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Clean up Regnum phylorefs #89

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Clean up Regnum phylorefs #89

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Commits on May 22, 2020

  1. Deleted unneeded phyloref_testcase.owl.

    @gaurav
    gaurav committed May 22, 2020
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Commits on Jun 30, 2020

  1. Imported some files from Anna's transcribed phylogenies.

    @gaurav
    gaurav committed Jun 30, 2020
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  2. Added phylogenies transcribed or obtained by Anna.

    @gaurav
    gaurav committed Jun 30, 2020
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Commits on Jul 13, 2020

  1. Standardized to file ID to seven digits rather than six. 

    This is the number used by the Gene Ontology, Uberon and other
ontologies.
    @gaurav
    gaurav committed Jul 13, 2020
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  2. Renamed from "REGNUM_" to "CLADO_". 

    Since the plan is for them to have these terms in the Clade Ontology.
    @gaurav
    gaurav committed Jul 13, 2020
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  3. Imported phylogenies curated by Anna.

    @gaurav
    gaurav committed Jul 13, 2020
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Commits on Jul 14, 2020

  1. Moved and renamed files with Newick errors.

    @gaurav
    gaurav committed Jul 14, 2020
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  2. Added expectation for Ascomycota.

    @gaurav
    gaurav committed Jul 14, 2020
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Commits on Aug 10, 2020

  1. Manually labeled one expected resolution.

    @gaurav
    gaurav committed Aug 10, 2020
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  2. Updated phylogenies with latest.

    @gaurav
    gaurav committed Aug 10, 2020
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  3. Improved debugging; removed two files with failing Newick strings.

    @gaurav
    gaurav committed Aug 10, 2020
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Commits on Aug 25, 2020

  1. Replaced generated filename from "REGNUM_" to "CLADO_".

    @gaurav
    gaurav committed Aug 25, 2020
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  2. Fix: specifier authorities now written correctly.

    @gaurav
    gaurav committed Aug 25, 2020
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  3. Removed folders named 'scripts/' from encryption.

    @gaurav
    gaurav committed Aug 25, 2020
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  4. Added a script for mass-converting Phyx files into OWL ontologies.

    @gaurav
    gaurav committed Aug 25, 2020
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  5. Changed default number of digits to 7. 

    This is the same as used by CDAO. Also made this into a command line
argument.
    @gaurav
    gaurav committed Aug 25, 2020
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Commits on Aug 26, 2020

  1. Fixed author separators.

    @gaurav
    gaurav committed Aug 26, 2020
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  2. Added script to fix part of Phyx file.

    @gaurav
    gaurav committed Aug 26, 2020
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  3. Fixed specifier authorities in Phyx files.

    @gaurav
    gaurav committed Aug 26, 2020
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Commits on Jul 2, 2021

  1. Moved encrypted Phylonym Phyx out of encrypted/. 

    This unencrypts it.
    @gaurav
    gaurav committed Jul 2, 2021
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  2. Deleted two test clade definitions.

    @gaurav
    gaurav committed Jul 2, 2021
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  3. Added a test for Newick strings in input files.

    @gaurav
    gaurav committed Jul 2, 2021
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Commits on Jul 11, 2021

  1. Add a GitHub action to test this repo.

    @gaurav
    gaurav committed Jul 11, 2021
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Commits on Jul 12, 2021

  1. Made some tests optional; fixed tests.

    @gaurav
    gaurav committed Jul 12, 2021
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