On its 4th birthday, we are excited to announce Release 2.0 of the CEDAR Workbench. This release has many new features, as well as production releases of existing capabilities, so we'll be telling you about many of them in more detail in coming weeks.
Look and Feel
One of the first things you may notice is that CEDAR looks a bit different. We continually try to improve the bits of the CEDAR User Interface that don't work quite as well as we'd like. A few simple examples you might have noticed: The list layout is a lot tighter, with the tool icon (the vertical ellipsis) on each item, refined icons, and column headers that sort the columns when clicked. When you are editing a template, there is more information available about imported fields and their descriptions. Oh! And the big red + button (in the lower right) to create new things is now a dark green 'New +' button (in the upper left). We hope these changes will be more intuitive to our users. Let us know if there's something you don't like (or really like!).
Versioning and Publication
This really refers to two features, and many of the versioning capabilities were added in our (silent) 1.9 release. First, your templates, template elements, and (new in 2.0!) template fields can be assigned versions. They start out as version 0.0.1, and then can be updated by publishing them. Any artifact that is published will have a little world icon after its modification date. There is a lot to learn about these features, and we will be producing a video about them soon in our YouTube channel. (At which point we will update the previous sentence.)
Fields and Their Improvements
You've always been able to put a field into a template, or in a template element. But it could never stand by itself. Now we've fixed that, with CEDAR's support for fields as first-class artifacts.
And you have a few more options for a field. We enhanced CEDAR text fields to allow the specification of minimum and maximum string length. The numeric field was also enhanced and now supports decimal place specification, minimum and maximum values, unit specification, and additional numeric datatypes.
CDE Support: Using Common Data Elements in CEDAR
CEDAR now supports Common Data Element-based fields exported from the National Cancer Institute caDSR system. These fields are based on the ISO/IEC 11179 metadata representation standard. This support allows users to incorporate caDSR CDEs as fields in a CEDAR template. Soon we hope to import much of the caDSR content into CEDAR, so that CDEs can be used by anyone to build or refine a template.
Our support for CDEs means that we have had to add a lot of other features to CEDAR, such as versions, stand-alone fields, string-length options, and a lot of enhancements for numeric fields. Users of the CEDAR workbench cannot create new CDEs at this point. Stay tuned for more CDE-related features in coming months.
Publishing AIRR data to NCBI
We've been talking about the ability to upload AIRR metadata to the NCBI repositories (SRA, BioSample, and BioProject) for a while, and even released some functional software. But now we really think everyone who can in the AIRR Community should start using it! For starters, the Submissions Release Date at the top of the form controls the release of all three submissions in the form. We have had a few early adopters submit their AIRR metadata and data to NCBI, and with one or two final adjustments, the metadata (and all 54 files of data in one case, and 30GB of data in another) made it into NCBI. While NCBI submissions can be complicated, we think we are taking care of many of the most common challenges, and we know we are making submissions a lot easier for the AIRR community!
If you want to submit your AIRR data through CEDAR, visit the CAIRR documentation page to start filling out your metadata.
List of Instances for Metadata Templates
This is really a part of the Info Panel description below, but it's soooo useful: If you look in the Info Panel for any metadata template, you can see how many instances have been created from the template, as well as a (clickable!) list of the instances you have access to! Great for curators and troubleshooters of metadata issues.
Under the Hood
OK, we'll just list a few of the more important behind-the-scenes changes to wrap up this big release:
- The underlying metadata model and validation is more robust, supporting attribute-value pairs and a number of more subtle improvements and fixes.
- The metadata information panel (opened and closed with the 'i' symbol at top right of the desktop) has been expanded to give detailed information about all CEDAR resources in the Workspace. Many resources listed in the Info panel are now clickable, allowing users to navigate between related resources.
- More metadata are being collected about the relationship of a template, element, or field to its predecessor. Is it a newer release, or just a copy? Now you can tell where it came from.
- And as always, bugs-be-gone as often as we can.
All tasks completed for the 2.0 release can be found at our GitHub issues list.
You can also review the GitHub release history for 2.0 page.