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[BUG] (a priori) Erroneous hierarchy for "qualsolid" [format:3610] #854

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M-casado opened this issue Oct 6, 2022 · 2 comments
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@M-casado
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M-casado commented Oct 6, 2022

Hi, I believe that the term "qualsolid" [format:3610] has the incorrect parental hierarchy based on its definition: "FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.".

If it does not contain indeed "sequences", I would argue the following hierarchy is wrong and it should not be included in "Sequence record format" [format:1919]. This last term is described as "Data format for a molecular sequence record.".
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@matuskalas matuskalas added bug Something isn't working high priority labels Oct 6, 2022
@matuskalas matuskalas added this to To do in release 1.26 via automation Oct 6, 2022
@matuskalas matuskalas added this to the 1.26 milestone Oct 6, 2022
@matuskalas
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Thank you so much for your detailed report @M-casado, this indeed needs to be reviewed 🙏🏽

@rioualen
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Hello,

In order to address this issue I propose to do the following:

  1. remove the "qual" nodes that are in the fastq-like branches (red strikes)
  2. remove 1 intermediate node in "Format (by type of data) > Sequence quality report format (text) > qualsolid" (green strike)
  3. Rename/map "Textual format > FASTQ-like format > qual" to "Textual format > FASTQ-like format > Sequence quality report format (text)" (purple strike)
  4. Add "FASTQ-solid" as a broad synonym of qualsolid (blue notes)
  5. Do the same with qual454, qualillumina and qualsolexa

What do you think about it @matuskalas ? If it's okay with you I can implement those changes myself in Protege.
issue854

@rioualen rioualen self-assigned this Dec 18, 2023
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