One big problem that I'm regularly facing is that URLs for downloading Bioinformatics data (e.g., RefSeq releases or NCBI genome releases) disappear.

Does anyone have any good solution for this?

  • 3
    $\begingroup$ Do you have examples of specific URLs that have stopped working? Some projects try very hard to provide permalinks. $\endgroup$ Jun 1 '17 at 2:50
  • $\begingroup$ Genome releases are versioned, so the URL may move but the data is still there. $\endgroup$
    – Devon Ryan
    Jun 1 '17 at 6:47
  • 1
    $\begingroup$ Could you specify which platform or which kind of data you are looking for a stable URL? Many sites provide a ftp server for big downloads $\endgroup$
    – llrs
    Jun 1 '17 at 7:19
  • 1
    $\begingroup$ I think this is a good question, maybe with minor modifications: URIs for big databases rarely disappear but stable identifiers aren’t always obviously marked (e.g. Ensembl defaults to “current” release rather than a stable URI). $\endgroup$ Jun 1 '17 at 9:45
  • 2
    $\begingroup$ The question should be flavoured with some examples, but it rises a very good point. $\endgroup$
    – Kamil S Jaron
    Jun 1 '17 at 12:15

The Persistent uniform resource locator or PURL is one such solution, these are designed to be a bit more robust than permalinks in so much as they are supposed to survive the change of domain name. The bio ontology community already use them http://purl.bioontology.org/docs/index.html


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.