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**DON'T MERGE -- ARCHIVE ** Build overhaul v4.0.0 #122

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**DON'T MERGE -- ARCHIVE ** Build overhaul v4.0.0 #122

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Commits on Dec 7, 2021

  1. adding metadata tracking doc

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    callahantiff committed Dec 7, 2021
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  2. adding chemical-disease metadata

    @callahantiff
    callahantiff committed Dec 7, 2021
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  3. adding chemical-phenotype metadata

    @callahantiff
    callahantiff committed Dec 7, 2021
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  4. formatting update

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    callahantiff committed Dec 7, 2021
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  5. updating chemical-disease and chemical-phenotype filtering

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    callahantiff committed Dec 7, 2021
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  6. adding back chemical-rna edges

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    callahantiff committed Dec 7, 2021
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  7. adding chemical-gene metadata

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    callahantiff committed Dec 7, 2021
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  8. updating filtering criteria

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    callahantiff committed Dec 7, 2021
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  9. fixing identifier columns

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    callahantiff committed Dec 7, 2021
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  10. fixing columns

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    callahantiff committed Dec 7, 2021
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  11. chemical-gene, chemical-protein, chemical-protein

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  12. chemi-gene/protein/rna

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  13. chemical-pathway

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  14. chemical-go

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  15. adding reverse edges

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    callahantiff committed Dec 7, 2021
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  16. updating evidence

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  17. disease-phenotype

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    callahantiff committed Dec 7, 2021
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  18. updating criteria

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    callahantiff committed Dec 7, 2021
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  19. gene-disease/phenotype

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  20. adding gene prefix

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  21. gene-gene

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Commits on Dec 8, 2021

  1. gene-pathway

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  2. updates for universal gene identifier mapping

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    callahantiff committed Dec 8, 2021
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  3. gene-protein/rna

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  4. gobp-pathway, pathway-gocc/gomf

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Commits on Dec 10, 2021

  1. updated processing code

    @callahantiff
    callahantiff committed Dec 10, 2021
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  2. updating processing criteria

    @callahantiff
    callahantiff committed Dec 10, 2021
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  3. refining processing pipeline

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    callahantiff committed Dec 10, 2021
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  4. protein-anatomy/cell and rna-anatomy/cell

    @callahantiff
    callahantiff committed Dec 10, 2021
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  5. fixing referenced columns

    @callahantiff
    callahantiff committed Dec 10, 2021
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  6. cleaning up file processing to add metadata

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    callahantiff committed Dec 10, 2021
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  7. protein-catalyst/cofactor

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  8. protein-catalyst/cofactor

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    callahantiff committed Dec 10, 2021
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Commits on Dec 14, 2021

  1. light reformatting and re-org

    @callahantiff
    callahantiff committed Dec 14, 2021
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  2. protein-gobp/gocc/gomf

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    callahantiff committed Dec 14, 2021
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  3. protein-pathway

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    callahantiff committed Dec 14, 2021
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  4. protein-protein

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    callahantiff committed Dec 14, 2021
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  5. rna-protein

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    callahantiff committed Dec 14, 2021
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  6. adding code to ignore file header metadata

    @callahantiff
    callahantiff committed Dec 14, 2021
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  7. updating clinvar data file

    @callahantiff
    callahantiff committed Dec 14, 2021
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Commits on Dec 23, 2021

  1. addressing unionOf bug

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    callahantiff committed Dec 23, 2021
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Commits on Dec 24, 2021

  1. improved testing dependencies

    @callahantiff
    callahantiff committed Dec 24, 2021
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  2. improving logic

    @callahantiff
    callahantiff committed Dec 24, 2021
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  3. partially complete clinvar changes

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    callahantiff committed Dec 24, 2021
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Commits on Dec 27, 2021

  1. adding clinvar datasets

    @callahantiff
    callahantiff committed Dec 27, 2021
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  2. adding file header and editing content

    @callahantiff
    callahantiff committed Dec 27, 2021
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  3. extended example

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    callahantiff committed Dec 27, 2021
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  4. updated script

    @callahantiff
    callahantiff committed Dec 27, 2021
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  5. improved spacing

    @callahantiff
    callahantiff committed Dec 27, 2021
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  6. making all dependencies "|" delimited

    @callahantiff
    callahantiff committed Dec 27, 2021
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  7. updating testing data

    @callahantiff
    callahantiff committed Dec 27, 2021
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  8. fixing language

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    callahantiff committed Dec 27, 2021
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  9. adding header and making "|"-delimited

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    callahantiff committed Dec 27, 2021
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  10. fixed typos and updated delimiter

    @callahantiff
    callahantiff committed Dec 27, 2021
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  11. improving def

    @callahantiff
    callahantiff committed Dec 27, 2021
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  12. improving column def

    @callahantiff
    callahantiff committed Dec 27, 2021
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  13. adding bioregistry function

    @callahantiff
    callahantiff committed Dec 27, 2021
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  14. place holder for ontology dbxref retrieval

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    callahantiff committed Dec 27, 2021
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  15. adding pyyaml to requirements

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    callahantiff committed Dec 27, 2021
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Commits on Dec 28, 2021

  1. adding biolink functionality

    @callahantiff
    callahantiff committed Dec 28, 2021
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Commits on Dec 30, 2021

  1. delaying build further

    @callahantiff
    callahantiff committed Dec 30, 2021
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  2. bumping lxml to match

    @callahantiff
    callahantiff committed Dec 30, 2021
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Commits on Jan 2, 2022

  1. removed additional parameter

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    callahantiff committed Jan 2, 2022
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Commits on Jan 3, 2022

  1. lowering the case of the variables

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    callahantiff committed Jan 3, 2022
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Commits on Jan 4, 2022

  1. extending bioregistry functionality

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  2. finalizing data

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    callahantiff committed Jan 4, 2022
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  3. updating clinvar resource filenames

    @callahantiff
    callahantiff committed Jan 4, 2022
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  4. modifying header and updating maps

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  5. better logic for ids missing from bioregistry

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    callahantiff committed Jan 4, 2022
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  6. removing unused arg

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Commits on Jan 5, 2022

  1. adding jsonl functions

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    callahantiff committed Jan 5, 2022
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Commits on Jan 6, 2022

  1. updating definitions

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  2. updating variable names

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    callahantiff committed Jan 6, 2022
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Commits on Jan 8, 2022

  1. renaming node metadata directory and files

    @callahantiff
    callahantiff committed Jan 8, 2022
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  2. fixing typo

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    callahantiff committed Jan 8, 2022
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Commits on Jan 19, 2022

  1. pulling better entity description

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    callahantiff committed Jan 19, 2022
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  2. adding pubmed ids

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    callahantiff committed Jan 19, 2022
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Commits on Jan 20, 2022

  1. improved explanation

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    callahantiff committed Jan 20, 2022
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Commits on Jan 25, 2022

  1. fixed identifier

    @callahantiff
    callahantiff committed Jan 25, 2022
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  2. complete overhaul and update

    @callahantiff
    callahantiff committed Jan 25, 2022
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Commits on Jan 28, 2022

  1. moving metadata file

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    callahantiff committed Jan 28, 2022
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  2. updating pathway to metadata file

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    callahantiff committed Jan 28, 2022
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  3. fixing edge type errors

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    callahantiff committed Jan 28, 2022
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Commits on Jan 29, 2022

  1. cleaned up file

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    callahantiff committed Jan 29, 2022
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  2. committing nearly complete data

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    callahantiff committed Jan 29, 2022
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Commits on Apr 1, 2022

  1. adding better tqdm

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    callahantiff committed Apr 1, 2022
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  2. adding ipywidgets

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    callahantiff committed Apr 1, 2022
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  3. alphabetizing

    @callahantiff
    callahantiff committed Apr 1, 2022
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  4. cleaning up linting errors

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    callahantiff committed Apr 1, 2022
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  5. sprucing

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    callahantiff committed Apr 1, 2022
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  6. light overhaul

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  7. adding analytic search examples

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    callahantiff committed Apr 1, 2022
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  8. Merge branch 'build_overhaul_v4.0.0' of github.com:callahantiff/PheKn… 

    …owLator into build_overhaul_v4.0.0
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  9. suppressing biolink functions 

    need to strongly consider whether to add biolink dependency
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  10. adding back org test data

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    callahantiff committed Apr 1, 2022
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  11. suppressing changes for testing

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  12. suppressing for testing

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  13. testing rollback

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  14. rollback for testing

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  15. fixed import error

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  16. addressing typing error

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  17. rollback for testing

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  18. rollback for testing

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  19. rollback

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  20. resolving typing errors

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  21. Merge branch 'master' into build_overhaul_v4.0.0

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  22. fixing parsing error

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Commits on Apr 4, 2022

  1. adding footnote

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  2. fixing header

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  3. Merge branch 'master' into build_overhaul_v4.0.0

    @callahantiff
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  4. bumping numpy

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  5. bumping numpy version

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  6. adding entity search helper functions

    @callahantiff
    callahantiff committed Apr 4, 2022
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  7. fixing numpy version error

    @callahantiff
    callahantiff committed Apr 4, 2022
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  8. Update build_requirements.txt

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    callahantiff committed Apr 4, 2022
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