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Use namespaces from identifiers.org #31

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3 tasks done
reece opened this issue Sep 17, 2018 · 1 comment
Closed
3 tasks done

Use namespaces from identifiers.org #31

reece opened this issue Sep 17, 2018 · 1 comment
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@reece
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reece commented Sep 17, 2018

The goal of this issue is to migrate namespaces to those used in identifiers.org. Those namespaces will become the standard in seqrepo. The namespaces are:

  • NCBIrefseq (for most accessions)
  • Ensemblensembl
  • LRGlrg

Implementation options:

  1. Abrupt db migration. Migrate namespaces in database in-place without a transition and release. Clients using old namespaces would break.
  2. Use optional API translation to transition. Use three releases in which the new namespaces are is 1) optional w/default off (no behavior change), 2) optional w/default on, 3) updated in db and API translation is removed.
  3. Automatic translation. In the first release (e.g., 0.5.7), add obligatory translation from new to old namespaces. Storing aliases would continue to use the old namespace. Finding would use translate new namespaces to old. Fetching alias records would add synthetic record for the new namespace. In a subsequent release (e.g., 0.6) invert the previous translation.

Option 3 seem pretty clearly the superior choice: it's easier to understand, requires less communication, and obviates client switches.

  • Translate from NCBI to refseq
  • Translate Ensembl to ensembl
  • Translate LRG to lrg
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@reece reece changed the title Use namespaces from indentifiers.org Use namespaces from identifiers.org Oct 20, 2018
@reece reece added this to the 0.6 milestone Jun 9, 2020
@reece reece closed this as completed in f2b48ef Jul 6, 2020
@reece reece mentioned this issue Nov 26, 2020
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