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Support for prefix declarations in OBO format #1102

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Support for prefix declarations in OBO format #1102

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Commits on May 10, 2023

  1. obo2owl: Treat replaced_by value as an IRI. 

    The value of the `replaced_by` tag in a OBO file should be an ID
according to the OBO Flat File Format specification, so we treat it as
such.
    @gouttegd @balhoff
    gouttegd authored and balhoff committed May 10, 2023
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  2. obo2owl: Follow idspace declarations. 

    When the header frame of a OBO file contains `idspace` tags, use them to
translate Prefixed-IDs (aka CURIEs) into full IRIs.
    @gouttegd @balhoff
    gouttegd authored and balhoff committed May 10, 2023
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  3. obo2owl: Treat consider value as IRI. 

    Process `consider` tags in a OBO file the same way as `replaced_by`
tags.
    @gouttegd @balhoff
    gouttegd authored and balhoff committed May 10, 2023
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Commits on May 11, 2023

  1. Remove injected OBO_REL prefix declaration; order is backwards so lik… 

    …ely never useful.
    @balhoff
    balhoff committed May 11, 2023
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Commits on May 12, 2023

  1. Roundtrip support for prefix declarations in OBO format.

    @balhoff
    balhoff committed May 12, 2023
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Commits on May 13, 2023

  1. Add null check.

    @balhoff
    balhoff committed May 13, 2023
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Commits on Aug 1, 2023

  1. Use prefix manager directly to compact IRIs to CURIEs.

    @balhoff
    balhoff committed Aug 1, 2023
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  2. Fix lookup for idspace prefixes.

    @balhoff
    balhoff committed Aug 1, 2023
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  3. Don't write default prefixes into OBO format.

    @balhoff
    balhoff committed Aug 1, 2023
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  4. Add OBO idspaces usage and roundtrip test.

    @balhoff
    balhoff committed Aug 1, 2023
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Commits on Oct 20, 2023

  1. Merge branch 'version4' into replaced-by-value-as-iri-v4

    @balhoff
    balhoff committed Oct 20, 2023
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  2. Ensure longest namespace match is used. Disallow prefixes that are su… 

    …bstrings of OBO namespace.
    @balhoff
    balhoff committed Oct 20, 2023
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Commits on Feb 1, 2024

  1. If a prefix is declared in idspaces, don't use # separator for "non-c… 

    …anonical" ids.
    @balhoff
    balhoff committed Feb 1, 2024
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  2. Drop conflicting id annotations rather than stuff into owl-axioms hea… 

    …der.
    @balhoff
    balhoff committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. Corrected key comparison in OBOFormatPrefixManager. Exclude OBO IRIs … 

    …from idspaces.
    @balhoff
    balhoff committed Feb 2, 2024
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  2. Remove debugging code.

    @balhoff
    balhoff committed Feb 2, 2024
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Commits on Feb 8, 2024

  1. Don't inject default semweb prefixes into OBO document format.

    @balhoff
    balhoff committed Feb 8, 2024
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Commits on Apr 29, 2024

  1. Test prefixes aren't injected.

    @balhoff
    balhoff committed Apr 29, 2024
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