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Record format machine readability: retention time #306

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meowcat opened this issue May 3, 2021 · 2 comments
Open

Record format machine readability: retention time #306

meowcat opened this issue May 3, 2021 · 2 comments

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@meowcat
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meowcat commented May 3, 2021

This concerns

  1. definition of the unit for RT in MassBank records
  2. automatic conversion of existing RT data to a defined unit

Concerning 2) it was highlighted that there is an issue when the given unit is not explicitly given (i.e. RETENTION_TIME is just a number). I suggested to add an .ini (or other) file to contributor folders to provide missing info to the autocuration process (which might be needed also for other values.) @sneumann you weren't a big fan; do you have a better idea?

@michaelwitting
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Why not simply demanding a unit with numeric value, e.g. min, s. If no unit is supplied it is an invalid field...

@meier-rene
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That would be the right thing to do. But we have a lot of legacy content in MassBank which does not define these units. Validation of all data is something like a unit test we use to ensure integrity of code and data on commits. Thats why we couldnt implement this test for the complete data. Lately I added -legacy as switch for the validator aa5b211 . Now our legacy content can be validated with less strict tests and I can implement this unit test for all new contributions. I will put this on my short term todo list.

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