Release Notes

For future functionality please see roadmap

2.0 (SNAPSHOT)

This is a full release. It adds both significant functionality in all areas of Tawny, has a significant clean up of the code base, but also includes a number of breaking changes.

The biggest change has been a reworking off the "default ontology" and "broadcasting" functionality. This results in a cleaner and hopefully in most cases faster code base. Many functions (such as owl-some and and), however, no longer have default ontology functionality and, as a result, can no longer accept string arguments; only the "main" functions (owl-class, object-property etc) are capable of creating new entities, which probably better reflects the original intentionality.

This release also includes further internationalization code, including full support for development of ontologies in Arabic (thanks to Aisha Blfgeh) and Italian. Other highlights include a much cleaner print output making Tawny easier to use and debug.

Support for "frame" functions like owl-class has been refactored; this means that new frame functions can be easily created, and existing functions can be easily extended with new frames. A new function, defgem has been added which gives additional support for facets. A new pattern called tier has been added which generalizes value-partition.

New Features

• defgem provides new support for facets
• frameify allows easy creation of frame oriented functions
• New pattern tier added
• New cleaner implementation of broadcasting, with three new first class functions: fontology, broadcast and broadcast-2
• Shorter macro names for definition: defno, defnb and defnb2
• defn* macros now all add :arglist to their var
• New shorter, cleaner print output for OWL API functions
• Tawny now supports translation into any language
• tawny.arabic: support for Arabic ontologies
• tawny.italian: support for Italian ontologies
• tawny.query.into-map now supports :object keyword
• tawny.query adds many new query functions operating on ontologies and owl entities
• tawny-name extractor function added
• tier pattern added

Bug Fixes

• fetch-doc works on ontologies correctly
• into-map now supports any Entityable object
• ontology now accepts multiple values for most frames
• object-property now parses correctly (and signals an error) when passed a single incorrect keyword

Breaking Changes

• Move to Clojure 1.7 because of fix for CLJ-1388
• Remove default-ontology functionality from all constructor functions (owl-some, only, and, or and not)
• :name frame now namespaced -- this "feature" was never documented.

1.6

Numerous small changes

New Features

• Value Partition now allows additional frames to be added to values.
• Patterns now now the entities they create
• Many improvements to tawny-mode.el
• Support for anonymouse individuals

Breaking Changes

• Protocols are now in their own namespace

Bug Fixes

• Logging message from SLF and ELK are off my default

1.5

The 1.5 release is mostly to move to the OWL API version 4.

New Features

• Save as turtle (thanks to Michael Gaare)
• Annotation now supports any object with an IRI

Breaking Changes

• tawny-owl update to OWL API 4
• tawny-mode update to CIDER 0.11

1.4

The 1.4 release extends Tawny's existing pattern functionality. Patterns created by tawny can now be annotated as belonging to a particular instance of pattern, which in turn makes it easy to find all the entities created by a pattern. As this capability uses OWLs annotation capabilities, this means that the pattern instances are also apparent in the saved OWL ontology so other tools can use this information also.

Tawny-OWL is not also partially documented using http://github.com/phillord/lentic[lentic]. While this is not complete, it does not make sense to delay the release until this is ready as it is developer documentation.

New Features

• Support for "facets" -- an easy mechanism for making existential relationships with a set of classes.
• The addition of tawny.pattern/pattern-annotator and associated functions, which links together all the entities in a pattern.

Bug Fixes

• Tawny now guesses the type of a statement better by looking at all arguments.

1.3

The 1.3 release adds three new features. First, we add support for axiom annotations. While this has always been possible through the direct use of the OWL API, this also circumvented many of the features of Tawny-OWL. This is now possible, through use of the tawny.owl/annotate function.

Second, support for building patterns has been reworked in the tawny.pattern namespace. The functions p and e allow easy expression of patterns in a way which can cope easily with optional frames, and also integrates well with pattern-generator which allows easy construction of macro'd versions of function based patterns; this allows easy interning of pattern entities and the use of symbols.

Finally, a new annotator function has been added to tawny.owl. This allows easy construction of short-cut functions like label and owl-comment which construct annotations of a specific type, while still supporting Tawny-OWLs default ontology functionality. The motivation for this functionality comes from Jennifer Warrender, who has shown that it is a common pattern in several ontologies.

New Features

• It is now possible to add annotations to axioms as well as entities. The primary entry point is annotate.
• A number of new functions have been added to tawny.pattern.

Breaking Changes

• tawny.pattern has been re-written, meaning that value-partition is now a function, with defpartition offering the same thing in macro form.

1.2

The main feature for the 1.2 release has been the incorporation of core.logic, through (ab)use of the Tawny's querying facilities. A tighter integration should be possible, having core.logic work directly over the OWL API, but this was relatively simple to implement. It is performant enough for most uses (the Gene Ontology renders to Clojure data structures in 1-2 seconds on my desktop).

Currently, this integration is used only by tawny.query, providing a query language for searching over the OWL data model. It should also pave the way for repurposing of other tools, though, including a linter like kibit.

One other substantial change is an aggressive micro-optimisation of default-ontology and broadcast-ontology functionality. These functions are called for almost every user function in tawny.owl but had a base call time in the microsecond range (rather than 10s of nanoseconds for a normal call). These micro-optimisations cost a slightly longer code-base; however they give a 3-5x speed increase. Loading a tawny rendered version of GO is now about only about 3x slower than reading the OWL file. These optimisations have resulted in two breaking changes to the broadcasting and default ontology behaviour, both of which now have alternatives.

Finally, rendering has now been cleaned up, so that the ontology form can also be rendered, and this form re-read. This has required a few additional changes.

New Features

• tawny.query now includes a number of core.logic predicates.
• tawny.render/as-form can now cope with any OWL object.
• tawny.render/as-form now takes options, producing output in several formats: two for evaluation or documentation, and two for querying. It is also possible to select the set of ontologies or ontology manager with which to render.
• tawny.render can now render OWLOntology objects.
• The ontology function now supports :import and :annotation frames which broadcast.
• direct-instances function added.
• defentity form added and made public.
• We now test against several versions of the OWL API.

Bug Fixes

• Tawny's own annotation ontology now uses defonce semantics which makes reloading easier.
• :versioninfo handling was broken on ontology.
• refine now uses default ontology
• ontology now adds a prefix even if one is not specified. This avoids a NPE when saving in a prefix format.
• as-form now renders multiple facts correctly
• Several bugs fixed with property chain support, as well as their rendering.
• Numeric restrictions now accept doubles
• tawny.fixture/ontology-and-reasoner didn't actualy work

Breaking Changes

• broadcasting functions no longer nil patch; previously nils were silent ignored. In practice, this was added for internal reasons (which are no longer necessary), and was probably a bug rather than a feature. Nils are now passed to OWL API, and generally cause fail early NullPointerExceptions.
• The default-ontology and broadcast-ontology mechanisms have been extensively micro-optimised; to enable this optimisation, I have deprecated one "feature" which was largely undocumented. Many functions which previously accepted an :ontology frame, no longer do, but still accept an ontology as the first argument. The defentity forms still accept this (as they must have a symbol as the first argument) but the :ontology frame must come first and have a single ontology.
• tawny.query has been extensively reworked, including changes to the underlying representation.
• tawny.render/form has gone (private). Extensions to tawny.render/as-form should work as a replacement.
• tawny.render/as-form is no longer a multimethod, just a function. In practice, this should have been an implementation detail anyway.
• Various dynamic vars in tawny.render have gone, replaced by options in the as-form call.
• tawny.render/as-form now returns a lazy list. In practice, this is should be breaking change only if you use str (in which case change to pr-str instead). The laziness may also cause some unpredictable issues if you store the form, and change the ontology, then realise the form.
• A number of functions which used to work on OWLNamedObject now support OWLOntology also. These include tawny.lookup/iri-to-var and associated functions.

Dependencies

• OWL API to 3.4.10
• Hermit to 1.3.8.4
• New dependency: core.logic 0.8.7

1.1

The 1.1 release has largely been about regularisation of the syntax, enhanced performance and added a few pieces of OWL missing from 1.0.

Regularisation is the biggest change and is, unfortunately, a breaking change. Original Tawny mimicked Manchester syntax; it's "subclassof" frame is back-to-front -- the filler is a superclass of the entity in question. Tawny now uses ":sub", ":super" as slot names; ":subclass" and ":subproperty" are deprecated and will be removed at a later date.

Documentation

• Have added more exemplar ontologies. The OWL primer ontology has now been ported to Tawny.

New Features

• Individual facts can now be defined by the is function (rather than fact) and owl-not (or tawny.english\not).
• Introduced new functions for declaring disjoint object and data properties. as-disjoint now supports all of these.
• Introduced new function, as-equivalent which works for classes, object or date properties.
• suboproperties',suboproperty?' and related functions added.
• Both equivalent? and disjoints? now work for data and object properties also.
• inverse function allows for anonymous reference to the inverse of a property expression.
• oneof now takes accepts strings, numbers and booleans as literals without requiring literal.
• Unqualified cardinality is now supported without using of owl-thing
• The JFact reasoner is now supported.
• New aliases have been added to tawny.english.
• All namespaces now load without reflection warnings, having been heavily type-hinted. This should introduce no changes but many namespaces run much faster; tawny.owl about 2x, tawny.render perhaps 5x for very approximate benchmarks.

Breaking Changes

• owl-not now also supports individuals -- this is technically a breaking change because owl-not previously had arity 1, now also has arity 2.
• disjoint-classes list has been removed, and disjoint-classes-list has been renamed to disjoint-classes!
• tawny.protege-nrepl has now been removed; its had dependencies that were not explicitly specified as it ran inside protege. It is now in a project of its own, called tawny.protege.
• add-subclass functionality has now reversed its functionality -- the second class is now the subclass rather than the superclass.

Bug Fixes

• rendering of object and data properties now reports superproperties.
• superclasses and subclasses no longer crash on circular class hierarchies
• datatype equivalents were limited to other datatypes. Now any datarange is usable.

Dependencies

• OWL API to 3.4.9. Hermit to 1.3.8.3
• Clojure 1.6

1.0

Code Changes

• Introduced integration_test namespace for errors that could be in several places.

Bug Fixes

• iequivalent-classes was removing top and bottom. This makes sense isuper and isubclasses but was breaking a pitfall example.
• individual-explicit was incorrectly declared as variadic and so silently ignoring all frames.
• with-suffix and with-prefix were only returning their last form which prevented their use within as-disjoints and equivalent.
• tawny.owl was not necessarily being loaded correctly, leading to profile violations. It is not loaded as a class resource lazily when necessary.
• tawny-emacs.el was crashing with "Track Entites" should now be fixed.

1.0 (rc1)

Code Changes

• Lookup implementation has been enhanced for performance. This also affects repl and render namespaces.
• All relevant functions should broadcast now.

Bug Fixes

• Support for datatypes was broken in a few areas.

Breaking Changes

• remove-axiom now takes a list, which most of the add-* functions returns
• characteristics on properties now use keywords (:functional instead of functional).
• function names have been regularised (see documentation) resulting in many name changes.
• The format for memorise.clj has changed significantly; this allows arbitrarily sized files to be created. There is no converter from the old file format, but I will write one if it is needed.
• The format for obo.clj has changed to using EDN, rather than a bespoke properties file. As with memorise.clj there is no converter.

1.0

New Features

• tawny-emacs.el now has explicit support for Protege
• A new protege-nrepl.clj namespace which hooks tawny into core Protege data structures.

0.12

This release is intended to be feature complete. New features will not be added for 1.0, although accidentally missing functionality may be added.

New Features

• Complete support for OWL 2, include data types
• OWL documentation can be queries as normal clojure metadata
• New namespaces, query and fixture
• Completion of rendering functionality
• Regularisation of interfaces: where relevant functions now take an ontology as the first argument.
• Updated to Hermit 1.3.7.3, OWL API 3.4.5

Breaking Changes

This version introduces a few breaking changes.

• The as-subclasses and as-disjoint macros are now functions, making them lexically scoped.

0.11

New features

• facts on individual are now supported
• documentation has been greatly extended
• OWL API 3.4.4

Breaking Changes

This version introduces a few breaking changes.

• isubclasses,isuperclasses have been changed to direct-subclasses, direct-superclasses in tawny.owl. This was to avoid a nameclash with tawny.reasoner
• *reasoner-progress-monitor* is now an atom. While this enables the use of reset!, it means an atom must be used in binding. Samples are given in the documentation