Biolink-model

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Added an enhanced Publication model
Replaced biolink-model.owl with biolink-model.owl.ttl
Differentiated mappings for classes into related, broad, narrow, close, and exact mappings
Differentiated mappings for slots into related, broad, narrow, close, and exact mappings
Fixed typos in class and slot definitions
Fixed inconsistent domain and range constraints
Added classes to represent food
Fixed parent for relation enables
Deprecate edge_label in favor of predicate
Added missing prefixes
Added guidelines to the documentation
Tidied the representation and use of mixins
Differentiated the mixin hierarchy from the class hierarchy
Rearranged properties like id, name, type, description to a generic grouping entity class

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Added genomic entities and common properties for these entities
Added mappings to GPI 2.0 specification
Fixed prefixes for mappings in the model
Fixed definition of interacts_with relation to be symmetric
Added missing predicates referenced in associations
Added entities and properties for representing sequence locations
Added mappings from Monarch Initiative
Added an inverse property of subclass_of
Fixed description for edge_label and relation slots
Added more mappings for different entities and relations
Added chi_squared_statistic and p_value association slots
Expanded the scope of correlated_with relation
Added clarification to RDF mappings
Fixed provided_by property to be multivalued
Added enables relation

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* association_id property should be an association property
* Added or updated id_prefixes for many types
* add caused by property as inverse of causes
* Chemical structure --> chemical substance
* adding has-output
* OBAN to all upper case. Fix Issue 271
* Adding RHEA to prefixes that can be used for reactions, 269
* First pass at chem2chem associations and hyperedges to catalysts,
* fixes 269
* adding node properties for exposure events
* added new associations for exposures
* identifier type changed to anyURI and linked to metamodel ElementIdentifier
* iri type changed to support both URI or Curie
* changed subclass of to reference an iri instead of a defined ontology class, and made it multivalued
* association_id now defaults to bnode so it doesn't have to be supplied
* range of association slot is named thing (meaning that it has to be typed in the model)
* systematic synonym changed to multivalued
* changed subject and object of association to named thing instead of just a iri
* changed relation type to uriorcurie vs. straight uri
* moved association_id in the association class so the creation order is subject, relation, object instead of association_id, subject, relation, object

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* fixed ID type
* adding support for samples and generic attributes
* tiny typo
* Change type off association\_id from identifier type (URI or CURIE) to nodeidentifier (URI, CURIE or BNODE)
* Newest biolinkml output + changes from dataset push
* TBD: tag looks like an JSON object tag - quote it!
* 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..

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

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* 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