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Make excelparser that converts a filled excel sheet to an ontology #309

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merged 34 commits into from
Dec 12, 2021

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francescalb
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@francescalb francescalb commented Dec 1, 2021

Description:

Type of change:

  • Bug fix.
  • New feature.
  • Documentation update.

Checklist of data that should be parsed in the minimal initial version that can be merged to master

Concepts

  • prefLabel
  • subClassOf
  • altLabels
  • comments
  • elucidatons
  • examples
  • relations
    Metdata
  • base_iri
  • imported ontologies
  • authors: currently added as contributors
  • contributors
  • versionInfo
  • license
  • title
  • abstract

Checklist:

This checklist can be used as a help for the reviewer.

  • Is the code easy to read and understand?
  • Are comments for humans to read, not computers to disregard?
  • Does a new feature has an accompanying new test (in the CI or unit testing schemes)?
  • Has the documentation been updated as necessary?
  • Does this close the issue?
  • Is the change limited to the issue?
  • Are errors handled for all outcomes?
  • Does the new feature provide new restrictions on dependencies, and if so is this documented?

Comments:

@francescalb francescalb linked an issue Dec 1, 2021 that may be closed by this pull request
@francescalb
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@jesper-friis @sygout
Here is the first example of the excelparser. Can you have a look and comment on what other things should be made available?

@sygout
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sygout commented Dec 7, 2021

I tried to run make make_microstructure_onto.py and it crashes.
if you removed a weird "1" in the prefLabel column, it seems stuck.

@francescalb
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The '1' is there only to test that it doe snot fail if prefLabel starts with a number, can be removed. However, if you remove it with a space you will get an error as you will effectively give it a prefLabel with space.

@francescalb francescalb closed this Dec 8, 2021
@francescalb francescalb reopened this Dec 8, 2021
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francescalb and others added 8 commits December 9, 2021 09:49
Co-authored-by: Jesper Friis <jesper-friis@users.noreply.github.com>
Co-authored-by: Jesper Friis <jesper-friis@users.noreply.github.com>
Co-authored-by: Jesper Friis <jesper-friis@users.noreply.github.com>
data  argument can either be metadata (pd.DataFrame)
or a row for a concept (pd.Series)
@francescalb francescalb marked this pull request as ready for review December 10, 2021 07:17
@francescalb francescalb changed the title [DRAFT] flb/close 302 excelparser Make excelparser that converts a filled excel sheet to an ontology Dec 10, 2021
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Very nice

@francescalb francescalb merged commit 4f6251f into master Dec 12, 2021
@CasperWA CasperWA deleted the flb/close-302-excelparser branch March 2, 2022 16:25
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make excel parser that creates and ontology from a filled excel file
3 participants