munging metadata

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. ...

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 fu...

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...