munging metadata

Last weekend was the 2nd HL7 FHIR Connectathon (Jan. 14 & 15) that included a Clinical Research Track and the 14th overall FHIR Connectathon. This event was hosted on the Riverwalk in San Antonio and featured over 200 attendees for a weekends worth of hacking. The primary purpose of the Connectathon events is to provide a forum for participants to develop and test software in an informal way. During the previous, inaugural Clinical Research Track < http://wiki.hl7.org/index.php?title=FHIR_Connectathon_13> only two of us participated.  By the end of the weekend we were able to use FHIR resources to demonstrate the pre-populate Medidata Rave-based demographics and concomitant medications CRFs. The Clinical Research Track at the 14th Connectathon generated quite a bit more participation interest with 8 attendees. Representatives from vendors, sponsors, and standards organizations participated. Beyond the pre-population of CRFs using EHR data retrieved using FHIR, sever...

As the CDISC XML Technologies team finalizes Define-XML v2.1 for internal review an old debate has re-surfaced: how much should the Define-XML specification focus on the regulatory submissions use case versus providing a more general specification that works for a broader set of use cases. As a standard that provides metadata to describe tabular datasets, Define-XML can be used to describe legacy datasets as well as datasets included for submissions. Define-XML has also been used as a specification for datasets. However, Define-XML became the most widely implemented ODM-XML based standard due its role as a required element of regulatory submissions. The importance of ensuring that Define-XML files included in a submission are complete and accurate makes a compelling case for adding rules that specifically target this use case at the risk of reducing its usefulness in other contexts. Having recently participated in the September HL7 FHIR connectathon in Baltimore, MD it strikes me ...

The SHARE API Pilot continues to make progress. A draft specification is being reviewed and a test server is running the API as currently specified. The pilot team will finalize the draft specification and spend the rest of the year testing and developing interfaces to the API. The SHARE team will also make use of the API to enhance tools in the SHARE ecosystem by making it easier for them to consume SHARE metadata. The SHARE API will be moved into production during Q2 of 2016. A few last development details are being cleaned up for the SHARE RDF export, and then we'll work to generate a test export for the community to review. The initial exports will include SDTM, CDASH, and Controlled Terminology. The RDF content will be posted to eSHARE, and will also be available for consumption via the API once it has been moved into production. The Biomedical Concept (BC) development tools have seen a number of upgrades this year. These tools are currently being used by the Collabor...

Lots of new initiatives showed promise at the CDISC 2015 Interchange conference in Chicago on November 9-13.  The EHR2CDASH (E2C) project demonstrated the potential of healthcare link technologies used with the CDISC standards. The E2C XPath statements used to grab HL7 C-CDA/CCD document content will be stored in SHARE to support the implementation of CDASH forms that can be pre-populated with EHR content. A group of CFAST TA standards development stakeholders reviewed the new processes and tools that will be used for developing the Prostate Cancer standard. BiomedicalConcepts continue to garner attention as a key element of the semantic layer in the CDISC standards model. The growing CDISC standards model so important to the SHARE work was on display during the poster session. Use of the ODM standard was highlighted, including an extension to support its use in modern hand-held devices. There was quite a bit of enthusiasm and interest in SHARE activities, as evidenced by the cr...

The theme of sharing clinical research data permeated a number of presentations at the CDISC International Interchange Conference this year. In fact, the opening plenary keynote presentation by General Peter Chiarelli, CEO of One Mind, highlighted the dire need for data sharing in clinical research and espoused a number of open science principles. One Mind defines open science as a “global movement to make scientific research, results and data available, and accessible to everyone.” The key goal behind this push for open science is to accelerate the research community’s ability to transform basic research into better clinical treatments for patients. You can find One Mind’s open science principles here http://onemind.org/Our-Solutions/Open-Science . One of One Mind’s open science principles involves adhering to widely accepted data standards. This makes sense because the standards help make the data useful. Sharing the data is not the end game. Using the data to accelerate the dev...

When people point to flaws in SDTM, they typically appear to me as gaps in the existing standard. In general, CDISC started defining standards by focusing on the basic structural metadata (e.g. domains, variables, code lists). This makes sense because this structural metadata is fundamentally useful, and relatively easy to understand and create. As the industry’s use of the standards has increased, so has the demand for standards that can be implemented more consistently and easily, as well as standards that are more computable. The limitations in the current standards are gaps, and addressing these gaps represents a natural evolution for the CDISC standards. As noted in my previous post “What’s in a SHARE Value Level Metadata Library?” CDISC does not currently contain Value Level Metadata (VLM) content, and this content represents a lot of new metadata. VLM is a gap in the existing standards. How do we know what variables are impacted by a specific –TESTCD? Much of that informati...

What’s in a Value Level Metadata (VLM) Library? SHARE has the capability to store and publish Value Level Metadata (VLM) content. Currently, the only CDISC standard describing VLM is Define-XML. Define-XML provides the structure for VLM along with some guidelines on when it’s useful, but it does not provide standard VLM content. The Define-XML v2.0 specification states that VLM should be applied when it provides information useful for interpreting study data, and that it need not be applied in all cases. Precisely what and where VLM should be used is determined by study implementers. Since there are no hard and fast rules describing when to use VLM, what should be included in a SHARE library of VLM content? It might be useful to ask, “where is VLM being used today?” Based on input so far, most implementers add VLM where they think the regulatory reviewers might want to see it. Since many organizations are not yet using Define-XML as a machine-readable specification, but are inst...