caDSR Update Curation Tool, CDE Browser, and 2012 Denise Warzel Semantic Infrastructure Operations, Data Standards Services July 11,

Metadata Software Engineering – caDSR Overview Description: Tools, utilities and APIs A Repository for storage and management of sharable human and computer readable descriptions of data from which Forms and Services needed to conduct a study can be produced automatically A Registry to facilitate registration and standardization of the information the Repository contains Preserves the meaning of and thus extends the value of data Deliverables: (10-11) CDE Browser; Form Builder; Curation Tool; cgMDR Excel Addin, Template and Bulk Loader; UML Model Browser; Sentinel Tool; caDSR Database Server; Domain Model, Object Cart and Freestyle APIs; Semantic Integration Workbench (SIW); UML Loader Background : 2001 Oracle DER (Data Element Registry): Admin Tool and Database 2003 extended Ed2 to a concept based system (11179 Ed 3-like) 2005 extended to support Forms Last 3-4 years O&M: Refactoring Code Base (Split Form Builder and CDE Browser), Tech Stack upgrades EVS API (4.0, then LexEVS 5.1), AntHill Build and Deployment Automation, AppScan Compliance, Firefox Compatibility, Bug Fixes Community Supported Community Involvement 5 NCI divisions, 8 NCI and caBIG program areas, 5 NIH Institutes, 19 External “programs” 47 Cancer Centers with over 33k “Released” CDEs/and a total of >47K 3.2k CRFs, 2.9k in “Released” 60 active curators in July 2011, 45 since Jan 2011

Distribution of content across user base 3,328 Forms created by the Community 2,923 CRFs in CTEP used in 611 trials 152 in CCR used in 322 Active Trials 102 in NHLBI 99 in caBIG® 92 in NIDCR 40 in DCP 29 in SPOREs 1M+ CRFs created in C3D from caDSR CDEs 1 in NICHD 1 in NINDS 1 in REDCap (Demography) 24,749 CDEs with Workflow Status of "Released” 114NICHD 129EDRN 288CIP 310NINDS 628SPORES 1113PS&CC 1373DCP 2007NHLBI 2272CCR 2333NIDCR 3491C3D 10462CTEP 26939caBIG

Current Release Plan Status Curation Tool 4.1 – August GF 7680 Allow edits to an element that is used on a CRF without having to first remove the element from every instance of use on the formGF 7680 GF 1333 Customizable Download adds ability to customize the download search results in Excel format by selecting which fields to download. For the Excel download also allow the user to rearranging the order of the columns.GF 1333 GF Allow the ability to download search results from Curation Tool searches including the ability to download DECs and VDs using the Customizable DownloadGF GF Add an alternate definition to the DEC and VD from the specific concept definitions selected in EVS search since these are not used in the component's preferred definition. (See Bug: GF30796)GF 30798

Current Release Plan Status Curation Tool 4.1 Cont. GF Move On-line Help to WikiGF GF The pop up Edit Menu should display in the primary portion of the UI, you should not have to scroll down to select an option.GF GF Change the label in the component/EVS search UI from “Use Selection” to “Link Concept” so its clearer that the selection is for the purpose of linking the caDSR item, not on selecting the specific definitions.GF GF Cannot remove a representation term qualifier from a Value Domain. All VDs must have a representation term, but you should be able to remove a rep term Qualifier and save the VD successfully.GF GF Displayed system generated definition changes between Curation UI, Validation UI and final CDE/DEC/VD. * Add a warning message on the validation page when this happens so curators know that the concept definitions they chose are not used.GF GF Cannot delete concepts from VM.GF 30758

Current Release Plan Status CDE Browser 4.1 – September GF 7743 DE Derivations: Improve ability to search/query for CDEs that are derivedGF 7743 In Advanced Search, added a "Search only Derived DEs" button next to "Exact Phrase", "All..." and "At Least.." options. GF Clean up Alternate Name/Definition Display for Data Element and Permissible Value (STILL WORKING ON THIS ONE)GF GF 1333 Make Customizable Download available for use with CDE Cart (both from Cart and search results)GF 1333 GF 7896 Add ability to select which items in the Cart to DownloadGF 7896 GF Add Alternate Definitions for VM to standard XML and Excel download.GF GF Allow search by public id or name without having to select a dropdownGF GF Rearrange/rename links so that tool links are on the main line, information links are up aboveGF GF Move Online Help to WikiGF GF Align Permissible Values vertically so the permissible values are under the CDE - shift as they go down the pageGF GF Change "What's New" to link to Release notesGF 30611

Questions on 4.1 Releases?

Metadata Software Engineering – caDSR Overview Community Feedback "The building block of semantic interoperability is the common data element.” – AHA/ACCF "For the metadata tags and identifiers, we recommend the use of the construct of the National Institutes of Health/National Cancer Institute Data Standards Registry and Repository” – AHA/ACCF Portal: “Need one place to find everything, not GME, CDE Browser, UML Model Browser” – ICR “Identify semantically similar CDEs” - Duke Simplify finding good reusable content – numerous “Allow model owners to share their models” – ICR “Allow discovery of touchpoints to other models” Simplification: “Simplified process for annotation and registration” - ICR “Modeling Tools (e.g. EA) tied to caDSR and EVS” - ICR “Allow models to be easily submitted for review without leaving the system” – ICR Fix productivity issues in Curation Tool – Curators Developing CDEs from Models takes too long - Duke “caIntegrator…represent the columns of … new datasets as CDEs in the caDSR so that the dataset can easily be interpreted and reused.” - ICR Strategic: Support harmonization with BRIDG and DAMs– CTMS Support use of Datatypes – CTMS “Authoring tools to help generate shim services” - ICR “allow application developers to validate their model against an existing standard supported by caBIG“ - SAIC “need an enterprise caliber local repository solution that can interoperate with caDSR and others” – MDACC Support *NEW* projects that need MDR capabilities CTSA – REDCap, CDISC, CDC/PHIN, PROMIS, AHA/ACCF, Radiation Oncology, Taiwan Cancer Registry (loaded model), State/Local Cancer Registries Provide SIv2 ready content for migration to new platform

caDSR 2012 proposed enhancements and modernization 1 Support Federated MDRs 2 Support manual/bulk loading aligned w/BRIDG and other targeted Models such as LS- DAM 3 Support NCI Datatypes so curators can populate constant values 4 Make use of CTS2 features around value sets (Curation, Form Builder, CDE Browser) 5 Form Builder: 5a support use of derivations and model fragments 5b Support "one-click" updates to questions on forms 5c Provide a way to view forms without logging in 5d Export Forms in add’l formats: XML, CDA format, REDCap 5e ability to copy questions 5f ability to add and view Contact Person and Organization 5g including support for module reuse 5h add layered semantics so that reusable generic CDEs and model fragments gain form semantic context 6 Data Standards Portal - simplify finding, reusing, comparing models and CDE standards such as content required by HIPPA, 21090, BRIDG etc

caDSR 2012 proposed enhancements and modernization 7 Support for Writeable APIs with less restrictive (partially complete) content to be added for use by DynamicExtensions and other similar use cases from AIM/NBIA, MediData - includes data elements and Forms; 8 Curation Tool: 8a Fix Bugs/design issues in Block Edit; 8b Fix Customizable download so that the XML Download works; 8c ability to edit Reference Documents name or definition and have it apply to all places where Ref Doc is referenced 8d make CSI IDs visible in edit Alt name/def classifications view 8e Allow selective copy of names/def and classifications when creating new for existing 8f Ability to set Preferred Name and Definition from previously curated items without having to cut and paste into long name and definition. 8g Add ability to store and share frequently used Customized Downloads descriptions 8h Enhance concept annotations so its easier to move mapped concepts around for OC and Prop

caDSR 2012 proposed enhancements and modernization 9 Excel Addin: add vocabs 9b improved searching 9c allow customization of h ow the annotations are added to spreadsheets (nanoTab) 10 Bulk Loader: allow large number of CDEs to be matched and uploaded 10b Allow batch register list of EVS Concepts in caDSR 10c Allow batch load of alternate names and definitions *Pathak J, Wang J, Kashyap S, Basford M, Li R, Masys DR, Chute CG "Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience", JAMIA doi: /amiajnl , May Support bulk/uml loading CDEs that use other terminologies/model alignment than NCIt concepts 12 Support loading models that are not Domain Models (classes with CDEs with different OC) 13 Value Domain and CDE Duplication: Enhance Curation Tool, Bulk Loaders to allow Value Domain updates and eliminate creation of Duplicate VDs and CDEs 14 Enhance search for value domains to look for a list of matching values

caDSR 2012 proposed enhancements and modernization 15 Enhance Browser and Curation search/query interfaces to make it easier to find reusable content 16 UML Model Browser: Allow end users to compare models side by side (list of classes and attributes) and download, similar to CDE Compare Matrix

caDSR Bug Fix, Steady State Support 1 Tier 2 and 3 support, problem determination and bug fixes 2 Technology Stack Upgrades including upgrade to LexEVS 6.1 in Browser, Admin, Curation, Bulk Loader, Excel Addin, possibly SIW to add add'l vocabs if still being used 3 "508" and AppScan remediation for frequently used production tools (Browser, Curation, Sentinel, Form Builder, Bulk Loader) 4 provide limited support for Open Source customers 5 work with content team to clean up/merge duplicate content based on duplicate Concept, OC, Prop and DECs 6 Support Federation: populate caDSR IRID in each item 7 Add regular/scheduled export of all caDSR Content (can't download all content via Browser due to Excel Limitations)

caDSR Bug Fix, Steady State Support 9 Update CDE Browser download to data element derivations 10 SIW: IF still being used: 10a Fix bug in SIW Flickers when CDE mapped to existing VD 10b allow "Integer::XX" concept mappings 11 patches as needed

Questions?