Posts

Loading Terminology in SHARE: What's the DIFFerence?

We load the CDISC Controlled Terminology (CT) published by the NCI Enterprise Vocabulary Services (EVS) into the SHARE metadata repository (MDR). When we're through catching up with our backlog we'll have more CT in SHARE than any other type of metadata, and we'll publish the quarterly CT content to the SHARE Exports page on the CDISC web site. One of the main differences in how we load the CT is that we load only the incremental changes. That is, we load the differences by generating diff files that contain only the changes between the packages published in the current quarter and those published in the previous quarter. The diff files are available for download, or they can be generated using the NCI's Diff program. This program is a Java application, and it is simple to set up on most machines.

The Diff application is easy to use and can generate diff files for any two versions of a delimited text CT package. The two packages used to generate the diff file do not ne…

Define-XML v2.1 – What do you think?

If you're wondering where the XML standards like Define-XML went on the CDISC website, they've moved. They're now located under Standards/Transport. If you go to the transport page you can select from a fairly extensive menu of transport standards. There are a few transport options located elsewhere, such as Lab and the Analysis Results Metadata Define-XML extension.

Our broad list of XML standards is in the process of welcoming a new version of Define-XML to the family. This new version of Define-XML, v2.1, will almost certainly be listed in the standards catalogs of regulatory authorities at some point, so all of you working on regulatory submissions should find this update interesting. There are a couple weeks left in the Public Review period (it ends on May 5th) so there's still time to add your comments. You can find the Define-XML v2.1 Public Review package along with instruction for adding JIRA comments on the CDISC wiki.

While Define-XML v2.1 is a minor point r…

Using the SHARE API to Grab the Latest CDISC Terminology Packages

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Keeping your repository up to date with the latest CDISC Controlled Terminology (CT) packages represents a challenge to many organizations. The SHARE API make it easier to retrieve the CT packages and initiate the process of updating your repository. In this post I'll walk through the process of finding and retrieving the CT from SHARE using the API. We'll use the default media type of XML. When requesting a full CT package the XML media-type uses the NCI EVS extended versionof ODM that includes the additional metadata needed to represent the CT content.
The following figure provides an overview of the steps taken to retrieve the latest CT packages using the SHARE API. The first step is to determine what CT Packages are available for loading. This can be done by using the Get Standard Terminology List API. The SHARE API is RESTful so this entails requesting the /terminology-packages resource. The default Lifecycle-Status parameter retrieves Approved Final content. Since the N…

Wanted: SHARE API Early Adopters

Having completed the SHARE API v1.0 pilot in 2016, CDISC recently announced the SHARE API Early Adopter Program for those interested in beginning to use the API right away. SHARE API access provides a RESTful web services interface to SHARE for retrieving new CDISC standards and terminology.

Having worked on the API pilot, I'm happy to see it released for general use. It's a significant step forward and marks CDISC's movement towards new ways of publishing machine-readable standards content.  As part of the Early Adopters Program new users will be asked to provide regular feedback and input into new features. The SHARE API is currently a v1.0 release meaning the essentials are there in terms of accessing metadata content, but we also have a lot more we'd like to do with it. The API Pilot team developed a list of user stories at the beginning of the project, and while most were implemented during the pilot, many were deferred and will become part of the roadmap for futu…

Clinical Research Track at the 14th FHIR Connectathon

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, several additi…

A Profile for Define-XML

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 tha…

SHARE 2015 Q4 Technical Update

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 Collaborative C…