source: trunk/ontoCAT/dist/release_notes.txt @ 506

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/>.