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ChangeLog
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CHANGES
=======
3.0.3
-----
add missing inverses or missing symmetric properties
add explicit mappings for phenotype and anatomical ontologies
add UMLS as an id prefix for requested class
3.0.2
-----
add side effect predicate
add 'abundance or activity' enum value
deprecate 'original knowledge source', add documentation to the description and examples
3.0.1
-----
minor syntax changes/typo fixes
adding requested attributes for COHD supporting data properties
3.0.0
-----
deprecated/refactored predicate hierarchy to move semantics from predicates into qualifiers (edge properties)
added several enumerations for qualifiers, depending on their usage in associations
added gene->chemical associations with restrictions on subject/predicate/object values (as defined in enumerations)
restructured annotations syntax to comply with LinkML including a change to canonical predicate and opposite syntax
2.4.7
-----
* add pydantic class to the wheel
* update LinkML dependency
2.4.5
-----
* add BioPlanet and Inxight prefixes
* rename pydantic class to model.py
2.4.4
-----
* updated documentation to reference the Biolink Model publication
* added molecular activity to pathway association
* added gene to pathway association
2.4.3
-----
* DRY refactoring of the biolink:ThingWithTaxon mixin by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1033
* Adding a biolink:GeneToPathwayAssociation by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1031
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v2.4.2...v2.4.3
2.4.2
-----
* fix exposure classes
* more documenation
2.4.1
-----
* bug fixes
2.4.0
-----
* make attribute a child of named thing
* add id to ontology class
2.3.1
-----
* reinstantiate food class with correct prefixes
* add pydantic gen to artifacts
2.3.0
----
* Define subject and/or object on several associations by @kevinschaper in https://github.com/biolink/biolink-model/pull/997
* Replace recursive category range on NamedThing with regex by @kevinschaper in https://github.com/biolink/biolink-model/pull/998
* fixes #1002 - remove underscores from some model components by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1004
* fixes #937 - deprecate approved_to_treat in favor of worldwide FDA status slot. by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1005
* add xref to named thing, fixes #934 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1006
* move around SEMMED mappings according to 936, fixes #936 fixes #935 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1007
* remove relation from association fixes #922 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1009
* add remaining inverses fixes #831 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1010
* Fix prefix mismatches by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1011
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v2.2.16...v2.3.0
2.2.16
------
small maintenance fixes, new prefixes, roles for chemical entities
2.2.15
------
update doc regeneration to use DocGenerator as a first pass.
fix annotations syntax.
2.2.14
------
small maintenance fixes, pin LinkML for testing purposes.
2.2.13
------
small refactors to better use description field consistently.
2.2.12
------
fix dependebot security announcement
remove subclass of from slot_usage
add canonical inverse for increased/decreased activity of pairs
and mondo disease susceptibility term to narrow mappings of disease
update license to apache 2.0
2.2.11
------
Update actions to use github user
2.2.10
------
mapping fixes - remove obsolete mappings, swap text based mappings with ids where applicable
add associated with predicate along with associated with sensitivity to predicates.
2.2.9
-----
many fixes to mappings
2.2.8
-----
add a prefix mapping file artifact generated with LinkML upgrade.
2.2.7
-----
get pypi releases working via github actions
2.2.6
-----
small new additions: several new prefixes, UMLS for chemical entity hierarchy, reactions and pathway additions.
remove drugbank, drugcentral from some members of the chemical hierarchy
added drug regulatory status world wide
added two new predicates under related to, related to at concept level, related to at instance level to
add ways of excluding concept level triples from instance level ones.
fixed chemical entity domain/range constraints after second round of chemical hierarchy refactor
added two new associations that help relate wellness gut/blood microbiome sampling to blood analytes
added literature co-occurence
added has_evidence to association object
fix KGX warnings
fix doc links
added pypi github action
2.2.5
-----
bug fixes: add FYPO prefix, add toxicant, add canonical tag to genetically_interacts_with
setup.py to include name variable in order to enable dependents graph
add README info including link to presention on biolink.
2.2.4
-----
bug fixes: various ID expansion cleanups, remove redundancy in ID prefixes (ie: DBSNP)
upgrade to linkml-1.0.5 to address some issues with the context.jsonld file
2.2.3
-----
bug fixes: inverse predicate is_a hierarchy for 'affects' vs. 'affected by'
2.2.2
-----
UMLS->STY prefix management
adding back in missing mixins for increases/decreases amount activity of.
2.2.1
-----
bug fixes: handling one-off prefix requests
added epistemic qualifier enumeration
2.2.0
-----
add original_subject and original_object edge properties
refactor id prefixes in chemical hierarchy
remove spurious mapping
2.1.0
-----
remove gene and polypeptide (and children) from chemical entity is_a hierarchy
add chemical entity and gene or gene product mixin
add chemical entity and polypeptide and protein mixin
add fda approval status enumeration and definitions
remove is_a parents from exposure classes
add prefixes back to protein
2.0.2
-----
First pass at property chain specification
2.0.0 bug fixes and documentation updates
Upgrade to linkml-1.0.0
2.0.1
-----
Add NCBIGene prefix (with correct capitalization) to accommodate jsonld context requirements
2.0.0
-----
Refactor of the 'Molecular Entity' and 'Chemical Substance' classes and hierarchy
New 'Information Resource' class and EPC slots
New 'reactions' associations and slots
Added inverses for the majority of biolink predicates
1.8.2
-----
Added documentation and examples for mixins
Added id_prefixes to gene, protein
Added id_prefixes to gross anatomical structure
1.8.1
-----
Fixed typo in 'treatement' -> 'treatment'
Removed UniProtKB from Gene class ID prefix list
Changed contact email from Deepak->Sierra
1.8.0
-----
BiolinkML->LinkML name change support
1.7.0
-----
Updated identifiers to canonical forms
Added predicates for increase/decrease expression predicates, opposite of predicate, generalized
domain for treats and transcription/translation predicates
Domain/range changes for 'interacts with' predicate
Add owlstart enumerations for logical interpretations
Fixed part of the documentation bug for 'types' (linkml changes in progress), added environmental context
as another doc fix
Bump urllib to 1.26.3
Added last broad mappings from wikidata to the model
1.6.1
-----
Corrected NCBIGene prefix (from NCBIGENE)
Reverted ontology taxon parent to named thing
1.6.0
-----
Corrected the exact mappings for CTD positive and negative correlation predicates
Refined the modeling of ontology class as a mixin
Removed slot_uri for 'subclass of' predicate
Moved CTD:therapeutic from 'exacerbates' to 'ameliorates'
Fixed range for category slot in the 'association' class
Cleaned up prefixes for INO and HANCESTRO
Removed commas in class and predicate names
1.5.0
-----
Fixed mapping for CTD
Added catalyst qualifier slot
Updated guidelines with examples
Extended the model to represent spatiotemporal exposures, outcomes, and cohorts
Added 'pathological process' class
Predicates that are symmetric are defined explicitly
Added a new 'activity' class
Fixed mixin hierarchy of transcript and RNA products
Extended the model to represent entities from MODs
Reorganized the chemical substance hierarchy
Added a class to represent siRNA
Improved the organization of 'pathological process'
Added more prefixes for various classes
Changed category slot required for 'named thing' and optional for 'association'
1.4.0
-----
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
1.3.9
-----
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
1.3.0
-----
* 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
1.2.5
-----
* 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..
1.2.1
-----
* Bump version to 1.2.1
* Fix typo
* Add ChangeLog
* Switched to png for UML images
1.2.0
-----
* 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
1.1.1
-----
* 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
1.1.0
-----
* 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
1.0.0
-----
* 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