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Generate RO-Biolink predicate mappings based on a particular Biolink model #104

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Generate RO-Biolink predicate mappings based on a particular Biolink model #104

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Commits on Jul 30, 2023

  1. Added a ro-to-biolink-local-mappings.tsv as a prereq.

    @gaurav
    gaurav committed Jul 30, 2023
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  2. Implemented a very basic command and added some documentation.

    @gaurav
    gaurav committed Jul 30, 2023
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  3. Reorganized code a little bit.

    @gaurav
    gaurav committed Jul 30, 2023
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  4. Added some data structures.

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Commits on Jul 31, 2023

  1. Moved over code to download predicate-mappings from Biolink.

    @gaurav
    gaurav committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. Partially implemented thing.

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  2. Something that works.

    @gaurav
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  3. Works correctly.

    @gaurav
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  4. Removed some unnecessary code.

    @gaurav
    gaurav committed Aug 1, 2023
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  5. Added Scope to manage Source. 

    As suggested in https://zio.dev/reference/resource/scope
    @gaurav
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  6. Added code to write out RO mappings.

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    gaurav committed Aug 1, 2023
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  7. Put relations into the right place.

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    gaurav committed Aug 1, 2023
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  8. Fixed generation and added ro-to-biolink-mappings.tsv.

    @gaurav
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  9. Added some manual mappings from cam-kp-api PR 640. 

    cam-kp-api PR 640: ExposuresProvider/cam-kp-api#640
    @gaurav
    gaurav committed Aug 1, 2023
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  10. Added new manually added predicates.

    @gaurav
    gaurav committed Aug 1, 2023
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  11. Added a missing Biolink prefix.

    @gaurav
    gaurav committed Aug 1, 2023
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Commits on Aug 14, 2023

  1. Commented out Biolink model mappings -- only predicate mappings for now.

    @gaurav
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  2. Added ro-to-biolink-predicate-mappings.tsv as a Makefile target. 

    Also deleted ro-to-biolink-mappings.tsv, which contains all the
mappings.
    @gaurav
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  3. Added explanatory log message.

    @gaurav
    gaurav committed Aug 14, 2023
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  4. Added current biolink-predicate-mappings to GitHub for reference. 

    This should be updated by the Makefile.
    @gaurav
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  5. Added export of all qualifiers into a single value.

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  6. Improved output with filtering and simplification.

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  7. Committed Biolink Predicate Mappings TSV to repo.

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    gaurav committed Aug 14, 2023
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  8. Added GOREL to list of prefixes we support.

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  9. Added GOREL, reorganized code. 

    Also added ro-to-biolink-predicate-mappings-all.tsv.
    @gaurav
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  10. Turn Biolink predicates into URLs too.

    @gaurav
    gaurav committed Aug 14, 2023
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  11. First stab at incorporating qualifiers into kg_edges output.

    @gaurav
    gaurav committed Aug 14, 2023
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  12. Removed redundant predicate.

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  13. Reduced storage space, added all predicate mappings.

    @gaurav
    gaurav committed Aug 14, 2023
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  14. Fixed syntax error.

    @gaurav
    gaurav committed Aug 14, 2023
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  15. Fixed path in Makefile.

    @gaurav
    gaurav committed Aug 14, 2023
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Commits on Aug 28, 2023

  1. Added local mapping reading code.

    @gaurav
    gaurav committed Aug 28, 2023
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  2. Upgraded dev.zio packages.

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    gaurav committed Aug 28, 2023
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  3. Replaced snake case with camel case to make it more Scala-y.

    @gaurav
    gaurav committed Aug 28, 2023
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  4. First stab at warnings.

    @gaurav
    gaurav committed Aug 28, 2023
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  5. Added additional duplication checks.

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    gaurav committed Aug 28, 2023
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  6. Added checks for invalid Biolink predicates.

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    gaurav committed Aug 28, 2023
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  7. Deleted RO:0002313 from local mappings. 

    As per #104 (comment)
    @gaurav
    gaurav committed Aug 28, 2023
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Commits on Nov 7, 2023

  1. Merge branch 'master' into kg-tsv-qualifiers

    @gaurav
    gaurav committed Nov 7, 2023
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