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
============
2010-06-25 - [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