Status Terminology

 

On the ENCODE Portal, statuses are used to indicate the processing phase of a specific object. In general, only objects that have been assigned a status of 'released,' 'revoked,' or 'archived' can be viewed by the general public. Objects that have been assigned a status of 'deleted' or 'replaced' can only be viewed by admins and not the general public. In general, objects with other statuses are accessible to data submitters, but cannot be viewed by the general public.

Experiment status

 

 
  • in progress - This assay has been started. 
  • submitted - This assay has all of its associated FASTQs submitted to the DCC.
  • released - This assay is released to the public. In order to transition to 'released' from 'ready for review,' there should be no red audits, the submitting lab and the data wrangler should be satisfied with the metadata and all orange audits should be explained.
  • archived - This assay was not revoked for being faulty, however, in most cases there is more current data available using more current methods. These experiments should have superseded_by value for the experiment that replaces them. Ideally, the reason for archiving will be found in the submitter_comments.
  • revoked - This assay was deemed erroroneous or significantly below standards after it had been released. A 'revoked' experiment should have its associated files and libraries 'revoked' as well. Ideally, the reason for revoking will be found in the submitter_comments.
  • replaced - This assay has been merged with another experiment and the experiments should now share accessions. This is usually the case when multiple objects were created for the same experiment. This state is special because the accession of a 'replaced' object is available for reuse and should be given to the new merged experiment as an alternate_accession.
  • deleted - This assay was removed before it was released. Information may possibly be found in the notes field.
 

File status

 

 
  • uploading - The file is uploading to the Amazon S3 bucket and awaiting format and uniqueness checks.
  • upload failed - The file failed to upload to the Amazon S3 bucket.
  • content error - The file failed format check or uniqueness checks.
  • in progress - The file has successfully uploaded and passed format and uniqueness checks.
  • replaced - This file object is merged with another. Either the files are duplicates in (content) md5sum or the format was found faulty and replaced with a remedied file. 'Replaced' is a special status because it allowes the accession to be reused. The replacing file should now have this accession in alternate_accessions.
  • deleted - This file was removed before it was released.
  • released - This file is released to the public. 
  • archived - This file is considered superfluous or outdated. There is nothing wrong with the file, but it is considered an extra to the experiment.
  • revoked - This file was deemed erroneous or significantly below standards after it had been released. A 'revoked' file should have some reason for revoking in the notes field.                         

Permissions status

 

Permissions statuses, which are visible to public users only if the object has not been 'deleted,' are assigned to objects that are created and edited only by admins, including: lab, award, user, organism, platform, and source.

 

 

Basic Object status

 

Basic object statuses are visible to public users if the object is 'released,' are assigned to objects including document, image, page, software, characterizations (donor, genetic modification, and biosample) and all quality metrics.

 

 
 

Experiment internal status

 

Experiment internal statuses, which are all visible to admins only, are assigned to experiments to track the experimental data's current stage of pipeline processing. These are assigned to experiment objects in addition to experiment status described above.

 

 
  • unreviewed - Experiment metadata and data have not yet been evaluated.
  • unrunnable - The data do not meet the criteria (format, quality, etc.) to be run through the appropriate pipeline.
  • no available pipeline - The ENCODE Consortium does not currently have a uniform processing pipeline for this data type.
  • requires lab review - Metadata and data have been reviewed and the experiment requires attention from the submitting lab before processing.
  • pipeline ready - Metadata and data have been reviewed and the experiment is considered ready for processing through the appropriate pipeline.
  • processing - Data is currently running through the appropriate pipeline.
  • pipeline error - Pipeline run was started but failed for a specific reason which is noted in pipeline_error_detail.
  • pipeline completed - Data was successfully run through the appropriate pipeline to completion.
  • release ready - The ENCODE DCC has approved this data for release.

Updated: November 2018