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Adding crawl and chain commands #826

Merged
merged 10 commits into from
Jan 31, 2025
Merged

Adding crawl and chain commands #826

merged 10 commits into from
Jan 31, 2025

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cmungall
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@cmungall cmungall commented Jan 30, 2025

  • Documentation
    • Added new notebook for generate-synonyms
    • Added new notebook for diff-associations
    • Added notebooks showing how to use OAK expressions on command line to make a subset generation pipeline
  • New commands
    • crawl
    • chains
  • New options on commands
    • Added --unmelt option to mappings command : Mappings can now be easily summarized by object_source, a column is created for every external prefix/database
    • Added --add-pipeline-step option to lexmatch
  • Query expression language
    • .numparents .numchild
    • `.multimrca'
  • Interface enhancements
    • Added invert option to relationships method
  • Implementation enhancements
    • AmiGOImplementation: including evidence, negation

Crawl Command

Check here once merged:

https://incatools.github.io/ontology-access-kit/examples/Commands/Crawl.html

Added new documentation notebooks
@matentzn
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Can you provide a brief summary about this very interesting sounding PR?

@cmungall cmungall changed the title Added crawl command. Multiple new features Jan 30, 2025
@cmungall cmungall changed the title Multiple new features Adding crawl and chain commands Jan 30, 2025
@cmungall cmungall merged commit 22ebc5c into main Jan 31, 2025
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@cmungall
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Updated the description, also added a (so far) quite minimal notebook

https://incatools.github.io/ontology-access-kit/examples/Commands/Crawl.html

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2 participants