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globalbioticinteractions / name-alignment-template

align names with known taxonomic resources
https://big-bee-network.github.io/name-alignment-workshop
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Doubled resolvedName output #3

Closed jtmiller28 closed 1 year ago

jtmiller28 commented 2 years ago

For the .txt file generated by the tool, the columns created contain identical names causing confusing labels. There are currently 2 columns named resolvedName, where the second is the fully resolved name output. I'm wondering what the first resolvedName column is for? Is it just removal of characters outside the species name? image image

jhpoelen commented 2 years ago

@jtmiller28 thanks for taking the time to record the duplicate columns names "resolvedName".

The first column named "resolvedName" is actually the outcome of an attempt to parse the provided Name .

The second column names "resolvedName" is the outcome of an attempt to align the parsed name with a Nomer support taxonomy.

I can see how this may be confusing.

What name / structure would make sense to you now that I've tried to explain what the valuables of the respective columns convey?

jtmiller28 commented 2 years ago

I think the first column named resolvedName being named parsedName would make sense to me since it would indicate its in the process of being broken down before resolution. That way users can also track through the columns whats occurring and backtrack potential issues that could occur with the first parsing step. The second column that is made with attempted aligned parsed name with nomer is clear with the name resolvedName since this matches previous syntax I've seen like correctedName, alignedName, etc.

jhpoelen commented 1 year ago

updated column names to be those listed in

https://github.com/globalbioticinteractions/globinizer/blob/f9c2096f552b7c5b0adfe5d57ccba5a9700a1a47/align-names.sh#L68

Please re-open / comment / create pull request if you'd like to change the column names.