PK w;: META-INF/PK w;:6jjMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.7.0 Created-By: 1.5.0_07-b03 (Sun Microsystems Inc.) PK &R;:WEB-INF/PK R;:WEB-INF/classes/PK +R;:WEB-INF/classes/sun/PK +R;:WEB-INF/classes/sun/kain/PK +R;:WEB-INF/classes/sun/net/PK +R;:WEB-INF/classes/sun/net/www/PK +R;:%WEB-INF/classes/sun/net/www/protocol/PK +R;:+WEB-INF/classes/sun/net/www/protocol/https/PK +R;:$WEB-INF/classes/sun/proxyurlhandler/PK +R;:WEB-INF/classes/uk/PK +R;:WEB-INF/classes/uk/ac/PK +R;:WEB-INF/classes/uk/ac/man/PK +R;:WEB-INF/classes/uk/ac/man/cs/PK +R;:!WEB-INF/classes/uk/ac/man/cs/img/PK ,R;:'WEB-INF/classes/uk/ac/man/cs/img/cohse/PK +R;:0WEB-INF/classes/uk/ac/man/cs/img/cohse/annotate/PK ,R;:.WEB-INF/classes/uk/ac/man/cs/img/cohse/locate/PK ,R;:4WEB-INF/classes/uk/ac/man/cs/img/cohse/locate/abner/PK ,R;:4WEB-INF/classes/uk/ac/man/cs/img/cohse/locate/oscar/PK ,R;:4WEB-INF/classes/uk/ac/man/cs/img/cohse/locate/quick/PK ,R;:5WEB-INF/classes/uk/ac/man/cs/img/cohse/locate/regexp/PK ,R;:0WEB-INF/classes/uk/ac/man/cs/img/cohse/ontology/PK ,R;:/WEB-INF/classes/uk/ac/man/cs/img/cohse/portlet/PK R;:-WEB-INF/classes/uk/ac/man/cs/img/cohse/proxy/PK R;:0WEB-INF/classes/uk/ac/man/cs/img/cohse/services/PK (R;: WEB-INF/lib/PK &R;:logs/PK %R;: resources/PK %R;:jjMETA-INF/context.xml PK R;:djj'WEB-INF/classes/COHSEPortlet.properties###Preferences knowledge-service = http://localhost:8080/ks/KnowledgeService #ontology = http://potato.cs.man.ac.uk/seanb/skos/diving-skos.rdf #ontology = http://thesauri.cs.vu.nl/eswc06/ipsv/rdf/ipsv.rdf ontology = http://www.cs.man.ac.uk/~puleston/neli.rdf #ontology = http://www.cs.man.ac.uk/~sjupp/ontologies/obo-in-skos/testneli.owl resource-service = http://localhost:8080/rs/ResourceService #Possible values: #Google - Google search engine will be used to identify link targets #COHSEDB - COHSE database will be used to get link targets resource-components = Google,Taverna-Entity-to-Pubmed reference-locator = Quick #reference-locator = RegExp #reference-locator = ABNER #reference-locator = OSCAR #Possible values: #true #false unique-terms = false #possible values are: #true #false show-source-info = true #Possible values are: #nested_list #plain_list link-box-technique = plain #Possible values: #overlay - blue highlight #icon - uses little COHSE icon link-embelishment-technique = overlay #This key can be obtained from: www.ontok.com/getkey ontok_key = 4cc20df99c7248a90 PK R;:10  -WEB-INF/classes/reference-locators.propertiesQuick = uk.ac.man.cs.img.cohse.locate.quick.QuickReferenceLocator RegExp = uk.ac.man.cs.img.cohse.locate.regexp.RegExpReferenceLocator ABNER = uk.ac.man.cs.img.cohse.locate.abner.ABNERReferenceLocator OSCAR = uk.ac.man.cs.img.cohse.locate.oscar.OSCARReferenceLocator PK +R;:@-WEB-INF/classes/sun/kain/KAINProperties.class1h 7 89: ;< => ? 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"javax/servlet/ServletException)Could not connect to the URL defined in " $fResponse was not committed at the end of the doGet() method. Unable to go further, called respondErrorMStart of doPost method, entering Try block around method 'makeConnection(..)'0Method 'makeConnection(..)' successfully called.PTry block around 'makeConnection(..) caught an exception and called respondErrorEAttempting to retrieve URL object from makeConnection's URLConnectionUTF-8Getting Character Encoding MK,Attempting to get and encode POST parameters NOP QL RSjava/lang/StringT UV=&*POST parameters were retrieved and encodedNSetting the URLConnection's 'setDoOutput(..)' method to TRUE for POST request. W-eTry Block around the URLConnection's 'connect()' method returned an exception and called respondError?Entering Try Block around the code to write to the POST stream.java/io/DataOutputStream XY Z [$ \ ]POST Stream successfuly writtenFAn error occured whilst trying to write the POST parameters :
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"#Entering the makeConnection method. ^K _K?/ `ainvalidjava/net/MalformedURLExceptionNo URL Defined : WXjava/net/ProtocolException-Protocol not understood or not found in URL: AEntering Try Block around the ProxyURLHandler's newURL(..) method: b1:// 'cd e3ProxyURLHandler's newURL method called successfully java/net/URLETry bock around ProxyURLHandler's newURL method returned an Exception fg 2hCopying Header fields across to the HttpServletResponse object xc vc Keep-AliveContent-Lengthchunked9Entering 'if' subsection of the header copying while looplocation y zq Set-Cookie  {q#org/apache/regexp/RESyntaxException@This shouldn't have happened... Something is quite out of whack.@A regex syntax error occured. Erm. This shouldn't be possible...Header Dealt With : Pragmano-cache |$ }g ~u/Entering Try Block to copy & Filter the content&Trying to get the standard inputStreamjava/io/BufferedReaderjava/io/InputStreamReaderjava/io/DataInputStream   Got the standard input StreamMFailed to get the standard Input Stream, trying to get the error Input Stream Got the error input Stream -> Could not get Error Reader: 2Failed to get any input stream. Sent headers only.!Trying to get the response writer *Got the response writer. Writing the data.  text/html text/xhtml ST ,- K + (1Finished writing the data, closing connections...Connections closed.0 --- No Content Present --- : Sent headers only kFlushing the response buffer : Writing all content & headers to output and closing the connection for good.Filtering Cookie : org/apache/regexp/RE; ; path= domain=Cookie successfully filteredUnable to filter cookie :  ; because : 2url\(/url( Kurl\("/url("url\('/url(' url\(http://http:// url\("http:// url\('http:// url\(https://https://url\("https://url\('https:// @import "/ @import "@import "http://@import "https:// @import '/ @import '@import 'http://@import 'https://src=/src=src="/src="src='/src=' src=http:// src="http:// src='http://href=/href=href="/href="href='/href=' href=http:// href="http:// href='http://action=/action= action="/action=" action='/action='action=http://action="http://action='http://url=/url=url="/url="url='/url=' url=http:// url="http:// url='http:// url=https:// url="https:// url='https://http:s//action=https://action="https://action='https:// href=https://href="https://href='https://\|/| D7Session is null, so the dom object will not be modifiedbaddCohseLinks: try to (1) create DOM, (2) add COHSE links, (3) return modified DOM as InputStream.sun/kain/TidyTransformerjava/io/ByteArrayOutputStream   Z HaddCohseLinks - TidyTransformer problem: couldn't create the DOM object. GTidyTransformer couldn't parse the document and the DOM object is null. 2TidyTransformer document - element object is null. _`DError obtaining proxySession, so the dom object will not be modified ***** Annotation in process***** pq JAnnotation in process and the proxySession couldn't handle the DOM object.[Annotation in process and the tidyTransformer couldn't turn DOM object to the OutputStream.java/io/ByteArrayInputStream    null  org/w3c/dom/Element classpageLink q   (original link)(original link) TKAINProxy - getLinkBox: TidyTransformer couldn't serialise the given document object $java/io/IOExceptionmKAINProxy - getLinkBox - IOException: Couldn't use PrintWriter to write back the HTML file for the linkBoxId=  V"KAIN URL-Forwarding Proxy Servlet.(

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KAIN Forwarding Proxy : Error

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You must include the 'http://' or 'https://'



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WK& YZ []"_3a9bC]IeLH3ij2NkLPQL`aG]> AlB8RBT Alm8RbcCn^oJ?+"#$MY&Y'()+*)+,MY,.,%2-Klnp2u3wL*[p3 [q?PQ?rsT ?rtcCuvwJ4+/0MYN6,-**,212 W-K}~,2L4 Nk4PQ4]>-xy%lBT %lmcCz{|J9*+3 M,(Y&Y'4)+)5)6)+,,K7L 9PQ9M>+}>c~J=+7MY&Y'9)+)+,MY&Y';)+)+,8!:K!"L*["[=PQ=}>cCPK +R;:QA @WEB-INF/classes/uk/ac/man/cs/img/cohse/locate/TextLocation.class1a ? @ AB AC D E F G AH IJKL M AN OPQRnode+Luk/ac/man/cs/img/cohse/locate/LocatorNode;offsetIsplitNodeBefore()Ljava/util/List;CodeLineNumberTableLocalVariableTablethis,Luk/ac/man/cs/img/cohse/locate/TextLocation; Signature?()Ljava/util/List;splitNodeAftergetNode-()Luk/ac/man/cs/img/cohse/locate/LocatorNode; getOffset()I/(Luk/ac/man/cs/img/cohse/locate/LocatorNode;I)VupdateForSplitZ(Luk/ac/man/cs/img/cohse/locate/LocatorNode;Luk/ac/man/cs/img/cohse/locate/LocatorNode;I)VbeforeafterpostSplitOffsetisBefore?(Luk/ac/man/cs/img/cohse/locate/TextLocation;Ljava/util/List;)ZothertextNodeSequenceLjava/util/List;LocalVariableTypeTable=Ljava/util/List;l(Luk/ac/man/cs/img/cohse/locate/TextLocation;Ljava/util/List;)ZisAftercheckValidIndex()V updateNode.(Luk/ac/man/cs/img/cohse/locate/LocatorNode;)VnewNode isNodeBefore>(Luk/ac/man/cs/img/cohse/locate/LocatorNode;Ljava/util/List;)Z otherNodek(Luk/ac/man/cs/img/cohse/locate/LocatorNode;Ljava/util/List;)Z SourceFileTextLocation.java  S TU VU $5 45 67 9: WXY Z#java/lang/ErrorIndex beyond end of text $[ \]^ _`*uk/ac/man/cs/img/cohse/locate/TextLocationjava/lang/Object)uk/ac/man/cs/img/cohse/locate/LocatorNodesplitTextNodeBefore(I)Ljava/util/List;splitTextNodeAftergetText()Ljava/lang/String;java/lang/Stringlength(Ljava/lang/String;)VaddTextLocationZ(Luk/ac/man/cs/img/cohse/locate/TextLocation;)Luk/ac/man/cs/img/cohse/locate/TextLocation;java/util/ListindexOf(Ljava/lang/Object;)I! 6 ***  6 **9   !/*D "#/*O $%a**+**ST UWX &'| * *+*,*Yd\^ _bdf*  ( ) *+,x(*+*+ *+,j ((-(./0 (.123,x(*+*+ +*,q ((-(./0 (.1245N** Y xz| 67H +*W*+   89:j,*,+ ;./0 .1<=>PK ,R;:YzzOWEB-INF/classes/uk/ac/man/cs/img/cohse/locate/abner/ABNERReferenceLocator.class1c 9:; < => ?@ A B C D EFG HIJ 9 KL MNO PQRS ONTOLOGY_IDLjava/lang/String; ConstantValueontology1Luk/ac/man/cs/img/cohse/ontology/DynamicOntology;()VCodeLineNumberTableLocalVariableTablethis;Luk/ac/man/cs/img/cohse/locate/abner/ABNERReferenceLocator; locateAll2(Luk/ac/man/cs/img/cohse/locate/LocatorDocument;)Vdocument/Luk/ac/man/cs/img/cohse/locate/LocatorDocument;block,Luk/ac/man/cs/img/cohse/locate/LocatorBlock;parser2Luk/ac/man/cs/img/cohse/locate/abner/ResultParser; ExceptionsT getOntology1()Luk/ac/man/cs/img/cohse/ontology/CohseOntology; invokeTool&(Ljava/lang/String;)Ljava/lang/String;inputoutputnormaliseToolOutput SourceFileABNERReferenceLocator.java  /uk/ac/man/cs/img/cohse/ontology/DynamicOntologyABNER U *uk/ac/man/cs/img/cohse/locate/LocatorBlock '0uk/ac/man/cs/img/cohse/locate/abner/ResultParser V WX 23 YUZ [\ABNER: Invoking process] ^U abner/Tagger _3ABNER: Process terminated 63\n|\r` ab9uk/ac/man/cs/img/cohse/locate/abner/ABNERReferenceLocator.uk/ac/man/cs/img/cohse/locate/ReferenceLocator8uk/ac/man/cs/img/cohse/locate/ReferenceLocationException(Ljava/lang/String;)V`(Luk/ac/man/cs/img/cohse/ontology/DynamicOntology;Luk/ac/man/cs/img/cohse/locate/LocatorBlock;)V getInputText()Ljava/lang/String;parsejava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintlntagABNERjava/lang/String replaceAll8(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;! !@**Y" # $%&'!w#Y+MY*, N-*- " !#"$#*#$%#() *+ ,-./01!/*"(# $%23!l" Y+M *,"-/13# "$%"4563!= +"8# $% 578PK ,R;:, *  QWEB-INF/classes/uk/ac/man/cs/img/cohse/locate/abner/ResultParser$WordResult.class1O . / 0 1 23 4 5 6 789 7:; 7< =>?@AwordLjava/lang/String;wordType conceptTypethis$02Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;G(Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis WordResult InnerClasses=Luk/ac/man/cs/img/cohse/locate/abner/ResultParser$WordResult; wordResult ExceptionsBprocess()V parseResult(Ljava/lang/String;)Vparsed[Ljava/lang/String; parseWordType SourceFileResultParser.java  &  '( O CD +& E FG\| HI- JKL MNjava/lang/String;uk/ac/man/cs/img/cohse/locate/abner/ResultParser$WordResultjava/lang/Object8uk/ac/man/cs/img/cohse/locate/ReferenceLocationExceptionequals(Ljava/lang/Object;)Z0uk/ac/man/cs/img/cohse/locate/abner/ResultParser access$000k(Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V access$100k(Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;Ljava/lang/String;Ljava/lang/String;)[Ljava/lang/String; access$200()Ljava/util/Map; java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object; l$*+***,**< 9=?A#C$!$"#$%&B** **  GH !#$'(d*+ M*,2 *,2L NOP !" )*#$+&h(** L*+2*+2TVW'X(!)*#$,- 7PK ,R;:1 FWEB-INF/classes/uk/ac/man/cs/img/cohse/locate/abner/ResultParser.class1 6 6 6 7 6 6 6 6 6 6 6    6  6O 6 6  ! ! !  ( +  WordResult InnerClassesEXTERNAL_DIVIDERLjava/lang/String; ConstantValueINTERNAL_DIVIDERWORDTYPE_DIVIDERINTERNAL_DIVIDER_SUBSTITUEBEGIN_REFERENCECONTINUE_REFERENCE NOT_REFERENCEconceptTypeIdsToNamesLjava/util/Map; Signature5Ljava/util/Map;ontology1Luk/ac/man/cs/img/cohse/ontology/DynamicOntology;block,Luk/ac/man/cs/img/cohse/locate/LocatorBlock; inputTextcurrentPositionI currentStartcurrentConceptType`(Luk/ac/man/cs/img/cohse/ontology/DynamicOntology;Luk/ac/man/cs/img/cohse/locate/LocatorBlock;)VCodeLineNumberTableLocalVariableTablethis2Luk/ac/man/cs/img/cohse/locate/abner/ResultParser; getInputText()Ljava/lang/String;parse(Ljava/lang/String;)Viresult wordResults[Ljava/lang/String; ExceptionscreateInputText splitOnce9(Ljava/lang/String;Ljava/lang/String;)[Ljava/lang/String;textdividerparsed processWord9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)VstartwordwordType conceptTypeskipWord(Ljava/lang/String;)I skipSpace()VgetConceptTypeName&(Ljava/lang/String;)Ljava/lang/String;idnamecheckConceptReferenceendtermcreateParseExceptionN(Ljava/lang/String;)Luk/ac/man/cs/img/cohse/locate/ReferenceLocationException;message access$000k(Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Vx0x1x2x3 access$100k(Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;Ljava/lang/String;Ljava/lang/String;)[Ljava/lang/String; access$200()Ljava/util/Map; SourceFileResultParser.java EF cd hi Rq NO PO Q; IJ KL bZ M; ;uk/ac/man/cs/img/cohse/locate/abner/ResultParser$WordResult R q vq Z\|: yz noB pq  java/lang/Stringjava/lang/StringBuilder&Unrecognised concept type identifier: Z 8uk/ac/man/cs/img/cohse/locate/ReferenceLocationException%ABNER output not of expected format: R\java/util/HashMapPROTEINProtein DNARNA CELL_LINE Cell-line CELL_TYPE Cell-type0uk/ac/man/cs/img/cohse/locate/abner/ResultParserjava/lang/Object-Osplit'(Ljava/lang/String;)[Ljava/lang/String;G(Luk/ac/man/cs/img/cohse/locate/abner/ResultParser;Ljava/lang/String;)Vprocess*uk/ac/man/cs/img/cohse/locate/LocatorBlockgetText replaceAll8(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;equals(Ljava/lang/Object;)Zlength()I substring(II)Ljava/lang/String;charAt(I)C java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString/uk/ac/man/cs/img/cohse/ontology/DynamicOntologyensureSubConceptW(Ljava/lang/String;Ljava/lang/String;)Luk/ac/man/cs/img/cohse/ontology/OntologyConcept; addReference(Ljava/lang/String;II)Zput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; 67:;< =;<>;<?@;<A;<B;<C;<DEFGHIJKLM;NOPOQ;RST&*****+*, ** U"\1 23]^`%aV &WX&IJ&KLYZT/* UeV WX[\T(+ M>,Y*,2*Ujlnl#q'rV* ]O(WX(^;!_`a(bZT9* UvV WXcdTh+, N- *+-U{} V*WXe;f;g`a(hiT2, *+W"**+6,**-U& &,1V4jO2WX2k;2l;2m;a(noT1**=*Y+`* *+ *+U )/V 1WX1k; (jOa(pqTL* * *Y`U V WXrsTu++ M,*!Y"#$+$%,U )V +WX+t; u;a(vqT<*6*<*=* N**-&W* -d'W*U" )6;V* .jO)wOx;<WXyzTO(Y!Y")$+$%*UVWX{;|}TP*+,-UV*~X;;;a(TE*+,UV ~X;;a(TUqT|L+Y,-./W00/W11/W23/W45/WU# '($)1*>+K,9 68PK ,R;:WOWEB-INF/classes/uk/ac/man/cs/img/cohse/locate/oscar/OSCARReferenceLocator.class1 G  F  F F F F    F           &  F F F   F F  F F   ONTOLOGY_IDLjava/lang/String; ConstantValueHTML_FILE_PREFIXHTML_FILE_SUFFIXHTML_TEXT_HEADHTML_TEXT_TAIL REFERENCEREFERENCE_SLOTREFERENCE_SLOT_NAMEREFERENCE_START REFERENCE_ENDBLOCKED_REFERENCEREFERENCE_LIMIT_PREFIX_LENGTHIontology1Luk/ac/man/cs/img/cohse/ontology/DynamicOntology;()VCodeLineNumberTableLocalVariableTablethis;Luk/ac/man/cs/img/cohse/locate/oscar/OSCARReferenceLocator; 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@ABC  @DE  =F G @H IJ IKL MNOPQRSTUVW X YZ[\]^_`abcdefghijklmnop qrstuvwxyz{|}~      L           ,              USER_ID_IDLjava/lang/String; ConstantValueKNOWLEDGE_SERVICE_ID ONTOLOGY_IDRESOURCE_SERVICE_IDRESOURCE_COMPONENTS_IDREFERENCE_LOCATOR_IDUNIQUE_TERMS_IDSHOW_SOURCE_INFO_IDLINK_EMBEL_TECH_IDLINK_BOX_TECH_IDknowlegeServiceontologyresourceServiceresourceComponents[Ljava/lang/String;referenceLocator uniqueTermsshowSourceInfo linkEmbelTech linkBoxTech check_saveZmessage resourceURLtab_confdefaultOptions/Luk/ac/man/cs/img/cohse/portlet/DefaultOptions;()VCodeLineNumberTableLocalVariableTablethis-Luk/ac/man/cs/img/cohse/portlet/CohsePortlet;doView>(Ljavax/portlet/RenderRequest;Ljavax/portlet/RenderResponse;)VsbLjava/lang/StringBuffer; kainProxyresourceComponentsSessioneLjava/lang/Exception;requestLjavax/portlet/RenderRequest;responseLjavax/portlet/RenderResponse; ExceptionsdoHelpdoEditiIelementitLjava/util/Iterator; componentsLjava/util/Set;selectedComponentNamesLjava/util/HashSet;errorMsgurlLjavax/portlet/PortletURL;cssFileLocationrs1Luk/ac/man/cs/img/cohse/services/ResourceService; allComponentsks2Luk/ac/man/cs/img/cohse/services/KnowledgeService; ontologiesLocalVariableTypeTable(Ljava/util/Iterator;#Ljava/util/Set; processAction>(Ljavax/portlet/ActionRequest;Ljavax/portlet/ActionResponse;)Vsuccessex"Ljavax/portlet/ValidatorException;prefs"Ljavax/portlet/PortletPreferences;ontologies_updatecomponents_update load_resourceLjavax/portlet/ActionRequest;Ljavax/portlet/ActionResponse;setPreferences!(Ljavax/portlet/PortletRequest;)VLjavax/portlet/PortletRequest;setSessionAttributessessionLjavax/portlet/PortletSession;getResourceComponentsString()Ljava/lang/String;s SourceFileCohsePortlet.java \] UV W@ X@ resourcesTab Y@-uk/ac/man/cs/img/cohse/portlet/DefaultOptions Z[ text/html java/lang/StringBuffer  java/lang/StringBuilderCOHSE: getRemoteUser:      http:// :  $
/kain/!
9
 URL: a `CYour Preferences:
Knowledge Service: K@
Knowledge Resource URL: L@Resource Service: M@Resource Service Components:  No component is selected...(Reference Locators (in priority order): P@Unique Terms: Q@3Show information about the source of the resource: R@Link Embellishment technique: S@!Link Box Presentation technique: T@   java/lang/Exceptionjavax/portlet/PortletException \z


:This portlet can be used to browse pages that are decorated by the extra COHSE links. These extra links are added by using the services that are specified in the preferences. Therefore before you use this portlet make sure that you set the preferences appropriately.'The following preferences will be used:"

    e
  • Knowledge service: specify the knowledge service URL.
    • ]
  • Ontology: specify the knowledge resource URL.
    • c
  • Resource service: specify the resource service URL.
    • e
  • Resource components: specify the resource components.
    • j
  • Reference locator: specify which reference-locator to use.
    • l
  • Unique terms: specify if terms will be identified only once.
    • 
  • Show source info: specify whether information should be displayed concerning source of resources.
    • x
  • Link presentation technique: specify how cohse links will be visualised.
    • ~
  • Link embelishment technique: specify how added cohse links will be visualised.
    • 


error  /resources/cohse.css
_
Resource
`
Knowledge
h
Visualisation
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ERROR: 
0