caDSR Update

Curation Tool, CDE Browser, and 2012

Denise Warzel

Semantic Infrastructure Operations, Data Standards Services

July 11, 20111

Metadata Software Engineering – caDSR OverviewDescription: 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 11179 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 base3,328 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”• 114 NICHD• 129 EDRN• 288 CIP• 310 NINDS• 628 SPORES• 1113 PS&CC• 1373 DCP• 2007 NHLBI• 2272 CCR• 2333 NIDCR• 3491 C3D• 10462 CTEP

• 26939 caBIG

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 form• 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 11372 Allow the ability to download search results from Curation Tool searches including the ability to download DECs and VDs using the Customizable Download

• GF 30798  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)

Current Release Plan Status

• Curation Tool 4.1 Cont.• GF 30445  Move On-line Help to Wiki• GF 29361  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 30799  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 30706  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 30796  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 30758  Cannot delete concepts from VM.

Current Release Plan Status

• CDE Browser 4.1 – September• GF  7743 DE Derivations: Improve ability to search/query for CDEs that are

derived• In Advanced Search, added a "Search only Derived DEs" button next to "Exact Phrase",

"All..." and "At Least.." options.

• GF 29360 Clean up Alternate Name/Definition Display for Data Element and Permissible Value (STILL WORKING ON THIS ONE)

• GF  1333 Make Customizable Download available for use with CDE Cart (both from Cart and search results)

• GF  7896  Add ability to select which items in the Cart to Download• GF 30784 Add Alternate Definitions for VM to standard XML and Excel download.• GF 30901 Allow search by public id or name without having to select a dropdown• GF 30903 Rearrange/rename links so that tool links are on the main line,

information links are up above• GF 31066 Move Online Help to Wiki• GF 30732 Align Permissible Values vertically so the permissible values are under

the CDE - shift as they go down the page • GF 30611 Change "What's New" to link to Release notes

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 21090 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 21090 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 referenced8d  make CSI IDs visible in edit Alt name/def classifications view8e Allow selective copy of names/def and classifications when creating new for existing8f 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 descriptions8h 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 searching9c allow customization of h ow the annotations are added to spreadsheets (nanoTab)

10 Bulk Loader: allow large number of CDEs to be matched and uploaded10b Allow batch register list of EVS Concepts in caDSR10c 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:10.1136/amiajnl-2010-000061, May 2011

11 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?