- [cjm] macro expansion in OWL

VERSION 0.12
============

2010-05-31	- [hsk] fix: 17 cols for GAF2.0. https://rt.cpan.org/Public/Bug/Display.html?id=57994
2010-05-31	- [hsk] no refs to undefs. https://rt.cpan.org/Ticket/Display.html?id=57997
2010-06-25	- [cjm] latest owl xslt fixes: URI treatment fixed. allow * idspace option. expansion tags

VERSION 0.13
============

2010-10-10	- [cjm] latest owl xslt fixes for annotation properties