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