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OntoCAT Java API Release Notes
==============================

Version 0.9.9.2 / / /
	Added <userIds> <obsoleteParent> fields to Bioportal's OntologyBean
	FIX for the inability of using encoded slashes in the URL proper when querying Bioportal
	Now passing them as string parameters, q=? pattern
	Added xrefs to annotations returned from OLS

Version 0.9.9.1 30/9/2011
	FIX: starting term now added on the appropriate side of a path in BioPortal
	Updated BP signatures to include isObsolete fields
	Now termpath will throw an exception if an unresolvable term is found rather 
	than adding null to the path
	Modified namespaces behaviour to be more consistent throughout and fixed
	os.getOntologies().get(0).getOntologyAccession() so that it can be used
	as ontologyAccesion (see example 18)

Version 0.9.9 30/08/2011
	Interface change, added getURI to OntologyTerm
	Updated BP OntologyBean's signature and changed warning on new fields to DEBUG level
	Minor fix for empty term paths causing an exception

Version 0.9.8 31/05/2011
	Added GNU and Apache license boilerplates to all source files
	
	Modified distribution package by adding a top-level directory to avoid polluting 
	the directory that it is unzipped into
	
	OntoCAT's default apikey is now added to all BioPortal REST queries
	(note that you can also use your private apikey by supplying it in the 
	alternative BioportalOntologyService constructor)
	
	As per OBO Foundry policy (http://www.obofoundry.org/id-policy.shtml)
	OBO accessions are now translated by OWL API into URIs. This results in
	colons (:) being replaced with underscores (_) in the accessions. In line with
	this policy OntoCAT leaves the accessions as is, however it it still possible
	to getTerm() by its OBO accession, e.g. GO:0000003, but the accession 
	on the retrieved corresponding OntologyTerm will be GO_0000003. 

Version 0.9.7.7 17/05/2011
	FIX: ReasonedFileOntologyService basic constructor was not being instantiated properly
	
	FIX: Another work-around for OWL API 3.2.2 introducing invalid object properties
	URIs and messing up with the reasoner. The new approach relies on removing unused 
	object properties rather than merging as it is difficult to predict which properties
	to merge with OBO namespace introducing another unknown into the object propery URI
	
	UPDATE: Updated BioPortal's OntologyBean signature with userAcl field

Version 0.9.7.6 26/04/2011
	FIX: Manual fix for EFO synonyms and definitions to be parsable through BioPortal
	
	Added an internal cache to BioportalOntologyService that stores the results of
	recent queries (LRU type, 100 queries capacity)
	
	Modified the way BioportalOntologyService accesses hierarchy to reuse ConceptBean
	rather than calling parents/children signatures (considerable speed improvement due
	to caching)

Version 0.9.7.5 05/03/2011
	UPDATE: Updated the OWL API dependency to 3.2.2, which removed the need to fix
	the "owlapi" prefixes in OBO ontologies, but the OBO parser now incorrectly
	loads the object property IRIs, which required a different fix.
	
	FIX: Added an override for the arbitrary limit in the SAXParser of 64k entity expansions
	when using RDFXMLParser (error message: The parser has encountered more than "64,000" 
	entity expansions)
	
Version 0.9.7.4 31/03/2011
	The owlapi prefix is now removed from OBO term accessions when using the 
	ReasonedFileOntologyService

Version 0.9.7.3 23/03/2011
	FIX: ReasonedFileOntologyService was incorrectly calculating root terms
	
	FIX: ReasonedFileOntologyService now also computes relationships for OBO ontologies
	
Version 0.9.7.2 15/03/2011
	FIX: ReasonedFileOntologyService was missing the OntologyService interface implementation
	preventing it from being decorated
	 
Version 0.9.7.1 11/03/2011/
	Some internal refactoring of ReasonedFileOntologyService
	
	Renamed ReasonedFileOntologyService.getRelationsShortcut() to getSpecificRelation()
	 
Version 0.9.7 9/03/2011/
	Change in OntologyService.getRelations signature from return Map<String, List<String>> 
	to Map<String,Set<OntologyTerm>>  
	
	Added ReasonedFileOntologyService, which uses the HermiT reasoner to infer hierarchy and relations
	
	Added support for individuals/instances/particulars to FileOntologyService
	
	FIX: OLS.getRelations() now returns a proper result set

Version 0.9.6.3 9/02/2011
	Removed system.exit() statements that were causing problems in external applications

Version 0.9.6.2 8/02/2011
	Added LocalisedFileService that harmonises and overwrites ontology accessions for FileOntologyService
	
	Updated to latest BioPortal REST signature
	
	FIX: property search was case sensitive in FileOntologyService
	
	FIX: sorting by similarity now includes properties in BioportalOntologyService and FileOntologyService

Version 0.9.6.1 24/11/2010
	Rolled out similarity enabled search (Levenshtein distance across normalised strings)
	
	Updated to the newest BioPortal ontology bean xml signature
	
	Customised XStream parser so that future BioPortal xml updates will no longer block the parser
	
	Fix for some of the issues with term context and service type 
	
	Fix for "The ontology could not be created:" error in FileOntologyService

Version 0.9.6 15/11/2010
	Updated OWL API dependency to 3.1
	
	On creation of FileOntologyService you can specify a user-defined ontology accession
	
	New utils package containing some convenience methods for the R ontocat package
	
	BioportalOntologyService.getOntologies() also lists the views
	
	FIX: Unnecessary warnings when searching OLS
	
	FIX: Occasional incorrect parsing of ontology accessions when searching OLS 
	
	FIX: FileOntologyService will throw exception if there are classes with no properties

Version 0.9.5.3 1/10/2010
	FIX: Colon in query would crash BioPortal
	
	FIX: CachedOntologyService -> OntologyTermContext was not serializable
	
	FIX: BioportalOntologyService would not populate ontologyAccession in getAllTerms()
	
	FIX: include sources inside the distribution so that javadoc shows up properly

Version 0.9.5.2, 24/9/2010
	FIX: Fixed inconsistency when getOntologyAccession() was not in the list of 
	possible accessions of an OWL file thus preventing some of the methods from completing
	
Version 0.9.5.1, 24/9/2010
	FIX: getAnnotations() would result in IndexOutOfBoundsException in some cases
	
	FIX: Updated to recent BioPortal web services signature for OntologyBean - authorSlot
	
	FIX: Various fixes to javadoc

Version 0.9.5, 22/9/2010
	Added support for labels being part of the class URI
	
	FIX: removed unnecessary eager fetching on some of the methods in BioportalOntologyService
	(e.g. getParents, getChildren where the return list was post-processed on 
	individual term	basis)
	
	FIX: updated to the latest BioPortal service signature, i.e. instances XML
	
	Less warnings on using unoptimised getAllParents and getAllChildren

Version 0.9.4, 10/08/2010
	Made FileOntologyService more OBO friendly
		-automatically recognises OBO definition and synonyms
		-drops metadata EXACT, RELATED [] etc from synonyms
	
	Removed a bottleneck in OLS.searchOntology to speed up queries
	
	Extended OntologyService interface with getAllTerms(), getAllChildren(), getAllParents()
		-FileOntologyService has optimised versions for all three
		-BioportalOntologySerice only implements getAllTerms() through paging
		-all other cases are emulated in a slow unopotimized fashion (a warning
		is issued)
	
	Added downloadLocation to OntologyBean (fix for a new field in BioPortal response)

Version 0.9.3, 9/07/2010	
	Extended BioportalOntologyService with the searchSubtree method
	
	Added OntologyContext to OntologyTerm
	
	Harmonised all services to return null values or empty lists on empty results
	
	Added full internal caching to FileOntologyService to improve performance

Version 0.9.2, 28/05/2010
	Added SearchOptions for searchAll() and searchOntology(): EXACT, INCLUDE_PROPERTIES
	
	Fixed maxnumhits setting in BioPortal query to arbitrary large number
	
	Updated BioPortal rest signatures to support URLs as concept IDs
	
	URL encoding parameters in BioPortal queries
	
	Some fixes to make BioportalOntologyService and CachedServiceDecorator thread safe

Version 0.9.1, 8/04/2010
	Re-implemented searchAll() in OLSOntologyService as it suddenly stopped working
	
	Consistent exceptions throwing for incorrect accessions

Version 0.9, 25/03/2010
	Updates to recent BioPortal web services signature
	
	Includes a number of improvements:
		-caching
		-ranking
		-namespace translation
		-multithreaded composite service

Version 0.8, 10/02/2010
	First public release.
	
COPYRIGHT & LICENSE
===================
Copyright (c) 2010 - 2011 European Molecular Biology Laboratory and University of Groningen

Contact: ontocat-users@lists.sourceforge.net
 
This file is part of OntoCAT

OntoCAT is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option) any
later version.
 
OntoCAT is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details.

You should have received a copy of the GNU Lesser General Public License along
with OntoCAT. If not, see <http://www.gnu.org/licenses/>.
Source: README, updated 2012-12-07