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Verify that ROBOT can do the QC currently handled by the PRO dB #152

nataled opened this issue Jul 5, 2019 · 0 comments


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commented Jul 5, 2019

Opening this ticket to document the progress on this issue. As discussed, we currently have several QC channels. The first is pre-database (done by @nataled). Next is the comparison of PRO dB output with the original input (done by @Julie-Cowart). Finally, ROBOT (done by @Julie-Cowart). Note that the ROBOT results are not currently part of a current release cycle (the output is reviewed for the next release). Also note that ROBOT can be run at any point in the cycle (that is, it doesn't need to wait until the end). As post-production QC is rate-limiting for the release, it is desirable to shift it earlier in the cycle. To this end, we have been systematically comparing the pre- and post-dB results, and fixes for any large-scale issues identified have been implemented in the pre-dB check (for PRO OBO only; the PAF changes are still fully dependent on the dB). The question is whether or not the dB step can be bypassed altogether. The following will need to be checked:

  1. @nataled to review PAF output from dB. Most of the issues in the past have been simply to fix the referenced names and synonyms. This can easily be done pre-dB. Any remaining issues will need to be checked.

  2. @Julie-Cowart to document the QC done using the dB. Much of it is already known because the output reveals the issues. However, it is possible that there are checks for things that never were issues (or are no longer).

  3. ROBOT is continually being revised to do more and more QC. Once we have a list of our own checks, these can be compared to ROBOT. Upon finding similarities, we can decide to offload our own QC in favor of it being done by ROBOT. If there are QC checks that we do that ROBOT does not, and we deem useful for other ontologies, we can request inclusion of such checks in a future ROBOT release.

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