Changeset 459


Ignore:
Timestamp:
05/31/11 15:16:34 (2 years ago)
Author:
tadamusiak
Message:

0.9.8 release

Location:
trunk/ontoCAT
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • trunk/ontoCAT/dist/release_notes.txt

    r458 r459  
    55        Add getUri method to OntologyTerm 
    66 
    7 Version 0.9.8 //2011 
     7Version 0.9.8 31/05/2011 
    88        Added GNU and Apache license boilerplates to all source files 
     9         
    910        Modified distribution package by adding a top-level directory to avoid polluting  
    10         the directory that it is unzipped into  
     11        the directory that it is unzipped into 
     12         
     13        OntoCAT's default apikey is now added to all BioPortal REST queries 
     14        (note that you can also use your private apikey by supplying it in the  
     15        alternative BioportalOntologyService constructor) 
     16         
     17        As per OBO Foundry policy (http://www.obofoundry.org/id-policy.shtml) 
     18        OBO accessions are now translated by OWL API into URIs. This results in 
     19        colons (:) being replaced with underscores (_) in the accessions. In line with 
     20        this policy OntoCAT leaves the accessions as is, however it it still possible 
     21        to getTerm() by its OBO accession, e.g. GO:0000003, but the accession  
     22        on the retrieved corresponding OntologyTerm will be GO_0000003.  
    1123 
    1224Version 0.9.7.7 17/05/2011 
    1325        FIX: ReasonedFileOntologyService basic constructor was not being instantiated properly 
     26         
    1427        FIX: Another work-around for OWL API 3.2.2 introducing invalid object properties 
    1528        URIs and messing up with the reasoner. The new approach relies on removing unused  
    1629        object properties rather than merging as it is difficult to predict which properties 
    1730        to merge with OBO namespace introducing another unknown into the object propery URI 
     31         
    1832        UPDATE: Updated BioPortal's OntologyBean signature with userAcl field 
    1933 
    2034Version 0.9.7.6 26/04/2011 
    2135        FIX: Manual fix for EFO synonyms and definitions to be parsable through BioPortal 
     36         
    2237        Added an internal cache to BioportalOntologyService that stores the results of 
    2338        recent queries (LRU type, 100 queries capacity) 
     39         
    2440        Modified the way BioportalOntologyService accesses hierarchy to reuse ConceptBean 
    2541        rather than calling parents/children signatures (considerable speed improvement due 
    … …  
    3046        the "owlapi" prefixes in OBO ontologies, but the OBO parser now incorrectly 
    3147        loads the object property IRIs, which required a different fix. 
     48         
    3249        FIX: Added an override for the arbitrary limit in the SAXParser of 64k entity expansions 
    3350        when using RDFXMLParser (error message: The parser has encountered more than "64,000"  
    … …  
    3552         
    3653Version 0.9.7.4 31/03/2011 
    37         The owlapi prefix is now removed from OBO term accessions when using the ReasonedFileOntologyService 
     54        The owlapi prefix is now removed from OBO term accessions when using the  
     55        ReasonedFileOntologyService 
    3856 
    3957Version 0.9.7.3 23/03/2011 
    4058        FIX: ReasonedFileOntologyService was incorrectly calculating root terms 
     59         
    4160        FIX: ReasonedFileOntologyService now also computes relationships for OBO ontologies 
    4261         
    … …  
    4766Version 0.9.7.1 11/03/2011/ 
    4867        Some internal refactoring of ReasonedFileOntologyService 
     68         
    4969        Renamed ReasonedFileOntologyService.getRelationsShortcut() to getSpecificRelation() 
    5070          
    … …  
    5272        Change in OntologyService.getRelations signature from return Map<String, List<String>>  
    5373        to Map<String,Set<OntologyTerm>>   
     74         
    5475        Added ReasonedFileOntologyService, which uses the HermiT reasoner to infer hierarchy and relations 
     76         
    5577        Added support for individuals/instances/particulars to FileOntologyService 
     78         
    5679        FIX: OLS.getRelations() now returns a proper result set 
    5780 
    … …  
    6184Version 0.9.6.2 8/02/2011 
    6285        Added LocalisedFileService that harmonises and overwrites ontology accessions for FileOntologyService 
     86         
    6387        Updated to latest BioPortal REST signature 
     88         
    6489        FIX: property search was case sensitive in FileOntologyService 
     90         
    6591        FIX: sorting by similarity now includes properties in BioportalOntologyService and FileOntologyService 
    6692 
    6793Version 0.9.6.1 24/11/2010 
    6894        Rolled out similarity enabled search (Levenshtein distance across normalised strings) 
     95         
    6996        Updated to the newest BioPortal ontology bean xml signature 
     97         
    7098        Customised XStream parser so that future BioPortal xml updates will no longer block the parser 
     99         
    71100        Fix for some of the issues with term context and service type  
     101         
    72102        Fix for "The ontology could not be created:" error in FileOntologyService 
    73103 
    74104Version 0.9.6 15/11/2010 
    75105        Updated OWL API dependency to 3.1 
     106         
    76107        On creation of FileOntologyService you can specify a user-defined ontology accession 
     108         
    77109        New utils package containing some convenience methods for the R ontocat package 
     110         
    78111        BioportalOntologyService.getOntologies() also lists the views 
     112         
    79113        FIX: Unnecessary warnings when searching OLS 
     114         
    80115        FIX: Occasional incorrect parsing of ontology accessions when searching OLS  
     116         
    81117        FIX: FileOntologyService will throw exception if there are classes with no properties 
    82118 
    83119Version 0.9.5.3 1/10/2010 
    84120        FIX: Colon in query would crash BioPortal 
     121         
    85122        FIX: CachedOntologyService -> OntologyTermContext was not serializable 
     123         
    86124        FIX: BioportalOntologyService would not populate ontologyAccession in getAllTerms() 
     125         
    87126        FIX: include sources inside the distribution so that javadoc shows up properly 
    88127 
    … …  
    93132Version 0.9.5.1, 24/9/2010 
    94133        FIX: getAnnotations() would result in IndexOutOfBoundsException in some cases 
     134         
    95135        FIX: Updated to recent BioPortal web services signature for OntologyBean - authorSlot 
     136         
    96137        FIX: Various fixes to javadoc 
    97138 
    98139Version 0.9.5, 22/9/2010 
    99140        Added support for labels being part of the class URI 
     141         
    100142        FIX: removed unnecessary eager fetching on some of the methods in BioportalOntologyService 
    101143        (e.g. getParents, getChildren where the return list was post-processed on  
    102144        individual term basis) 
     145         
    103146        FIX: updated to the latest BioPortal service signature, i.e. instances XML 
     147         
    104148        Less warnings on using unoptimised getAllParents and getAllChildren 
    105149 
    … …  
    108152                -automatically recognises OBO definition and synonyms 
    109153                -drops metadata EXACT, RELATED [] etc from synonyms 
     154         
    110155        Removed a bottleneck in OLS.searchOntology to speed up queries 
     156         
    111157        Extended OntologyService interface with getAllTerms(), getAllChildren(), getAllParents() 
    112158                -FileOntologyService has optimised versions for all three 
    … …  
    114160                -all other cases are emulated in a slow unopotimized fashion (a warning 
    115161                is issued) 
     162         
    116163        Added downloadLocation to OntologyBean (fix for a new field in BioPortal response) 
    117164 
    118 Version 0.9.3, 9/07/2010 
     165Version 0.9.3, 9/07/2010         
    119166        Extended BioportalOntologyService with the searchSubtree method 
     167         
    120168        Added OntologyContext to OntologyTerm 
     169         
    121170        Harmonised all services to return null values or empty lists on empty results 
     171         
    122172        Added full internal caching to FileOntologyService to improve performance 
    123173 
    124174Version 0.9.2, 28/05/2010 
    125175        Added SearchOptions for searchAll() and searchOntology(): EXACT, INCLUDE_PROPERTIES 
     176         
    126177        Fixed maxnumhits setting in BioPortal query to arbitrary large number 
     178         
    127179        Updated BioPortal rest signatures to support URLs as concept IDs 
     180         
    128181        URL encoding parameters in BioPortal queries 
     182         
    129183        Some fixes to make BioportalOntologyService and CachedServiceDecorator thread safe 
    130184 
    131185Version 0.9.1, 8/04/2010 
    132186        Re-implemented searchAll() in OLSOntologyService as it suddenly stopped working 
     187         
    133188        Consistent exceptions throwing for incorrect accessions 
    134189 
    135190Version 0.9, 25/03/2010 
    136191        Updates to recent BioPortal web services signature 
     192         
    137193        Includes a number of improvements: 
    138194                -caching 
    … …  
    146202COPYRIGHT & LICENSE 
    147203=================== 
    148  
    149204Copyright (c) 2010 - 2011 European Molecular Biology Laboratory and University of Groningen 
    150205 

  • trunk/ontoCAT/src/uk/ac/ebi/ontocat/bioportal/BioportalOntologyService.java

    r458 r459  
    135135         * Instantiates a new bioportal service. 
    136136         *  
    137          * @param email 
    138          *            the email 
    139          */ 
    140         public BioportalOntologyService(String email) { 
     137         * @param apikey 
     138         *            the apikey required by BioPortal for REST queries 
     139         */ 
     140        public BioportalOntologyService(String apikey) { 
    141141                // Now map the xml to the java beans 
    142142                // FIXME level? 
    143                 urlAddOn = "&email=" + email + "&level=1"; 
     143                urlAddOn = "&apikey=" + apikey 
     144                + "&level=1"; 
    144145                configureXstream(); 
    145146        } 
    146147 
    147148        /** 
    148          * Shorthand that uses ontocat-svn email to instantiate the service 
     149         * Shorthand that uses ontocat apikey l to instantiate the service 
    149150         *  
    150151         */ 
    151152        public BioportalOntologyService() { 
    152                 this("ontocat-svn@lists.sourceforge.net"); 
     153                this("c6ae1b27-9f86-4e3c-9dcf-087e1156eabe"); 
    153154        } 
    154155 

  • trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example2.java

    r458 r459  
    3737        public static void main(String[] args) throws OntologyServiceException { 
    3838                // Instantiate BioPortal service 
     39                // Note that this uses ontocat's default apkikey 
     40                // but you can pass your private apikey into the service 
     41                // by using the alternative constructor 
     42                // new BioportalOntologyServcie( "your apkiey" ); 
    3943                OntologyService os = new BioportalOntologyService(); 
    4044 

  • trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Sandbox.java

    r458 r459  
    2424import jargs.gnu.CmdLineParser.UnknownOptionException; 
    2525 
    26 import java.io.File; 
     26import java.net.URI; 
    2727import java.net.URISyntaxException; 
    28 import java.util.Set; 
    2928 
    3029import org.apache.log4j.Logger; 
    … …  
    3231import uk.ac.ebi.ontocat.OntologyService; 
    3332import uk.ac.ebi.ontocat.OntologyServiceException; 
    34 import uk.ac.ebi.ontocat.OntologyTerm; 
    3533import uk.ac.ebi.ontocat.file.ReasonedFileOntologyService; 
    3634 
    … …  
    5149 
    5250                OntologyService os = new ReasonedFileOntologyService( 
    53                                 new File( 
    54                                 "C:\\work\\EFO\\EFO on bar\\ExperimentalFactorOntology\\ExFactorInOWL\\releasecandidate\\efo_release_candidate.owl") 
    55                                 .toURI(), "efo"); 
    56                 Set<OntologyTerm> organisms = os.getAllChildren("efo", "OBI_0100026"); 
    57                 log.info("Organism has " + organisms.size() 
    58                                 + " children"); 
     51                                URI.create("http://www.geneontology.org/GO_slims/goslim_generic.obo")); 
    5952 
    60                 for (OntologyTerm t : organisms) { 
    61                         if (!t.getAccession().contains("NCBITaxon")) { 
    62                                 System.out.println(t.getLabel() + "\t" 
    63                                                 + t.getAccession()); 
    64                                 for (String syn : os.getSynonyms(t)) { 
    65                                         System.out.println(syn + "\t" 
    66                                                         + t.getAccession()); 
    67                                 } 
    68                         } 
     53                log.info(os.getTerm("GO_0000003")); 
     54                if (os.getTerm("GO:0000003") == null) { 
     55                        log.warn("NULL"); 
    6956                } 
    7057 
    7158        } 
    7259 
    73         public static String getURI(OntologyTerm term) { 
    74                 return "http://purl.org/obo/owl/CL#" + term.getAccession(); 
    75                 // return ((ConceptBean) term).getFullId(); 
    76         } 
     60 
    7761} 

  • trunk/ontoCAT/src/uk/ac/ebi/ontocat/file/FileOntologyService.java

    r458 r459  
    612612        protected OWLEntity getOwlEntity(String termAccession) 
    613613        throws OntologyServiceException { 
    614                 return cache.get(termAccession); 
     614                OWLEntity result = cache.get(termAccession); 
     615                if (result == null){ 
     616                        // try replacing : with _ as per the OBO Foundry 
     617                        // id policy http://www.obofoundry.org/id-policy.shtml 
     618                        result = cache.get(termAccession.replace(":", "_")); 
     619                } 
     620                return result; 
    615621        } 
    616622 
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