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Commits on May 12, 2025

• Add sphinx config to docs

  bgyori

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  3dcaf39

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• Merge pull request #155 from gyorilab/ner_download

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  bgyori

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• Add NER download as CSV option

  bgyori

  committed
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• Bump version to 1.4.1

  bgyori

  committed
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Commits on Mar 20, 2025

• Merge pull request #153 from gyorilab/fix

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  bgyori

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• Fix corner case with trailing space in synonym

  bgyori

  committed
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Commits on Oct 29, 2024

• Bump version

  bgyori

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Commits on Aug 29, 2024

• Merge pull request #151 from cmungall/patch-1

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  bgyori

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• Update tests.yml to use new punkt file from NLTK

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  cmungall

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Commits on Jul 26, 2024

• Merge pull request #148 from galileosteinberg/ner-benchmark

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  bgyori

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• Added readme output.

  galileosteinberg

  committed
  b915c1c

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• Removed debugging print statements and unused imports

  galileosteinberg

  committed
  67e13dd

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• Update annotation test for new stopwords

  bgyori

  committed
  c05e872

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• Reorganize imports

  bgyori

  committed
  9fe059d

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• Adjust test for updated stopwords

  bgyori

  committed
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• Sort NERN stoplist alphabetically

  bgyori

  committed
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• Change more indentation

  bgyori

  committed
  9a725f1

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• Fix indentation

  bgyori

  committed
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• NER script derives BioIDBenchmarker class

  galileosteinberg

  committed
  99a327e

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• Fixed formatting issues

  galileosteinberg

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Commits on Jul 25, 2024

• Extended stopwords; moved stop words file to resources and logic into ner module

  galileosteinberg

  committed
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• Annotate not accepting spans <= 1, added progress bars

  galileosteinberg

  committed
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• Changes to app.py

  galileosteinberg

  committed
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• Modified to work with annotation objects

  galileosteinberg

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• Committing changes to app.py with NER class.

  galileosteinberg

  committed
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• Commit with changes to gilda evaluation logic. Returns metrics for both top matches and all matches.

  galileosteinberg

  committed
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• Make annotation return a list of scored matches

  

  bgyori

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  galileosteinberg

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• dded implementation of a stoplist for NER, set membership for for matching reference annotations, counter for most common false positives in bioid_ner_benchmark.py. Implemented a condition in the N…

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  galileosteinberg

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• Initial implementation of NER benchmark.

  galileosteinberg

  committed
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• Merge pull request #147 from gyorilab/use-coords

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Commits on Jul 24, 2024

• Update docstring

  kkaris

  committed
  4bcb4ea

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• Fix typo

  kkaris

  committed
  56c0e61

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• Use specific variables for start and end coordinates for clarity

  kkaris

  committed
  9caa293

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• Assume splitter function returns coordinates instead of sentences

  kkaris

  committed
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• Merge pull request #146 from gyorilab/ner_improve

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  bgyori

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