Release Notes caCORE Version 3.0 March 31, 2005 National Cancer Institute Center for Bioinformatics ================================================================ Contents ================================================================ 1.0 caCORE Introduction and History 2.0 caBIO 2.1 Release History 2.2 New Features and Updates 2.3 Bugs Fixed Since Last Release 2.4 Known Issues 3.0 caDSR 3.1 Release History 3.2 New Features and Updates 3.3 Bugs Fixed Since Last Release 3.4 Known Issues 4.0 CSM 4.1 Release History 4.2 Features 4.3 Bugs Fixed Since Last Release 4.4 Known Issues 5.0 EVS 5.1 Release History 5.2 New Features and Updates 5.3 Bugs Fixed Since Last Release 5.4 Known Issues 6.0 Bug Reports and Support 7.0 Documentation 8.0 NCICB Web Pages ================================================================ 1.0 caCORE Introduction and History ================================================================ caCORE 3.0 -- 31 March 2005 caCORE 2.1 -- 28 May 2004 caCORE 2.0.1 -- 19 December 2003 caCORE 2.0 -- 31 October 2003 caCORE 1.2 -- 13 June 2003 caCORE 1.1 -- 7 February 2003 caCORE 1.0 -- 29 August 2002 caCORE consists of four main components: Cancer Bioinformatics Infrastructure Objects (caBIO), Cancer Data Standards Repository (caDSR), Common Security Module (CSM), and Enterprise Vocabulary Services (EVS). Each component has both standalone functionality as well as integration points with the rest of caCORE. caCORE is a product of the NCI Center for Bioinformatics and its partners. Visit the caCORE web site for more information: -- http://ncicb.nci.nih.gov/core. ================================================================ 2.0 caBIO ================================================================ ---------------------------------------------------------------- 2.1 Release History ---------------------------------------------------------------- caBIO 3.0 -- 31 March 2005 caBIO 2.1 -- 28 May 2004 caBIO 2.0.2 -- 18 March 2004 caBIO 2.0.1 -- 15 December 2004 caBIO 2.0: -- 31 October 2003 caBIO 1.2.1 -- 27 June 2003 caBIO 1.2 -- 13 June 2003 caBIO 1.1.1 -- 11 April 2003 caBIO 1.1 -- 7 February 2003 caBIO 1.0 -- 29 August 2002 caBIO .91 -- April 2002 caBIO .90 -- October 2001 ---------------------------------------------------------------- 2.2 New Features and Updates ---------------------------------------------------------------- caBIO/caMOD/common Domain Objects: ---------------------------------- New Objects -- CloneRelativeLocation, Cytoband, CytogeneticLocation, GeneRelativeLocation, GenericReporter, GenericArray, HomologousAssociation, Location, NucleicAcidSequence, PhysicalLocation, PolulationFrequency, ProteinAlias, ProteinSequence, DatabaseCrossReference, InternetSource, Provenance, PublicationSource, ResearchInstitutionSource, Source, SourceReference, URLSourceReference, WebServicesSourceReference. Removed Objects -- CMAPOntology, CMAPOntologyRelationship, ConceptSearch, ConcensusSequence, Contig, ESTExperiment, EVSInterface, Expressable, ExpressionLevel, ExpressionExperiment, ExpressionFeature, ExpressionLevelDesc, ExpressionMeasurement, ExpressionMeasurementArray, GeneHomolog, GeneInterface, MapLocation, Ontologable, ProteinHomolog, ReadSequence, Relationable, SearchCriteria, SearchResult, TraceFile, and all *SearchCriteria objects. Modified or Renamed Objects -- DiseaseOntology (formerly Disease), DiseaseOntologyRelationship (formerly DiseaseRelationship), GeneOntology (formerly GoOntology), GeneOntologyRelationship (formerly GoOntologyRelationship, OrganOntology (formerly Organ), OrganOntologyRelationship (formerly OrganRelationship). Interface Pattern: ------------------ Every domain object has a corresponding interface object. Server Architecture Change: --------------------------- RMI has been replaced by HTTP tunneling as the mechanism for connecting to the caCORE server. Search Paradigm: ---------------- The SearchCriteria search paradigm has been replaced with an application service layer. Additionally, the Hibernate API is available for complex querying. WebServices: ------------ The individual web service classes corresponding to each domain object in caCORE2.1 have been replaced by a single web service class.caBIO/caMOD/common ---------------------------------------------------------------- 2.3 Bugs Fixed Since Last Release ---------------------------------------------------------------- No bugs fixed since last release ---------------------------------------------------------------- 2.4 Known Issues ---------------------------------------------------------------- -- There will be no weekly update for the caCORE 3.0 database due to the complexity of supporting both caCORE 2.1.2 and caCORE 3.0. -- caCORE 3.0 will only return up to 1000 records at a time. If multiple level search is conducted, each level will return up to 1000 records. For instance, if the search is Chromosome -> Gene -> Protein, only up to 1000 Genes will be returned, and only Proteins within this 1000 Gene will be returned, i.e. 265 Protein objects will be returned. Chromosome chr = new ChromosomeImpl(); List resultList = appService.search("gov.nih.nci.cabio. domain.Protein,gov.nih.nci.cabio.domain.Gene", chr); -- When searching for a large number of NucleiAcidSequence, Protein, Location objects, it may take a very long time. For example: Get a sequence with sequence id equal to 2 will take about 35 seconds: NucleicAcidSequence nuc = new NucleicAcidSequenceImpl(); nuc.setId(new Long(2)); List resultList = appService.search( "gov.nih.nci.cabio.domain.NucleicAcidSequence", nuc); Get all sequences will take about 15 minutes: NucleicAcidSequence nuc = new NucleicAcidSequenceImpl(); List resultList = appService.search( "gov.nih.nci.cabio.domain.NucleicAcidSequence", nuc); Get all locations for all genes that on chromosome 2 returns 751 records in about 7 minutes: Chromosome chr = new ChromosomeImpl(); chr.setId(new Long(2)); List resultList = appService.search( "gov.nih.nci.cabio.domain.Location,gov.nih.nci.cabio. domain.Gene", chr); -- When navigating uni-directional, many-to-one or one-to-one relationships, Java API may throw the following exception: Test client throws Exception = org.hibernate.LazyInitializationException: could not initialize proxy - no Session For example, the following program will throw the org.hibernate.LazyInitializationException. Chromosome chr = new ChromosomeImpl(); chr.setId(new Long(1)); List resultList = appService.search( "gov.nih.nci.cabio.domain.Gene", chr); Gene gene = (Gene) resultList.get(0); Taxon t = gene.getTaxon(); System.out.println(t); Workaround: Chromosome chr = new ChromosomeImpl(); chr.setId(new Long(1)); List resultList = appService.search( "gov.nih.nci.cabio.domain.Gene", chr); Gene gene = (Gene)resultList.get(0); //Workaround resultList = appService.search( "gov.nih.nci.cabio.domain.Taxon", gene); Taxon t = (Taxon)resultList.get(0); System.out.println(t); Here is a list of uni-directional relationship with many-to-1 or 1-to-1 mapping: InvivoResult(camod) Agent(cabio) ScreemingResult (camod) Agent(cabio) Therapy (camod) Agent(cabio) Promoter(camod) Gene(cabio) Location(cabio) Chromosome(cabio) ProtocolAssociation(cabio) Disease(cabio) RegulatoryElement(camod) Taxon(cabio) Xenograf(camod) Taxon(cabio) -- setMaxResultsCount() method of ApplicationService can only set the MaxResultCount() up to 1000. -- All searches are case sensitive, i.e., When you are searching with a field that is defined as a string, the search is case sensitive. For instance, GeneImpl.setSymbol("NAT2") will return a result, but "nat2" will not. -- NucleicAcidSequence's value attribute and Pathway's description fields are defined as CLOBs, and are currently not searchable in 3.0. When searching according to these two fields, a NullPointerException will be thrown. NucleicAcidSequence nas = new NucleicAcidSequenceImpl(); nas.setValue("test"); List resultList = appService.search( "gov.nih.nci.cabio.domain.NucleicAcidSequence", nas); -- The current model does not support getting a Gene object from a SNP object. -- You cannot currently get the ParentRelationship from OrganOntology OrganOntology g2 = new OrganOntologyImpl(); g2.setId(new Long(8)); List resultList = appService.search( "gov.nih.nci.cabio.domain.OrganOntologyRelationship", g2); It returns 0 relationships even though, grom table ORGANONTOLOGYRELATIONSHIP, we know that Cerebellum ( tissue_code = 8 ) is a child of brain ( tissue_code = 7 ). -- When you create an association between two objects, and then try and use ApplicationService to search with the objects you have created, you will get a gov.nih.nci.system.delegator.DelegateException: local class incompatible. This will happen with all object relationships. For instance: Chromosome chr = new ChromosomeImpl(); chr.setId(new Long(2)); Taxon tax = new TaxonImpl(); chr.setTaxon(tax); List resultList = appService.search( "gov.nih.nci.cabio.domain.Chromosome", chr); -- Wrong Protocol Type may be returned when search protocol from library. Library g2 = new LibraryImpl(); g2.setName("NCI_CGAP_Pr4"); List resultList = appService.search( "gov.nih.nci.cabio.domain.Protocol", g2); The result returned is: [java] ID is 18 [java] Type is TISSUE [java] Number of records is 1 The protocol type should be Library. -- Cannot directly search for PhysicalLocation or CytogeneticLocation or any objects that have a generalization relationship. For example, to get PhysicalLocation objects from SNP, users have to adopt the following code: SNP snp = new SNPImpl(); snp.setId(new Long(34053)); List rs1 = appService.search( "gov.nih.nci.cabio.domain.Location",snp); for (Iterator i = rs1.iterator(); i.hasNext();) { Object result = (Object)i.next(); if (result instanceof PhysicalLocation) { PhysicalLocation phyLoc = ( PhysicalLocation)result; System.out.println("Start PhysicalLocation is - " + phyLoc. getChromosomalStartPosition()); System.out.println("End PhysicalLocation is - " + phyLoc. getChromosomalEndPosition()); } } -- When conducting multi level search, the different objects have to be specified by fully qualified names and be separated by commas with no spaces. For example: appService.search("gov.nih.nci.cabio.domain.Protein,gov .nih.nci.cabio.domain.Gene", chr); is a correct search, while appService.search("gov.nih.nci.cabio.domain .Protein, gov.nih.nci.cabio.domain.Gene", chr); and appService.search("Protein,Gene", chr) are incorrect searches. -- WSDL file contains an invalid namespace: Due to a known Axis defect, a namespace/type "tns2:" shows up in the wsdl file (for example, "tns2:Taxon") instead of the correct type "xsd:anyType". The value "tns2" is undefined in the WSDL. This causes a client side failure when generating domain objects. Workaround: Save a local copy of the wsdl file, change all "tns2:" to "xsd:anyType" and run WSDL2Java against this updated wsdl file. -- Due to the previous limitation (invalid namespace), the method to set the domain object should not be used on the server side in setting search results. An example of this is Gene.SetTaxon(). If these methods are used on the server side in packaging search results, the webservice client will throw an exception. However, these methods CAN be used on the client side for nested search purpose. -- Currently, all domain objects defined in the web services use the bean serializer/deserializer, so they must conform to the bean pattern. However, this is not the case in our implementation of get/set associated object collection methods, such as GeneImpl.getLibraryCollection() method; they contains business logic (search logic). Thus, these methods do not work on the client side. -- Web services interface only returns 100 objects. -- We recommend using JVM 1.4.x. We have encountered NULL pointer exception when consuming a web service using JVM 1.5. -- When running a query using web services, SocketTimeoutException may occur. We recommend usubg call.setTimeout(new Integer(300000)) to increase the socket timeout. -- No deserializer error for EngineeredGene and Party may occur when using web services APIs; please add all of their parent and children serializers and deserializers. ================================================================ 3.0 caDSR ================================================================ ---------------------------------------------------------------- 3.1 Release History ---------------------------------------------------------------- caDSR 3.0 -- 31 March 2005 caDSR 2.1 -- 28 May 2004 caDSR 2.0.1 -- 19 December 2003 caDSR 2.0 -- 31 October 2003 caDSR 1.2 -- 13 June 2003 caDSR 1.1 -- 7 February 2003 caDSR 1.0 -- 29 August 2002 ---------------------------------------------------------------- 3.2 New Features and Updates ---------------------------------------------------------------- +------------------------------------+ | Admin Tool and caDSR Repository | +------------------------------------+ Updated Features ---------------- -- The following changes were made to the repository to support Concept Class, the new Administered Component added to the caDSR model - A new Concepts Table was added to the model. This supports complex Object classes, Properties and Representations with more than one Qualifier term. - Existing EVS codes and data in the Designations (Alternate Name) Table have been moved to the new Concepts Table. In the presence of more than one type of EVS alternate name for a given administered item, preference was given to the NCI_CONCEPT_CODE type alternate name which formed the basis of the related Concept class, the other EVS alternate names were dropped. - Existing Data Element Concepts with Object Class and Property Qualifiers were converted to the new complex Object class and Property Constructs. - Value Meanings that were associated with EVS concepts were converted to the new Concept Class. - Value Domains may now have a Concept associated with the Value Domain, serving as a Parent Concept for either a non-enumerated reference, or as the Parent for an enumerated value domain. - Object classes, Properties and Representation terms previously unassociated with concept classes have been fixed and are now associated with EVS concepts. -- The following tables are now associated with Concepts - Object classes - Properties - Representations - Value domains - Value Meanings - Qualifiers -- A table was added to capture Object Class Relationships. This new table is an administered component. Object Class Relationships are a key component supporting UML Model metadata. Views of this administered component are not yet available in caDSR but will be added after 3.0 as a change order. -- Field Max Length Changes: CSI Name has been extended to 255. Alternate Name has been extended to 255. Description for Workflow status and Registration Status has been extended to 2000 -- New tables were added to support classification of designations and definitions. This feature is key to supporting different names and definitions for reused components from multiple UML Modes. -- Registration Status and Workflow status now have a preferred display order so that data elements can be displayed in the preferred order with those most fully and approved within the registry are presented first in the search results of the CDE Browser. -- Changes to Dates: Begin Date and End Date were added to individual values in the Value Domain Permissible Values table. Thus the permissible value table was brought into compliance with the ISO 11179 Part 3 metamodel, allowing each permissible value within a Value Domain to have their own start and end dates. -- Improved handling of Delete/Latest Version Flag: The delete button has been removed from the AC maintenance screens. All ACs that were previously marked as deleted now have a workflow status of 'Retired Deleted' and a Change Note indicating that these items were previously deleted using the now defunct Admin tool "Delete" function button. -- New Business Rules Enforced when Creating a New DEC: The Admin Tool now requires that an Object Class be specified when creating a Data Element Concept. In addition, the application will not let you create a new DEC with the same Object Class and Property combination used by an existing DEC in the same context. An error message will appear when this occurs. This helps to reduce semantically redundant DECs and encourages reuse of existing DECs. -- New Functionality for Using Contexts: A context that is using an Administered Component (AC) owned by another context can now assign its own alternate names and add reference documents to the AC. -- Related Data Element Concepts: A new page has been added to list DECs related to an AC. This page can be accessed from the DEC, Object Class, and Property maintenance screens. -- Related Value Domains: A new page has been added to show list of Related VDs for Representations. This page is accessible from the Representations maintenance screens. -- Long Name Used Instead of Preferred Name: Where appropriate, we use or display Long Name instead of Preferred Name. When searching for ACs, the default now is to search on Long Name rather than on Preferred Name. In addition, on the DEC maintenance screens, object class and property class Long Name is displayed instead of Preferred Name. -- Excluded Data: Object Classes and Properties with a Workflow Status of Retired Phased Out are not included on the available list of values on DEC maintenance screens. -- EVS link has been removed from maintenance pages for Object Class, Property and Representation. -- System generated DEC and VD Preferred Names can be generated from DEC and VD maintenance screens. System generated names are composed of the public ids of underlying components. Since Long Names are the caDSR preferred name from an ISO 11179 perspective, this reduces the burden of maintaining multiple names. -- Object Class Qualifier and Property Qualifier have been removed from the DEC maintenance screen. Representation qualifier has been removed from the VD maintenance screen. Compound Object Class and Property (one or more qualifiers) can be created as a byproduct of DEC creation using the Curation Tool. The same is true of Representation Term and Qualifier in that these compound type representation terms can be created as a by-product of Value Domain creation using the Curation Tool. -- A link has been added to OC, PROP and REP maintenance screens to show related concepts. -- Copy Feature Enhancement: The DE Copy feature has been enhanced so that users can select specific Alternate Names (if any) to be included as part of the new copy. -- Admin Info: An Admin Info page has been added for Conceptual Domain, Object Class, Property, and Representation Term. This page includes information such as when the Administered Component was created and last modified. -- New Search Criteria: - Conceptual Domain has been added as a new search criteria for Value Domains. - DECs, VDs can be searched by Version Number. - Classification Scheme and Classification Scheme Item has been added as a new search criteria for Object Class. -- Set UML Loader Defaults: The UML Loader Defaults link has been removed from the Other Links section of the Main menu. These defaults are now set using the UML Loader Submission Worksheet. -- Form/Template Link: The Form/Template option was removed from the Other Links section on the Main menu. To work with forms, use the CDE Browser or Form Builder applications. Reference Documents can be uploaded and attached to forms and templates using Form Builder. -- A link to the new Sentinel Tool has been added to the Other Links section. -- An "Opt-Out" feature has been added to user accounts for use with the Sentinel Tool. The default is set to receive Alert Reports. This can be changed so that a user account does not receive Alerts except their own. This option is managed through the NCICB help desk by the caDSR account administrators through a UI. -- Label Changes: The label on the Protocol search results has been changed from "Cooperative Group" to "Organization." The label "Display Format" on the Value Domains page has been changed to "Format." +------------------------------------+ | CDE Browser | +------------------------------------+ Updated Features ---------------- -- New Look and Functionality for the Search Page. Based on user feedback, the CDE Browser search page has been redesigned to look and function more like a standard search site, such as Google, MSN, or Yahoo. There is now a Basic Search page and an Advanced Search page. The Basic Search can be set to search by 'name' or search by 'public id'. -- Search Preferences. We have added a Search Preferences link to the Search Page. You can use this feature to view and modify a set of default search parameters. For example, you can choose to include or exclude data owned by the Test or Training Contexts. -- Test and Training Data Excluded from Search Results. Data Elements owned by either Test or Training are excluded now by default from the Browser. As a result, neither the Test nor Training Context will appear in the caDSR Search Tree. In addition, DEs owned by either of these contexts will not be returned as matches when you run a search. -- New Place to Look for Existing Forms. A Catalogue of Published Forms has been added to the caDSR Search Tree to make it easier to find existing forms. Forms are placed into or removed from the Catalogue using a new Form Builder feature, "Publish/UnPublish". When a form is viewed from the CDE Browser, a list of the CDEs in the form is displayed in the search results. If a document of type "image" has been attached to the form using Form Builder, a "Download Template" icon appears next "Download Data elements to XML" icon. -- Additional Search Criteria. Three new search criteria have been added to the Browser, making it easier for you to find the Data Elements you need. You can now search on the Advanced Search page for data elements based on Concept, Object Class, or Property. -- Registration Status of RETIRED or a Workflow Status of CMTE APPROVED, CMTE SUBMTD, CMTE SUBMTD USED, RETIRED ARCHIVED, RETIRED PHASED OUT, or RETIRED WITHDRAWN are excluded by default. You can view or change the set of exclusion criteria by using the new search preferences feature described below. As before, the workflow status of RETIRED DELETED is excluded and not available in the choice list. -- New Default Sort Order for Search Results. The search results are listed using a default sort order to ensure that the most appropriate DEs appear near the top of the list. -- Sorting the Search Results. You can sort the search results as needed by clicking on any of the search result table column headings. -- CDE Compare Tool. The new CDE Compare Tool allows you to view a selected set of Data Elements in a convenient, side-by-side format. CDEs are placed into the Compare Matrix, then viewed side by side. In addition, the CDE comparison table can be downloaded to Excel for offline use. -- Hitting the "Enter" key will now initiate a search when you are on the Search Page. This works from both the Basic and Advanced Search Pages. -- "Designations" sub heading has been renamed "Alternate Names". -- Added Concept information in CDEBrowser details screen for Object Class, Property, Value Domain and Permissible values. The concept code is hyperlinked to EVS. -- Links to other commonly used caCORE tools have been added at the top. -- After completing a search, the number of matches is displayed at the top of the window and the screen automatically jumps to the search results. The "n matches" can also be clicked to jump to search results. -- Contexts are now listed in alphabetical order. +------------------------------------+ | Form Builder | +------------------------------------+ Updated Features ---------------- -- Guest Account. All users can access Form Builder now. If you don’t have your own account, you can log onto Form Builder as a guest. When you log in as a guest, you can view all public forms and templates. As a guest user, you can also create forms and templates and save them in the TEST context. -- Exporting Forms and Templates to Excel. Forms and templates can be downloaded to Excel. The form’s data elements and most of its structural information (such as headers, footers, instructions, and grouping of questions into modules) are included as part of the export. -- Publishing Forms. If you own a form or template, you can publish it from Form Builder. When you publish a form, it gets added to the Forms Catalogue, a list of all existing forms that can be viewed by the general public. "Guest" user will not be able to publish/unpublish forms. -- Form Instructions. You can now add instructions to forms and templates using Form Builder. Instructions can be added at several different levels: to the header, footer, modules, questions, and enumerated valid values. -- Reference Documents. Reference documents can be uploaded and attached to forms and templates. Once created, these documents can be viewed, edited, and downloaded by users who have access to your forms. A special reference document type "Image" can be used to link an attachment to the "Download Template" function viewable/accessible from the CDE Browser view of the form. -- Search Results Sorting. Search results in Form Builder can be sorted by column headings. -- Improved Form Navigation and Editing. We have made several enhancements to the way you view and modify the list of valid values associated with the DEs on your forms. Now, by default, when a DE is added to a form, its valid values are sorted alphabetically. Also, you can now quickly select and delete multiple valid values. In addition, we have changed the way the Form Builder application behaves when you are editing valid values, questions, or modules. Now, instead of being returned to the top of the page after adding/editing a module, question or valid value you remain at the same place in the page where you made the edit. -- Protocol LOV displays all protocols. Prior to 3.0 release Protocols with workflow statuses 'RETIRED PHASED OUT' and 'RETIRED DELETED' where filtered out. -- Hitting the "Enter" key will now initiate a search when you are on the Search Page. +------------------------------------+ | caDSR UML Model | +------------------------------------+ Items added to the caCORE caDSR UML Model now accessible via caCORE 3.0 caDSR APIs: ------------------------------------------------------------ -- Classes ClassificationSchemeItemRelationship ClassificationSchemeRelationship ComponentConcept Concepts ConceptDerivationRule Definition DefinitionClassSchemeItem DataElementRelationship DesignationClassSchemeItem Instruction ObjectClassRelationship ValueDomainRelationship -- Associations Multiplicity Multiplicity on new on existing New Class Class Side New Class Side Existing/New Class ------------------------------------------------------------------------------------------- ClassificationSchemeItemRelationship 0..* 1..1 ClassificationSchemeItem ClassificationSchemeItemRelationShip 1..* 1..1 ClassificationSchemeItem ClassificationSchemeItem 0..* 1..1 ClassificationScheme ClassificationSchemeItem 1..* 1..1 ClassificationScheme ComponentConcept 1..* 1..1 ConceptDerivationRule ComponentConcept 0..* 1..1 Concept ConceptDerivationRule 0..1 0..* Representation ConceptDerivationRule 0..1 0..* Property ConceptDerivationRule 0..1 0..* ConceptualDomain ConceptDerivationRule 0..1 0..* ObjectClass ConceptDerivationRule 0..1 0..* Qualifier ConceptDerivationRule 0..1 0..* ValueMeaning ConceptDerivationRule 0..1 0..* ValueDomain ConceptDerivationRule 0..* 1..1 DerivationType ConceptDerivationRule 1..1 0..* ComponentConcept Concept 1..1 0..* ComponentConcept DataElementRelationship 0..* 1..1 DataElement DataElementRelationship 1..* 1..1 DataElement Definition 0..* 1..1 Context Definition 0..* 1..1 Administered Component Definition 1..1 0..* DefinitionClassSchemeItem DefintionClassSchemeItem 0..* 1..1 Definition DefintionClassSchemeItem 0..* 1..1 ClassSchemeItem DesignationClassSchemeItem 0..* 1..1 Designation DesignationClassSchemeItem 0..* 1..1 ClassSchemeItem Instruction 0..* 1..1 CaseReportForm Instruction 0..* 1..1 ValidValue Instruction 0..* 1..1 Module Instruction 0..* 1..1 ProtocolFormTemplate Instruction 0..* 1..1 Question ObjectClassRelationship 0..* 1..1 ObjectClass ObjectClassRelationShip 1..* 1..1 ObjectClass ValueDomainRelationship 0..* 1..1 ValueDomain ValueDomainRelationship 1..* 1..1 ValueDomain -- Attributes added to Existing Classes Class Attribute Type ---------------------------------------------------------------------- ProtocolFormsTemplate displayName protected :String ValueDomainPermissibleValue beginDate protected :Date ValueDomainPermissibleValue endDate protected :Date -- New Associations Added to Existing Classes Existing Class Multiplicity Multiplicity on existing on existing/ Class Side New Class Side Existing/New Class -------------------------------------------------------------------------------- Reference Documents 0..* 1..1 Context ValueDomain 1..1 0..* Question ValueDomainPermissibleValue 0..* 1..1 Concept -- Deletions made to the Model - Attributes beginDate from PermissibleValue endDate from PermissibleValue +------------------------------------+ | CDE Curation Tool | +------------------------------------+ Version 3.0 of the Curation Tool incorporates enhancements to: -- Search from Main Menu -- EVS Search Functionality -- UI Design on Create/Edit/Validation Screens, Create/Edit Administered Components, and Block Edit Administered Components. Updated features: ----------------- Search from Main Menu: -- Conceptual Domain may be used as a filter for searching Data Element Concepts and Value Domains. -- Users may enter a specific version number for Data Element, Data Element Concept, Value Domain, and Conceptual Domain searches. -- Searches may be conducted using multiple Context filters. -- Object Class search results include a column displaying the names of Data Element Concepts using the Object Class. Semantic Integration of caDSR and EVS Vocabularies: -- A Data Element is formed by a concept that takes on a specific representation. In ISO/IEC 11179 terms, this translates into the combination of a specific Data Element Concept and a specific Value Domain. caDSR administered items are backed by the use of externally defined terminologies and controlled vocabularies. NCI has developed vocabulary services that are accessed via API (application to application interfaces) to provide touch points during the creation of the content. This results in administered components that are bound to immutable concept codes. These touch points are currently implemented at the Object Class, Property, Representation Term, Value Domain and Valid Value levels of the metadata model. Expanded EVS Search Functionality: -- EVS vocaublaries form the basis for naming and defining administered components in caDSR. Specifically during creation of Data Element Concepts and Value Domains, access to EVs is critical to ensure unambiguous semantics of Data Elements. In 3.0, enhancements to the search of the NCI Terminology Server vocabularies and the NCI Metathesaurus have been added. Enhanced EVS-related features of the CDE Curation Tool for this release include the following: -- From the NCI Terminology Server vocabularies the following updates were made: - UWD Visual Anatomist: This vocabulary is being dropped from the DTS vocabularies and is no longer available from the Curation tool. - MedDRA: Curation tool users may now search for terms directly from MedDRA (Medical Dictionary for Regulatory Activities) international medical terminology, developed under the auspices of the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Enhanced EVS-related features of the CDE Curation Tool for this release include the following: -- Users may search the NCI Metathesaurus using EVS concept codes. -- Retired concepts are excluded by default for results returned from the NCI Thesaurus. The user has the option to include Retired concepts, if desired. -- If a concept does not have a definition, search results from the NCI Thesaurus and Metathesaurus contain the text 'No Value Exists' in the appropriate search result field. -- When a user searches for related components in constructing Administered Items, the search results windows for those that search both the caDSR database and EVS vocabularies include separate columns for 'Public ID' (caDSR results) and 'EVS Identifier' (EVS results). In this release, the caDSR results also displays the EVS identifier upon which it is based. -- The following are updated or new EVS vocabularies that users now have the ability to access from the Curation Tool: - MedDRA (new) - LOINC (updated features) - MGED Ontology (updated features) -- Users have the ability to search EVS vocabularies by using a tree structure. This tree structure facilitates using Root Concepts and their collections of sub-concepts in the construction of caDSR metadata. -- When a user is creating or editing a Value Domain, they may select one or more search results from the EVS vocabularies to be used as Permissible Values. -- Users may create Non-enumerated Referenced Value Domain. This type of value domain provides the ability to indicate that the values must come from a referenced concept list but without copying/maintaining the values en mass in the caDSR. -- Users may create a 'Parent' concept to constrain Permissible Value selection. Only subconcepts of the Parent are allowed to be used as Permissible Values. Users may create Non-EVS Parent concepts to reference sources outside the EVS (e.g. World Health Organization). -- A Parent Concept from the NCI Metathesaurus may be used for a Non-Enumerated Value Domain. If a Parent Concept from the NCI Metathesaurus is selected from a search result filtered by a Meta Concept Source, for example ICD-9, the filtering source is retained and displayed on the Non-Enumerated value Domain screen. -- The EVS Concept Codes for Qualifiers, Object Class, Property, and Representation Terms selected from an EVS vocabulary are displayed on Data Element Concept and Value Domain screens. These Concept Codes are also hyperlinked to the EVS tree structure. Clicking the hyperlink causes a name component search window to display the appropriate tree structure focused on the selected EVS concept. -- If a concept from the NCI Metathesaurus is selected as a naming component and it also has an NCI Thesaurus concept code, the Thesaurus Concept code is used as the basis for the concept link instead of the Metathesaurus UMLS CUI. -- In order to support integration with the UML Loader, Administered Component create, edit and version screens employ a new naming convention comprised of three choices for Preferred Name: - System Generated: - Data Element: Public ID and version of the Data Element Concept concatenated with the Public ID and version of the Value Domain. (e.g. 1234567v1.0:987654v1.0) - Data Element Concept: Public ID and version of the Object Class concatenated with the Public ID and version of the Property. (e.g. 1234567v1.0:987654v1.0) - Value Domain: Parent Concept(s) Concept ID (if Parent Concept is present) concatenated with the Public ID and version of the Value Domain. (e.g. C:67253:1234567v1.0:987654v1.0) - Abbreviated: - Preferred Name is constructed in the same way it is in version 2.1.1. - Existing Preferred Name: - This is a user-editable field and initially displays the existing Preferred Name on 'edit', 'create new using existing' and 'version' screens. -- User Interfaces have been updated for Data Element Concept and Value domain creation and maintenance to support Compound Object Class, Property and Representation terms. Instead of a single concept being associated to an OC, P or Rep Term, and up to one Qualifier for each term, Compound items have a Primary Concept and may have one or more Qualifier Concepts. The Primary concept is shown in one edit window, the Qualifier terms in another. The UI displays both the concept name and its EVS identifier, displayed as a hyperlink. If more than one Qualifier concept exists, the concept code for the highlighted concept name is displayed. Business Rule Implementation: -- Business Rules implemented in the Curation Tool pertain both to the creation and maintenance of all Administered Components. The following is a list of enhancements that have been made to the business rules enforced by the Curation Tool. - End Dates for Administered Component creation and editing are mandatory if the Administered Component has a Workflow Status of Retired Archived, Retired Deleted, or Retired Phased Out. (End Date is not currently required for Retired Withdrawn). - The Data Element Concept Validation screen displays a warning stating that an Object Class should be present for a Data Element Concept. The Object Class is not mandatory unless its associated Data Elements have a Registration Status of Standard, Candidate, or Proposed. Conversely a Data Element cannot be promoted to Registration Status of Standard, Candidate, or Proposed if its Data Element Concept does not have an Object Class. - To promote better versioning practices, a hyperlink to the NCICB Business Rules webpage has been included next to the Version attribute on all create, edit and versions screens. - To promote better versioning practices, a message is displayed suggesting the selection of an appropriate Workflow Status when the user block versions by a point or whole. - To promote better versioning practices, the Workflow Status pick-list does not have a default value. - Until additional business rule validation can be added to the Block Edit Data Element function, the feature has been altered to prevent creation of poorly formed data in the following ways: - 'Select Data Element Concept Name' is disabled. - 'Select Value Domain Long Name' is disabled. - 'Check Box to Create New Version' is disabled. - CANDIDATE & STANDARD are not available from the Registration Status pick-list. This avoids inadvertently circumventing the mandatory Object class for Data Element Concepts of Data Elements promoted to these Registration Statuses, but by request, allows promotion of a block of Data Elements to "Proposed". UI Design on Create, Edit, and Validation Screens: -- On Value Domain screens, naming component fields have been labeled to indicate which components are retained and which are not retained. Object Class and Property are labeled as 'Optional Name Components (will not be saved or displayed later)'. -- All success messages display the Long Name and Public ID of the Administered Component. -- Value Meaning Description and EVS Concept Code are displayed on all Enumerated Value Domain screens. -- The ‘re-using Permissible Value’ message is no longer displayed if the user creates an exact duplicate of a Value, Value Meaning, Value Meaning Description combination already present in the caDSR. -- Effective End Date is now below the Effective Begin Date attribute. -- Workflow Status is now above the Version attribute. Administered Components Create and Edit: -- Components classified by a Classification Scheme (CSI) Item in a hierarchical order automatically inherits the parent of the selected CSI. Users have the ability to remove the parent if desired. -- Create New Using Existing screens open with the Version set to '1.0' and without the following attributes from the template Administered Component: - Classification Schemes/ Classification Scheme Items - Workflow Status - Registration Status (Data Element) -- Permissible Values may have Begin/End dates and Origins unique to a Value Domain. Designations: -- Alternate Names and Referenced Documents may be associated to the Used By Context. -- May assign Classification Scheme Items as part of the initial Designation process. +------------------------------------+ | CRT | +------------------------------------+ The reviewer Action of 'Draft Modified' has been removed. Administered Components with Workflow Statuses of RELEASED are displayed at the top of search and match results. Viewing of search results has been improved by making the results windows larger and by auto-adjusting row height and column widths to improve the display. Row heights and column widths are also manually adjustable. Data Element search and match results may now be sorted by clicking on column headings. +------------------------------------+ | caDSR Sentinel Tool | +------------------------------------+ The caDSR Sentinel Tool is a new tool which provides for the automated notification of changes within a caDSR database. Please refer to the online Help for a complete description of current features. ---------------------------------------------------------------- 3.3 Bugs Fixed Since Last Release ---------------------------------------------------------------- +------------------------------------+ | Admin Tool | +------------------------------------+ -- Version Number was not being displayed correctly on all screens. This has been fixed. Version Number now displays as XX.xx on all screens. -- Value Meaning was missing from "Details" display on VD maintenance page. This has been fixed. -- Users were unable to enter permissible values from the value domain screen. This has been fixed. -- When opening a detail view to edit or maintain, or select from an LOV, the pop up window was writing over an open window instead of opening a new window. This has been fixed. -- The Document Language default has been set to "English." -- All forms created in Form Builder were not viewable in the Admin Tool. The Form/Template link has been removed from Form Builder. The Form Builder tool has been enhanced to permit users to upload and attach documents to form or templates. -- Conceptual Domain was being populated with a key instead of name. This has been fixed. -- The image on the CSI tree was incorrect. It has been changed to say AC instead of DE. +------------------------------------+ | CDE Browser | +------------------------------------+ -- The Excel download file was not displaying properly for rows where the text has double quotes (" ") in it. This problem has been fixed. -- The CDE Browser Excel download did not sufficiently label columns related to the Data Element. Columns related to the DEC and VD were fully described, while those relating to the Data Element are named 'Version', 'Context', 'Public ID', etc. This has been fixed. We have added "Data Element" to these column headings. -- The CDE Browser was missing links to some of the other caDSR tools. These links have been added to the Browser. -- The "Download Template" link in the CDE Browser appeared only for templates. The "Download Template" link now appears for forms as well. +------------------------------------+ | Form Builder | +------------------------------------+ -- Adding CDE's with more than 999 valid values to a Form: This problem has been fixed. You can add CDEs with more than 999 valid values to a form in Form Builder. However, it may take several minutes to save a form that contains CDEs with large sets of valid values. -- Duplicate Valid Values: Valid values were being added more than once when a user was trying to update or change the association between a question and CDE. This has been fixed. -- Adding Valid Values: While editing a form’s module, users were not always able to add valid values by clicking on the '+' icon and then saving the module. This has been fixed. -- Rearranging Modules: A bug was preventing users from changing the order of modules, questions, or valid values when the display order was stored incorrectly in the caDSR repository. This has been fixed. -- Privileges: Certain non-CTEP users were able to view CTEP forms. This has been fixed. When users were assigned 'Admin' privileges to a context using the Admin Tool, Form builder was not granting corresponding privileges to the user. This has been fixed. -- CRT Tool and Discoverer Reports: If you edited a form in Form Builder after it was loaded using the CRF Loader, the form sometimes did not display properly in the CRT Tool or in certain Discoverer reports. This problem has been fixed. -- Logging Out: Under certain circumstances, an exception report was generated while logging out of Form Builder. This has been fixed. +------------------------------------+ | CDE Curation Tool | +------------------------------------+ -- Secondary windows open or opened after the session timeout has expired no longer display the Logon screen. The secondary windows direct the user to logon using the main screen. -- Derived Data Element attributes are retained after the user creates a new Data Element Concept or Value Domain from the Create Data Element screen. -- The Creator and Modifier pick-lists are in alphabetical order. -- Underlying code used to access the CDE Browser is dynamic rather than hard-coded. -- Designation function works as designed when user launches it from a screen displayed after clicking the 'Back' button from a Get Associated search. -- The 'Back' button is always displayed on appropriate Get Associated search results screens. -- The search result screen heading is always correct when using the Get Associated function. -- User-sorted results are retained on the source result screen after clicking the 'Back' button on a Get Associated search result. -- Get Associated results screens are no longer retaining filters used to return the source results. -- Data Element attributes 'Historic_CDE_ID' , 'Creator', and 'Date Created' are displayed on the results screen after an edit Data Element function has been submitted. -- Name component search windows are no longer initially displayed with a previous search’s filters selected. -- The Workflow Status pick-list is always initially focused on the blank space on all Block Edit screens. -- API_101 and API_102 errors are no longer being returned from the database. -- Sorting by the 'Reference Documents' column has been disabled. -- An API error is no longer displayed when a Name Component (a Derived DE attribute) is removed after navigating to the Validation screen. ---------------------------------------------------------------- 3.4 Known Issues ---------------------------------------------------------------- +------------------------------------+ | Admin Tool | +------------------------------------+ -- The default version type for Data Element Concept is not indicated in the user interface. It is 'All' versions. +------------------------------------+ | CDE Browser | +------------------------------------+ -- The tree takes 15-20 seconds to display the first time you enter a CDE Browser session or refresh the tree. No workaround. This is due to the new Catalogue feature and the need to build two sorted list of forms to support two views: alphabetically by form name and forms listed by Protocol. Alternatives to improve performance are being investigated and will be deployed to production as soon as possible. -- Downloading Large Sets of Data Elements: You may run into problems when downloading very large sets of Data Elements. Excel has a limit of 65,000 rows. If your Excel format download exceeds this limit, the download will not be successful. With the XML download, the download process may hang during very large downloads. We will correct this problem in a future release. To work around this problem, download the required data elements as several separate files. -- Test and Training Context Forms/Templates shows up under caBIG Catalog node even when the user has selected to exclude Test and Training context using search preferences. -- Data Element Details Screen: For some NCI Concept code hyperlinks for Object Class and Property component concepts does not open the NCI Thesaurus. This is due to a known issue in the Curation tool that will be fixed after the release. -- Sorting on Public Id sorts alphabetically: 1, 15, 100, 1000, 20007, 21, 2100, 2100058, 2093, instead of sequentially by number: 1, 15, 21, 100, 1000, 2100, 2093, 20007, 2100058. No workaround, this will be fixed after the release. +------------------------------------+ | Form Builder | +------------------------------------+ -- Saving CDEs that contain more than 50 but fewer than 1000 valid values: It may take several minutes to save a form to which you’ve added a CDE with a large set of values. Typically, you will notice this problem when adding a CDE that has 50 or more valid values. -- Saving CDEs that contain more than 1000 valid values: At this time you cannot successfully add a CDE to a form if that CDE contains more than 999 valid values. You will be able to add the CDE to the form, but you will not be able to save the form until you remove the CDE in question. This will be fixed as a change order in the near future. +------------------------------------+ | caDSR UML Model | +------------------------------------+ -- The caDSR 3.0 UML Model exposes most caDSR classes and attributes. Some classes and attributes are not exposed. For example "instruction" class is not included. +------------------------------------+ | CDE Curation Tool | +------------------------------------+ Block Edit: Classification Schemes removed during a block edit are temporarily displayed on a single edit screen opened immediately after the block edit was submitted. -- The Classification Scheme is removed. Get Associated: Edit Selection button is displayed on an Object Class (or Property) search results screen after a Get Associated Data Element Concept search is conducted, followed by an edit to the DEC, followed by a return to the Object Class (or Property) results screen by clicking on the Back button displayed on the DEC results screen. Clicking this Edit Selection button on an Object Class (or Property) results screen triggers a series of Java-Script errors to display. -- Do not click an Edit Selection button displayed on an Object Class (or Property) results screen. Main Search: If a user initiates a second search while previous search results are still displayed, the user can click 'More >>' link in the previous search results. However, this action terminates the second search while leaving the 'Searching, please wait' message and hourglass-cursor displayed. -- Avoid clicking a 'More >>' link after initiating any search. If the link is inadvertently clicked, click the main menu Search button to begin another search. Main Search: An 'Error on page' message displays if a new search is initiated before the screen fully refreshes. For example, if 'CRF Questions' is selected as the 'Search For' and the screen is still refreshing, and the user clicks the Enter button, the error will be displayed. -- Avoid initiating a search before the screen has refreshed completely. If the error is displayed (will either be a pop-up message or just text in the lower left corner of the IE window), click the main menu Search button and start again. Edit Component: Date picker calendars can display too large inside the default display window size if the IE Browser Text Size is set higher than Medium. -- Expand the Date Picker window to make it large enough to see all the dates or change the Text Size through the IE View/ Text Size menu. Select Medium to Smallest to ensure the entire calendar displays inside the default display window size. Derived Data Elements: When submitting a new or edited Data Element where a Component DE has been removed a user may receive an exception message stating that the Component DE was not removed. -- No workaround. The Component DE is actually removed. Changing VD Type: If a user is editing an Enumerated Value Domain and they select 'Non-enumerated' as a Value Domain type, the screen will refresh with all the values removed. If the user then re-selects Enumerated as the Value Domain type, the screen refreshes without the Valid Values. -- Click the Clear button to restore the Permissible Values. Naming Wizard: Any user-entered changes to Definition are removed if a naming component is selected after the user-entered text is added. -- Select all desired naming components first and then update the Definition manually. Naming Wizard: Preferred Name is not automatically truncated to 30 characters if the name type is toggled from System Generated to another type; then back to System Generated. -- Manually edit Preferred Name to fit 30 character limit. EVS Search: Using only a wildcard by itself during an EVS search will prevent EVS results from being returned. -- Avoid using a '*' in the search term field. EVS Search: The 'Set Meta Returns Limit' filter resets to '100' after a search is conducted. -- Select the desired Metathesaurus returns limit before conducting another search. EVS Search: Users may see intermittent and random EVS search results in terms of the number of terms returned including whether a term is returned from one search to another search. Performance times may also vary. This can occur with Synonyms and Identifier Code searches as well as Metathesaurus searches filtered by Source. -- Conduct the search again. This occurs when a user clicks on a concept name in the EVS tree structure while another user’s term search is simultaneously handled by the RMI server that processes EVS searched from the Curation Tool. EVS Search: The '.' acts as a wildcard during the NCI Metathesaurus portion of an EVS search. Since the standard wildcard for searches in the Curation Tool is '*', this can inadvertently cause the search string to be truncated. (E.g., '123.4*' would be searched as '123.' for the Metathesaurus portion of a search.) -- Do not include '.' in search terms. EVS Search: On an EVS search window with 'Search In' focused on 'None' for caDSR and 'Code (Metathesaurus)' for EVS; results from caDSR matching a term entered instead of a Metathesaurus Source Code will be returned. -- No workaround. Enter the desired Metathesaurus Source Code. EVS Search: Clicking on an EVS Concept name in the results area is designed to open the tree structure for the corresponding vocabulary showing the Concept’s place in the hierarchical order. The concept should be displayed in bold-font for easy identification. Concept names in the tree structure are not always displayed in bold-font. -- Use the internet browser’s 'Find' function to locate the Concept name When hyperlinked Concept names are clicked on a Select "Parent search" window, the window refreshes with 'Thesaurus/Metathesaurus' selected in the EVS Vocabulary filter. EVS Vocabulary filter. No results are displayed. -- No workaround. Do not click on hyperlinked concepts in "Parent Search" results. Search for term again. View the term's hierarchical place using the DTS Browser. This does not occur if the Concept is 'treed' in multiple locations in its source's tree structure. For example, the Concept 'Strand Invasion' (GO:0042148) from the Go Taxonomy is placed in at least six different locations in the GO tree structure. -- View the term's hierarchical place using the DTS Browser. EVS Search: When searching for EVS concepts and selecting the 'Subconcepts' function the screen refreshes with the expected Subconcepts in the results area, however, the Tree structure is displayed with the last tree search viewed by the user. For example, if the tree for GO was viewed last, and the user later conducts a 'Term Search' in the Thesaurus; selects a Thesaurus term and selects 'Subconcepts' function, the screen refreshes with the expected Subconcepts from Thesaurus displayed in the results area, but the window's left column is displaying the GO tree structure. -- Click on one of the Subconcepts in the results area. This causes the window to refresh with the expected Vocabulary’s tree structure. The Super/ Subconcepts relationship will be visible in the tree. If desired, click on the Superconcept and conduct another Get Subconcepts search. The window will refresh with the expected results and Vocabulary’s tree structure. Block Edit: The block edit for Data Elements Validation function does not enforce all of the business rules enforced during a single Edit Data Element function but the Registration Status of "Proposed" is still in the picklist. -- No workaround. If the data element violates any business rules the single edit function will catch it or the Block Edit will ultimately prevent the selection of "Candidate" or "Standard". Edit Data Element: Registration Statuses Standard and Candidate are no longer present in the Registration Status pick-list on Create, Edit, or Version Data Element screens after a Block Edit Data Element screen has been opened. -- No workaround. User must start a new Session to restore these two Registration Statuses. Data Element Concept Creation: The EVS_SOURCE column in the Concept Class table is not always being populated when an Object Class, Property, or Representation Term is created from NCI Metathesaurus concept for which and NCI Concept code also exists. This results in the display of a blank cell for EVS Source in the Admin tool "Show Concepts" screen and also in the CDE Browser, which is unable to open the concept hyperlink as a result. -- No Workaround. This will be fixed as a Change Order and a database script will be run to populate EVS_SOURCE for those Concepts lacking the data. Search for Permissible Value "error on Page": When searching for permissible values as a means to find Data Elements or Value Domains, if "All Attributes" has been selected in the "Display Attributes" window a JavaScript "Error on Page" message is displayed and the "Get Associated" function does not work - the results data may also be misaligned. -- Remove the attribute "EVS Identifier" from the list of displayable attributes and click "Update". To see the Permissible Value's EVS Identifier, perform a Get Associated Value Domain search (after EVS Identifier has been removed from display) and open the Value Domain on an Edit screen, where the Permissible Value's EVS Concept Code is displayed. Edit Value Domain: If a quotation mark is added to a Value's Name, the Name will be displayed in the Edit Permissible Value screen truncated after the quotation mark. This only occurs on the Edit PV screen. The enter Value's Name is written to the database correctly. The full name is displayed in search results and on Value Domain screens using it. -- No workaround. If a quotation mark is needed, go ahead and use it. Designations: Alternate Name and Reference Document not saved on "Designations". -- The "Add Selection" button must be selected to add each Alternate Name or Reference Document before the "Update Designations" function is selected. You should be able to see the new item added to the list of existing Alternate names or Reference Documents before selecting "Update Designations". The names and reference documents will be associated with the context named in "1) Designate in Context". If a "used by" designation does not exist, one is created. Designations: "API_DES_00 Unable to designate in the same context as the owning context" error message when attempting to add Alternate Name, Reference document or classification scheme using the "Designate" feature in Curation tool. -- This should be worded as a warning only. The Alternate name, Reference Document and Classifications, if entered, are saved to the database and correctly associated with the owning context. Pop up Blocker: Microsoft Windows XP Service Pack 2® has a pop-up window blocker engaged by default. This can interfere with some success messages produced by the CDE Curation Tool; preventing them from being displayed. -- Follow these steps to allow the CDE Curation Tool to display the success messages blocked by SPII’ s Pop-up Blocker: 1. Select 'Internet Options' from the browser’s 'Tools' menu. 2. Select the 'Privacy' tab. 3. Click the 'Settings' button in the 'Pop-up Blocker' area. 4. Copy and paste this URL into the 'Address of Web site to allow' http://cdecurate.nci.nih.gov 5. Click the 'Add' button on the 'Pop-up Blocker Settings' window. 6. Click the 'Close' button on the 'Pop-up Blocker Settings' window. 7. Click the 'OK' button on the 'Internet Options' window. +------------------------------------+ | CRT | +------------------------------------+ In the 'Match' and 'Search results' windows, Data Elements with multiple 'Long Name Document Text' entries appear multiple times. The Data Element appears once for each instance of 'Long Name Document Text.' The 'Long Name Document Text' field that is originally displayed may not be the same one that is shown once the entry is selected. -- In cases where a Data Element has multiple Long Name Document Texts the user should note that the Long Name Document Text ultimately displayed on the spreadsheet display of the CRF may not be the same as the one displayed to the user. The Data Element and all the 'Long Name Document Text' entries are not affected. +------------------------------------+ | caDSR Sentinel Tool | +------------------------------------+ A negative integer may be entered into the Specific Version field on the Monitor tab of Edit Alert. There is no adverse effect except other tools do not allow version numbers to be negative integers. -- No workaround. Avoid entering negative integers into the Specific Version field. Both icons at the top of the window open to Cancer.gov site. This is inconsistent with the Curation Tool, which has independent working icons for the NCI & caDSR. -- No workaround. Change Note/ Comment Text are displayed in the Alert report as a string of random characters. -- Use the Public ID and version provided in the Report to examine the Data Element in the CDE Browser. ================================================================ 4.0 CSM ================================================================ ---------------------------------------------------------------- 4.1 Release History ---------------------------------------------------------------- CSM 3.0 -- 31 March 2005 ---------------------------------------------------------------- 4.2 Features ---------------------------------------------------------------- CSM provides a flexible, comprehensive solution to common security objectives. Development teams can use CSM services rather than creating their own independent security methodology. +------------------------------------+ | CSM APIs | +------------------------------------+ Features -------- This CSM release provides the following services: -- Authentication - validating and verifying a user’s credentials to allow access to an application. CSM currently supports two credential providers: - Lightweight Directory Access Protocol (LDAP) - Relational Database Management Systems (RDBMS) The Authentication Service provides the following features: - It allows the application developers to configure single or multiple credential providers for various applications. - It authenticates user credentials against the configured providers. -- Authorization - granting access to data, methods, and objects. CSM incorporates an Authorization schema which holds the authorization data for a particular application. At run-time, CSM uses this data to make a security decision. The Authorization Service provides the following features: - Object level security check. - Attribute level security check. - Creation of Protection Elements at run-time. - Association of Protection Elements to Protection Groups at run-time. - Obtaining references to entities such as Protection Elements, Protection Groups, Users, etc. - Obtaining the collection of Privileges for a user for a Protection Element. - Obtaining principals for a user. +------------------------------------+ | User Provisioning Tool (UPT) | +------------------------------------+ Features -------- -- CSM provides a web-based UPT that can easily be integrated with a single or multiple applications and authorization databases. The UPT provides functionality to create authorization data elements like Roles, Privileges, Protection Elements, Users, etc., and also provides functionality to associate them with each other. The runtime API can then use this authorization data to authorize user actions. The User Provisioning Tool provides the following features: - Register an application and assign application administrators (Super Admin mode). - Create, Read, Update, and Delete authorization data elements. - Search using relevant criteria. - Group elements together. Assign users to groups, privileges to roles, and protection elements to protection groups. - Form associations between elements. For example, Assign a Protection Group and Roles to a User. ---------------------------------------------------------------- 4.3 Bugs Fixed Since Last Release ---------------------------------------------------------------- Initial release ---------------------------------------------------------------- 4.4 Known Issues ---------------------------------------------------------------- +------------------------------------+ | CSM APIs | +------------------------------------+ -- The getSubject method of Authentication Manager has not been implemented. -- Certain thrown exceptions may display hibernate-specific error messages. -- The connection pool provided by hibernate (c3po connection pool) shows inconsistent behavior in different environments. +------------------------------------+ | UPT Tool | +------------------------------------+ -- In the Protection Element and User section, when adding object details, if you press enter you'll be taken back to the object's home page. -- After logging in, the main menu is displayed in two rows instead of one. -- In the super admin mode, the admin mode home page displays if you click on the logo in the header or enter the home page url after logging in. ================================================================ 5.0 EVS ================================================================ ---------------------------------------------------------------- 5.1 Release History ---------------------------------------------------------------- NCI Thesaurus V 05.01d (monthly, concurrent with caCORE 3.0) -- 31 March 2005 NCI Metathesaurus V P050224 (monthly, concurrent with caCORE 3.0) -- 31 March 2005 NCI Thesaurus V 04.03n (monthly, concurrent with caCORE 2.1) -- 28 May 2004 NCI Metathesaurus V P040517 (monthly, concurrent with caCORE 2.1) -- 28 May 2004 NCI Thesaurus V 2.0 (released in caCORE 2.0) -- 31 October 2003 NCI Thesaurus V 1.1 (released in caCORE 1.1) -- 7 February 2003 NCI Thesaurus V 1.0 (released in caCORE 1.0) -- 29 August 2002 CTRM V 6.5 (released in caCORE 1.0) -- 29 August 2002 ---------------------------------------------------------------- 5.2 New Features and Updates ---------------------------------------------------------------- New vocabularies ---------------- -- MGED Ontology V 1.1.9 -- MedDRA V 6.0 the details on the Ontylog representation of these terminologies is available in the addendum to the Technical Guide documentation being made available in the caCORE 3 release. In addition, the HL7 V3 vocabulary is being made available to users of the NCICB's HL7 SDK; documentation for this vocabulary will be provided on request. DTSRPC V 2.0 ------------ The DTS (Apelon) terminology server used internally by the EVS has been upgraded to version 3.1. The DTSRPC 2 (which supports the caCORE EVS API), has been upgraded to serve vocabulary with the new Apelon API. Among the new Apelon features surfaced in the DTSRPC are: -- Associations (non-inheritable binary relations between concepts) -- Role hierarchies -- Property and Association qualifiers -- Role groups -- Concept hierarchy (tree) retrieval and caching In addition, the DTSRPC includes -- support for Clinical applications search requirements (paged resultset retrieval, retrieval by kind, allows filtering by term type) -- Boolean queries -- Graph as well as tree retrieval and caching. Small trees can be retrieved with virtually no performance penalty at runtime. However, with large trees or to further increase retrieval performance, we request users to advise us of their needs in this regard as we will be able to pre-cache their trees at initialization. Because of memory concerns, we currently allow only one Graph to be pre-cached; again, we request advise on whether to pre-cache a graph during initialization. NCI Terminology Browser ----------------------- The web browser used to visualize the terminologies served by the EVS has undergone two major changes: it is now compliant with NCICB User Interface (UI) standards (this will be the major change observed by users), and it does not call the Apelon API, instead, it queries vocabularies entirely through the DTSRPC layer. The latter is one of the small steps we are currently taking in order to be able to release in the future a vocabulary browser independent of commercial APIs. ---------------------------------------------------------------- 5.3 Bugs Fixed Since Last Release ---------------------------------------------------------------- No bugs fixed since last release ---------------------------------------------------------------- 5.4 Known Issues ---------------------------------------------------------------- We are aware of some non-critical issues that affect the performance of the DTSRPC. It is possible under some circumstances for a DTSRPC client to receive the resultset from another client that issued a request but was terminated before it received its resultset (an "interference" effect). Another issue is related to Firefox rendering the NCI Terminology Browser pages. Under some circumstances Firefox will render a web page entirely with the NCI banner image normally seen only at the top of the page. This is related to session cookies; currently the only workaround is to exit Firefox and start a new session. ================================================================ 6.0 Bug Reports and Support ================================================================ Send email to ncicb@pop.nci.nih.gov to request support or report a bug. In addition, mailing lists are used by the caCORE developer and user community to exchange ideas and make announcements. You can subscribe at these addresses: caBIO users -- http://list.nih.gov/archives/cabio_users.html caBIO developers -- http://list.nih.gov/archives/cabio_devel.html caDSR users -- http://list.nih.gov/archives/sbr_users.html EVS users -- http://list.nih.gov/archives/ncievs-l.html ================================================================ 7.0 Documentation ================================================================ The caCORE 3.0 Technical Supplement can be downloaded via FTP: -- ftp://ftp1.nci.nih.gov/pub/cacore/ caCORE3.0_Tech_Supp.pdf ================================================================ 8.0 NCICB Web Pages ================================================================ The NCI Center for Bioinformatics -- http://ncicb.nci.nih.gov/ NCICB Application Support -- http://ncicbsupport.nci.nih.gov/sw/ NCICB Download Center -- http://ncicb.nci.nih.gov/download/ caCORE -- http://ncicb.nci.nih.gov/core caBIO -- http://ncicb.nci.nih.gov/core/caBIO caDSR -- http://ncicb.nci.nih.gov/core/caDSR -- http://ncicb.nci.nih.gov/xml CSM -- http://ncicb-dev.nci.nih.gov/core/CSM EVS -- http://ncicb.nci.nih.gov/core/EVS //end