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Fix examples of SSSOM/TSV files. #362

Merged
merged 4 commits into from
Apr 21, 2024
Merged

Fix examples of SSSOM/TSV files. #362

merged 4 commits into from
Apr 21, 2024

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gouttegd
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The examples provided in the SSSOM/TSV section of the "overview" document are full of errors and would fail the most basic validation by our own tools:

  • use of Lexical instead of semapv:LexicalMatching in the mapping_justification field (probably a remnant of the time prior to the adoption of the SEMAPV vocabulary);
  • bogus IRI prefix for the SKOS namespace (missing terminal #);
  • use of a full-length identifier (instead of a CURIE) for creator_id.

This PR fixes those errors. In addition, it also ensures that the fields are listed in the recommended order. It’s not critical but if we take the time to recommend that fields be sorted in a given order, the least we can do is to follow our own advice in our examples.

While we are at it, we also add a small note about the requirement for using CURIEs in the SSSOM/TSV format, since that requirement currently does not appear anywhere but is already enforced by sssom validate.

This is a band-aid until the docs are completely overhauled as part of #330.

  • docs/ have been added/updated if necessary
  • [ ] make test has been run locally Not applicable
  • [ ] tests have been added/updated (if applicable) Not applicable
  • [ ] CHANGELOG.md has been updated. Not applicable

The examples provided in the SSSOM/TSV section of the "overview"
document are full of errors and would fail the most basic validation by
our own tools:

- use of "Lexical" instead of "semapv:LexicalMatching" in the
  mapping_justification field (probably a remnant of the time prior to
  the adoption of the SEMAPV vocabulary);
- bogus IRI prefix for the SKOS namespace (missing terminal '#');
- use of a full-length identifier (instead of a CURIE) for `creator_id`.

This commit fixes those errors. In addition, it also ensures that the
fields are listed in the *recommended order*. It's not critical but if
we take the time to recommend that fields be sorted in a given order,
the least we can do is to follow our own advice in our examples.

While we are at it, we also add a small note about the requirement for
using CURIEs in the SSSOM/TSV format, since that requirement currently
does not appear anywhere but is already enforced by `sssom validate`.
matentzn
matentzn previously approved these changes Apr 12, 2024
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@matentzn matentzn left a comment

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Perfect, thank you!

@matentzn matentzn requested a review from ehartley April 18, 2024 13:08
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@joeflack4
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joeflack4 commented Apr 19, 2024

Approve; Everything LGTM.

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The SKOS namespace is built-in, so canonically formatted files should
not include it.
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Make sure that embedded SSSOM/TSV examples use tabs in the source
document -- even if they are all converted to spaces in the resulting
HTML code.
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@ehartley ehartley left a comment

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Everything looks good! Thanks!

@gouttegd gouttegd merged commit 376c272 into master Apr 21, 2024
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@gouttegd gouttegd deleted the fix-tsv-examples branch April 21, 2024 15:12
@gouttegd gouttegd mentioned this pull request Jul 2, 2024
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4 participants