What’s going on related to CEDAR?

CEDAR Release 2.4

We released version 2.4 of the CEDAR Workbench on September 6, providing more user features and enhancements.

OpenView offers public option for CEDAR artifacts

OpenView of metadata instanceDid you ever want to show your template or metadata values to a colleague, without logging in? Do you want to view all your metadata on the web? Or maybe you’d like an IRI that anyone can use to see your work?

Now you can make your CEDAR artifact—metadata instance, template, element, or field—visible on the web. CEDAR’s OpenView service presents the CEDAR artifact as a publicly visible web page, with pop-up metadata descriptions and access to JSON and RDF views of the content. To make public your template, element, or field, simply enable OpenView from the workspace menu for the artifact. For now, if you want to make your metadata public, the template it’s based on must also be public—we can help you with this.

Instructions for CEDAR’s OpenView feature may be found at its CEDAR manual page.

Find field names in templates, elements, and fields

Adding to CEDAR’s ability to search for field names in CEDAR instances, you can now search for field names in CEDAR templates, elements, and fields.

Just like searching for field names in metadata instances, a colon after the string indicates a search within field names. The syntax ‘namestring:’ in CEDAR’s search bar will find the templates containing ‘namestring’ in the title. In the CEDAR search syntax, an asterisk matches any string and a question mark matches any character:

  • title:*, or simply title: Search for fields containing "Entity Identifier"
  • Publish*:
  • "Contact Email":
  • to?ic:

This functionality is documented in more detail here.

AIRR Community NCBI Pipeline

We improved the CAIRR pipeline for submitting MiAIRR data to NCBI. The AIRR community has documented CEDAR-driven MiAIRR submissions to NCBI in the MiAIRR-to-NCBI Submission Manual, the primary user documentation for submitting AIRR metadata. In the SRA section, the pipeline now checks user-entered file names against the names of files actually submitted, and alerts the user if they do not match, and file type options have been updated to reflect NCBI expectations. Finally, members of the AIRR community have validated that submissions appear appropriately in NCBI repositories.

Added Human Tissue NCBI Pipeline

CEDAR added a second NCBI submisssion pipeline for submitting metadata on Human Tissue studies. The template for this pipeline is modeled on the AIRR Community pipeline, but is customized to the NCBI BioSample Human Package 1.0.

Submission to Repository window with NCBI Human Tissue selected as defaultThe template and template elements used by this pipeline are publicly available in the following CEDAR folder: All/Shared/Shared by CEDAR/CEDAR-to-NCBI Pipeline. Documentation of the pipeline may be found in the CEDAR pipelines documentation page.

Inside News

Categories for Artifacts

To handle categorization of CDE fields, we have designed a category system that can be used by different communities to categorize CEDAR artifacts according to their own hierarchical labels. The API for this system has been implemented, and its user interface is planned for the next release.

Performance

We improved CEDAR’s performance for more search types in BioPortal class hierarchies.

Inside Inside News

We refactored code to handle resources (artifacts, users, groups, and folders) in a uniform way. And this release also incorporates some bug fixes.

All the tasks completed for the 2.4 release series can be found with this GitHub search, or by visiting the GitHub release page for release-2.4.

Drone Metadata and CEDAR at ESIP Summer Meeting

You can find the CEDAR team at ESIP’s Summer Meeting this July, thanks to the Linked data And Networked DRoNeS (LANDRS) community.

Simple Drone minimum information model
The Drone Minimum Information framework contains basic elements describing drones and their missions.

We’ll support the Small Unmanned Aircraft Systems’ Data Interest Group at the Drone Data Hackathon on Tuesday July 16. During the hackathon we will help create drone metadata templates and terms, and perhaps help model the metadata model used by the group.

CEDAR template with Drone metadata fields
After: CEDAR represents drone metadata.

 

 

 

Then we (and BioPortal) will roam the grounds until the UnConference (Thursday afternoon July 18) and Semantic Committee work (Friday July 19).





Publication: CEDAR offers metadata recommendations from mined rules

Marcos Martinez-Romero and his co-authors have published a new paper describing CEDAR’s updated implementation of intelligent authoring. The new methods use rule mining to generate recommendations based on previously entered metadata in the CEDAR system, and offer the users only the most likely recommendations given previous metadata entries for the template.

Suggested values seen by users
The intelligent authoring metadata recommendations take into account rules derived from previously entered metadata with the same values.

You can find instructions for setting up this capability in the CEDAR User Manual page Understanding the Suggestion System.

Martínez-Romero M, O’Connor MJ, Egyedi AL, Willrett D, Hardi J, Graybeal J, Musen MA. Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databasesDatabase. Volume 2019, 10 June 2019. https://doi.org/10.1093/database/baz059.