Data access policy

  1. General information
  2. Release policy
  3. Release date changes
  4. Removal of data from the public domain
  5. ArrayExpress data access accounts

1. General information

Experiments (sets of assays) and array designs in ArrayExpress are either 'public' or 'private' (often pre-publication and under peer review). Data will be kept private until a specified release date, or until an associated paper containing the experiment or array design accession number is published. Access to private data is possible via submitter and reviewer login accounts created by ArrayExpress upon successful loading of an experiment or array design into the database.

For sensitive data from human samples and individuals that can potentially lead to the identification of the donors (e.g. genomic DNA sequences), ArrayExpress 'private' data sets and submitter/reviewer login accounts cannot provide the high level of data encryption and access control required. In such cases, there should be a data access committee overlooking data privacy issues, and the data should be submitted to the European Genome-phenome Archive (EGA).

Human-identifiable data can still be submitted to ArrayExpress if the data has been consented for public release. Such approvals typically would be given by the relevant ethics committees and ensuring this is the responsibility of the submitters.

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2. Release policy

Experiments are made public when

  • the specified release date is reached
  • the submitter emails to tell us that the data can now be released (usually this is when an associated publication is accepted or published)
  • we identify a publication in which the ArrayExpress experiment accession number is cited

Array designs are made public when

  • the specified release date is reached
  • the submitter emails to tell us that the data can now be released
  • when an experiment the array design is linked to is made public
  • we identify a publication in which the ArrayExpress array design accession number is cited

When an experiment or array design is made public the data is available through the ArrayExpress web interface and the FTP site. There are more information on this ArrayExpress FTP downloads help page.

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3. Release date changes

Reminders about experiment and array design release dates are sent to submitters 7, 30 and 60 days before the current release date.

Microarray experiment submitters: Release date can be changed using this access control tool. Simply login with the data access account details which we emailed you when curation was completed, double-click at the private experiment that you would like release date changed, and follow on-screen instructions. You would normally have used these account details to log in to the ArrayExpress website and view your private experiment(s). Don't worry if you have forgotten the username and/or password, you can retrieve login details using your submitter's email address and the experiment accession number.

Sequencing experiment submitters: Release date still needs to be changed by ArrayExpress cuartors to make sure the sequence read records at the European Nucleotide Archive are kept in sync. Please continue to write to us at arrayexpress@ebi.ac.uk and include the revised release date in YYYY-MM-DD format to avoid ambiguity.

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4. Removal of data from the public domain

Data may be be made private again in ArrayExpress (removing both web interface and FTP access) in the following circumstances

  • submitters realise after their experiment or array design is made public that they failed to request a change to the release date. Note we import data regularly from the Gene Expression Omnibus (GEO) and any data that GEO notify us as being withdrawn will also be withdrawn from ArrayExpress.
  • data is found to be incorrect e.g. sample annotation or sample-data file associations are wrong. The data will be removed from ArrayExpress until the data can be corrected.
  • data are found to have been submitted to ArrayExpress without the permission of the rightful owner; this is expected to be extremely rare and requires formal institutional contact with the submitting institution.

Data is made private again at the next daily update of ArrayExpress where possible. As the data will have been distributed previously as public, ArrayExpress cannot exercise any control on the resultant use of the data by third parties.

Array designs cannot be made private again if they are linked to a public experiment. Array designs will be kept private if they are linked only to private experiments.

Experiments that have been public may be included in the Expression Atlas . If an experiment is later made private again in ArrayExpress then it will also be removed from the Atlas. However, the Atlas has a monthly, rather daily, release schedule and data will be only removed at the next release unless there are extenuating circumstances.

High throughput sequencing read data that is submitted to ArrayExpress, but transferred to the European Nucleotide Archive (ENA) is subject to their data release policies. In general, ENA does not turn a public experiment private again unless there is an exceptional reason. Please also refer to our policy on updating/cancelling a sequencing experiment for more details.

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5. ArrayExpress data access accounts

Submitters are sent details about their own access accounts and those for journal reviewers after a pre-published experiment or array design is loaded into the ArrayExpress database. Submitters can view all their private experiments and array designs using one login. Each reviewer account only gives access to a single experiment or array design.

Please refer to this page on accessing private data on how to use the access accounts, and how to retrieve login details if you've lost them.

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