CHANGES
=======

v1.2.4
------

* Change type off association\_id from identifier type (URI or CURIE) to nodeidentifier (URI, CURIE or BNODE)

v1.2.3
------

* Newest biolinkml output + changes from dataset push
* TBD: tag looks like an JSON object tag - quote it!

v1.2.2
------

* first passing test
* Make run against new model
* Adjustments to type system and association
* Fix merge issue on contextn
* Add native URIs and shexJ format
* Add context that uses metamodel uris instead of slot\_uri and class\_uri
* Add context that uses metamodel uris instead of slot\_uri and class\_uri
* Fix JSON object/array parsing conflict
* SIO:010004 duplication resolved
* Needed double quotes around string..

v1.2.1
------

* Bump version to 1.2.1
* Fix typo
* Add ChangeLog
* Switched to png for UML images

v1.2.0
------

* Update .gitignore
* Update setup.cfg
* Revert "Update setup.py"
* Use the official uniprot PURLs for uniprot entries
* Update setup.py
* Update remaining artifacts
* Update Makefile and tests
* Rename biolinkmodel folder to biolink
* Switch to newer biolinkml
* Fix issue #227
* Point travis at tests (vs. test)
* Fix issue #225
* Backing up to Travis 3.6
* updating index docs
* Update UML diagrams
* Change travis build to 3.7
* Build from new makefile
* Update biolink-model.yaml
* Update biolink-model.yaml
* Fixes #212
* Undoing committed change, intended to open pull request
* Fixes #212
* Update tests for Semantic Net updates
* Commit cosmetic changes so we can merge the latest Semantic Net elements
* Added UMLS Semantic Types and Codes to the Biolink YAML model (#209)
* Update all content for model changes
* Update documentation (#194)
* remove useless evidence instance and use evidence type for has evidence to fix https://github.com/biolink/biolink-model/issues/153 (#195)
* Add description for population (#196)
* Update biolink-model.yaml (#203)
* Add Gitter badge
* Fixed null pointer exception
* Regen tests (#192)
* model refactoring (#187)
* Add Python 3.7 badge to README
* Fix issue #188.  Use non-aliased slot names in RDF (#190)
* Update tests, requirements and version
* chembl id prefixes (#180)
* Adding PMID as id prefix for publications (#181)
* Resolve merge conflicts
* Detect ALL unused prefixes (#183)
* Partial fix for issue #175 - missing prefix fix
* Partial fix for issue #175 - missing prefix fix
* Changed ANCESTRO to HANCESTRO
* Update tests to reflect changes
* Fixing type in RO mapping of the 'prevents' slot
* Changed graphviz output to .gv and .svg.  Fixes issue #176 (#177)
* extend mappings with new slots (#173)
* Change base URI to  http://w3id.org/biolink/vocab
* Detect ALL unused prefixes
* merge
* Update secondary files Also removed a few more false change positives
* Test and build of patch change
* Remove GMODChado mapping
* Make category an IRI type
* Fix issue #163.   Also added pipenv files and fixed make file bug
* Checkpoint
* Added comparefiles tool and added to makefile
* Sort markdown index files
* Sort markdown output
* Sample test code for RDF files
* Update tests to reflect ancestors fix
* Fixed scope error
* Correct error in shex compact grammar generation
* Update to fix a bug in the shexc generator
* Updates ShEx testing and generation
* Fixed issue in ShEx generation
* Fix for issue #138.  Also updated version number
* Remove a debug statement
* Make test file case sensitive
* Fix issue #131 by changing the name of the test script and adding a pattern to the Makefile
* Add COLUMNS to travis build
* Fixes issue #133 and does complete build
* Updated tests to reflect issue 120 fix
* Fix for issue #119.  Also includes a complete make
* Fix for issue #119.  Also includes a complete make
* Fixed issue #120
* Updated version for ShExJSG
* Update requirements to match setup
* Update biolink-model.yaml
* Update images
* Build fix
* Resync build
* adding 48 new predicates to support CTD data
* Start of documentation for using the schema loader
* fixed erroneous BFO:0000066  mappings
* Fix for issue #106 - regenerate all documents
* Completely merge biolink-model.yaml
* Set the test refresh\_files variable to false
* Completed the biolink-model.yaml merge and regenerated the ouutput
* Conflict resolution
* Order related differences?
* Integrated last change to biolink-model.yaml on biolink repository
* Remove contrib PNG's and use direct reference
* docs
* Everything is more or less solid
* Everything is more or less solid
* Get the right context for the metamodel
* Added a RDF directory to the make file
* Checkpoint. Metamodel seems completely sound in JSON/RDF and the like
* RDF generating from JSON-LD
* Updated the python to type the slots
* First cut at ShEx generator
* Theoretically complete except for ShEx
* Undoing earlier name fix -- need another approach
* Fix for issue #14
* Undo fix for issue #12
* Fix for issue #12
* Fix for issue #12
* Fix for issue #11
* Fix for issue #10
* Update test and make output to reflect changes in json schema generator
* Fixed a typo in Generator.visit\_all\_\_class slots
* Fixes issue #9
* Test files updated to reflect biolink-model.yaml refactoring for issue #8
* Misc test files that were missed in previous submissions
* Temporary fix for issue #8 -- added expected failure decorators
* Fix for issue #7
* Fixes for issue #5
* Fixes for issue #4
* Additional changes for yuml determinacy problem
* Fixed non-determinacy issue in emission order
* Cleaned up contextgen comments and clicktestcase editing of it
* Fix issue #6
* Part of issue 2 fix
* Removed Generator.root\_closure, as it was only called from here
* Fix Issue #3 - extra asterisk
* Fix Issue #5
* Fix Issue #2
* Added link to the metamodel markdown documentation
* Approaching beta version of markdown and yuml diagrams
* Switch to inline UML
* Update to YUML and markdown generators
* OWl Generation is close to working
* Set theme jekyll-theme-dinky
* Updated the docs
* Passes 3.6 and 3.7 tox tests
* Removed bin directory and added scripts to setup.py
* Checkpoint -- all generators running
* Checkpoint -- YUML generator approaching complete
* Checkpoint -- Generating everything through markdown
* Checkpoint -- generating complete python for metamodel and biolink
* Checkpoint -- metamodel is (almost) self generating
* Proposed dataclasses representation of metamodel
* test for shex etc

v1.1.1
------

* added generated docs for new elements
* Additional association paths
* Added zenodo badge, see #87
* added predisposes and has input slots
* added missing generated docs
* evidence
* Additional mappings
* semweb prefixes
* Ensure all prefixes added
* regen
* add 'in taxon' slot to translator\_minimal subset
* imports
* trim leading 'is' from several predicate names
* changing in\_subset values to lists
* regen
* Fixes #77
* Added example property for chemical entity, fixes #64
* pop2pop
* Update biolink-model.yaml
* regen docs
* fix syntax errs
* stub code for generating nested objects in contextld
* Fixed invalid YAML file
* update treats condition->treats
* fix typos, minor updates to deescriptions
* Added in\_subset and  inverse annotations to TKG min predicates, and WD and SemMedDB mappings
* added in\_subset and inverse slot definitions
* renamed 4 predicates, deprecated two predicates, added numerous new predicates
* re-prioritized
* re-prioritized
* Added chembl, fixes #65
* added links to context file, see #65
* missing docs
* Using reactome for now, but see https://github.com/monarch-initiative/dipper/issues/582
* include all prefixes
* JSON-LD context generation
* link to kgx

v1.1.0
------

* docs
* regen
* fix typo
* updated docs
* Added grouping for BP+MF, fixes #59
* Update biolink-model.yaml
* add SEMMEDDB:PRECEDES mapping
* neo4j-names
* proposed for #49
* tr
* Added UMLS Semantic Group LIVB as a mapping
* category
* expanding UML
* new classes
* restored
* regen
* variant to pop frequencies
* add missing
* Use correct UPHENO Phenotype IRI
* upgraded marshmallow
* fixed typo
* Added metabolite, fixes #35
* Fix upheno mapping, fixes #41
* Update biolink-model.yaml
* Update biolink-model.yaml
* Update biolink-model.yaml
* nu
* yUML
* variants
* protobuf
* regen
* regen
* regen
* regulates
* local-names
* Adding predicates
* NT: haplotype
* sequence variant changes, from #21
* Update biolink-model.yaml
* Issue #26
* regenerated
* regenerated
* regen
* ontol
* regen
* ontology iri
* license
* license
* license
* adding license

v1.0.0
------

* regenerated derived artefacts
* fixing typo
* removing occupation, was added for #7
* First pass at modeling isoforms in schema, see also discussion at https://github.com/The-Sequence-Ontology/MSO/issues/1
* improved metamodel def
* reorganized README
* regen
* Fix list typo
* add\_wikidata\_class\_mappings
* sio mappings
* Added mappings from @micheldumontier in https://github.com/NCATS-Tangerine/translator-knowledge-beacon/pull/45
* pheno qualifiers
* Added mappings to the small number of Wikidata concept types
* Gitignore local Eclipse IDE configuration
* first pass at ShEx, #12
* csvs
* moved docs from top level
* csv export
* regen
* regen
* docs
* moved
* moved
* remove stale
* split some out into contrib
* additional mappings
* doc
* regen
* Added md doc generator, md docs and regenerated all
* test-docs
* test-docs
* Set theme jekyll-theme-dinky
* Set theme jekyll-theme-dinky
* Exemplar SIO mapping see #1
* Adding some mappings for bio2rdf association types, see #1
* regen
* fix typo
* adding space and time
* add attributes
* Update biolink-model.yaml
* Add microRNA type
* regen
* Adding new types Annotating types with identifiers #2
* regen
* mixins
* regen
* regen
* graphql
* sample
* fixed link
* regen with color coding
* regen-gv
* regen
* regen
* schemagen
* using manager methods
* regen
* regen
* travis-badge
* travis
* generation of owl, new classes, travis
* docs
* regen
* adding expression example
* adding expression example
* initial commit
