search

Lioscro / alaska-parse

Automated and friendly RNA-seq analysis (migrated to Parse Server)
http://alaska.caltech.edu
1 stars 0 forks source link

Incomplete submissions to GEO #18

Open dangeles opened 5 years ago

dangeles commented 5 years ago

If samples are automatically submitted to a GEO repository, it is not hard to imagine that the data is deemed useless or the project remains unfinished and the repository should in fact be deleted.

Maybe we should talk out an agreement with the GEO staff to have the repository be deleted after 3 years if the authors have never contacted the staff. This is actually a really tough problem and may be almost impossible to solve, since the purpose of GEO is to NOT delete data, but there's also no point in making incomplete, unfinished or (worst of all) duplicate repositories.

Lioscro commented 5 years ago

If the user deems a project useful and uploads it to the GEO, they must make a voluntary effort to contact the GEO about their submission (by either sending them an email about the submission or submitting the FTP transfer form).

Additionally, the GEO submission guidelines say, Un-announced files will be automatically deleted from the server after two weeks. https://www.ncbi.nlm.nih.gov/geo/info/submissionftp.html

dangeles commented 5 years ago

Uhhh.. Neither of those is the same as the scenario I envision.

Imagine authors submit to GEO, contact GEO to establish repo. Then decide to add new analyses. How could they add to the GEO repo? Our response would probably be to suggest they decline the automated upload, and do it manually using the old repo as provided previously. We could add this in the FAQ.