Ontology Common API Tasks (OntoCAT)

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/>.