munging metadata

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

Despite just being released in Q2 of 2014, a number of freely available tools are already available to work with Dataset-XML files. The recently-introduced CDISC Dataset-XML standard enables the interchange of tabular datasets, like SDTM or ADaM, using ODM-based XML, and provides a convenient alternative to SAS V5 XPORT files. Tools supporting Dataset-XML are listed on the publicly accessible CDISC Dataset-XML Resources page on the CDISC Wiki. Early versions of many of these tools were available before Dataset-XML was released as a final standard. The speedy availability of these tools highlights the CDISC community’s culture of innovation as inspired by the availability of machine-readable standards. The availability of software tools with the release of Dataset-XML enabled the FDA to begin planning the "Transport Format for the Submission of Regulatory Study Data” pilot prior to the standard’s final release. In order to test Dataset-XML’s suitability as a replacement for SA

CDISC SHARE is a metadata repository (MDR) that supports the development, governance, publishing, and consumption of the CDISC standards in human and machine-readable formats. For more information about SHARE see the   CDISC Website . eSHARE and iSHARE are parts of the overall SHARE system. They represent two separate ways to access SHARE content, as shown in the diagram below. Interactive SHARE, or iSHARE , is the tool used by the CDISC standards development community for developing, governing, and publishing the standards. iSHARE is a cloud-based MDR configured for the CDISC standards that includes a number of standards management and development tools. Prior to accessing the tool, CDISC standards team members receive both on-line and interactive iSHARE training. Each standards development project works with the SHARE Metadata Curators to create and publish new CDISC standards. As new standards, and new versions of existing standards, are created iSHARE provid

During May and June the SHARE team has been busy on a number of fronts. In June we plan to begin beta testing the eSHARE site for machine-readable downloads of the CDISC standards.  The eSHARE site will be part of the new CDISC web site that will be launched in June. The SHARE team has also been actively designing new forms of standards content for SHARE, including Research Concepts and explicit Value Level Metadata representations. A white paper describing our initial solution for Research Concepts will be distributed for review in June. Also during June we plan to complete an initial proof-of-concept project towards a long-term Research Concept solution. Value Level Metadata (VLM) blog postings started in May and will continue through June. We plan to publish a white paper describing how VLM content will be represented in SHARE, and exported in Define-XML format, later in the summer. The SHARE Metadata Curators continue their work with the foundational standards teams to load a

As part of the work to implement Value Level Metadata in SHARE, as well as to author a Define-XML Implementation Guide article, this will be the first of a series of posts on the topic of Value Level Metadata. These posts target a more technical audience, however the Define-XML IG article will include less technical jargon. Future posts will cover additional Value Level Metadata topics and examples. Value Level Metadata (VLM) is metadata that constrains a variable definition based on the value of another variable(s). VLM was originally specified in Define-XML v1.0 as a mechanism for providing the additional metadata needed for software to more accurately interpret these constrained variables.  For example, VSORRES is a variable with structural metadata of  DataType=”Text” and Length=”200”. However, when VSTESTCD=”DIABP” that definition is constrained by VLM to use DataType=”integer” and Length="3". In this case, the value of DIABP in VSTESTCD has triggered the application o

Since the R1 library was moved into production at the end of January, the SHARE team has been hard at work on the R2 deliverables. Broadly speaking, R2 is focused around three main themes: (1) loading the remaining foundational standards, (2) publishing machine-readable standards to eSHARE, and (3) designing a solution for research concepts. On the first theme the SHARE curators are working with the SDS team to load SDTMIG 3.1.3, in addition to working on the import of SDTM IG 3.2. The curators are also working on the first controlled terminology update with the March release. On the second theme the team has implemented features to provide machine-readable standards exports, and has been testing these. The new CDISC web site will host this content for subscribers, and will be available for use this summer. Finally, on the third theme the team has been working on the requirements and a solution alternative for research concepts. A prototype of this solution will be implemente

SHARE is no longer merely a vision, idea, or plan. After nearly 6 months of implementation work SHARE R1, our first production library, has been completed. Woot woot! This is a major milestone. We've taken the first step on a long journey towards realizing the vision of transforming the CDISC standards into an end-to-end, interoperable set of metadata all available in a machine-readable format. Both SDTM 1.2 (IG 3.1.2) and CDASH 1.1 have both been loaded into the production SHARE Library. Using SHARE R1 we will load SDTM 1.3 (IG 3.1.3) and SDTM 1.4 (IG 3.2) in the coming weeks. Although the CDISC Controlled Terminology development and governance processes will remain unchanged, we will continue to load each newly released terminology package into SHARE. BRIDG 3.2 and the ISO 20190 data types have also been loaded into the R1 library. The theme for R1 was Machine-Readable Standards. The SHARE Team plans to publish metadata from SHARE for subscribers to download by the end o