SSSOM-Java 1.0.0

Changes since version 0.9.0:

• sssom-core:
  • The core module is now strictly dedicated to the implementation of the SSSOM specification. All additional features (such as SSSOM/Transform) have been moved to a new module called sssom-ext. This is so that library users who just need to read and write mapping sets and perform their own operations on mappings can do so without bringing the whole SSSOM/Transform or OWL-related features that they may not need.
• SSSOM/Transform:
  • Add the possibility to define filter functions, to filter mappings by executing some custom, application-specific code.
  • Add the possibility to define callback functions, to execute custom code intended to have side-effects on the SSSOM/T engine.
  • Add optional named arguments (“flags”) to function calls.
  • Two features that were previously specific to the SSSOM/T-OWL dialect have now been consolidated and generalised into the base SSSOM/T lamguage:
    • placeholder substitutions in function arguments, e.g. the possibility to write "%{subject_id}" to insert the subject ID of the current mapping;
    • the possibility to define variables that can be dereferenced in a placeholder substitution.
  • Add experimental support for URI Expressions.
• New functions in SSSOM/T-OWL:
  • exists, to check whether an entity exists in the ontology and is not obsolete;
  • is_a, to check whether an entity is a descendant of another entity;
  • annotate, to add arbitrary annotations on entity.

Breaking change for SSSOM/T-OWL users

Variables dereferenced within a call to create_axiom should no longer be enclosed in angled brackets, as this will prevent them from being successfully recognised by the Manchester syntax parser. To dereference a variable in a call create_axiom, use either the un-bracketed form without angled brackets (%MY_VARIABLE), or the (new in this version) bracketed form with angled brackets (<%{MY_VARIABLE}>).