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Add Biomedical NER data sets #1513

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24 tasks done
leonweber opened this issue Apr 6, 2020 · 1 comment
Closed
24 tasks done

Add Biomedical NER data sets #1513

leonweber opened this issue Apr 6, 2020 · 1 comment
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@leonweber @yetinam @mariosaenger
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@leonweber
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leonweber commented Apr 6, 2020 •
edited by yetinam
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This issue tracks the progress of integrating the HUNER data – a collection of 34 biomedical NER data sets – into flair.

  • BioCreative 2 Gene Mention
  • BioInfer
  • Biosemantics
  • CDR
  • CellFinder
  • CEMP
  • CHEBI
  • CHEMDNER
  • CLL
  • DECA
  • FSU-PRGE
  • GELLUS
  • GPRO
  • IEPA
  • JNLPBA
  • Linneaus
  • Loctext
  • miRNA
  • NCBI disease
  • OSIRIS
  • S800
  • SCAI chemicals
  • SCAI disease
  • Variome
@leonweber leonweber added the feature A new feature label Apr 6, 2020
leonweber added a commit that referenced this issue Apr 6, 2020
@leonweber
GH-1513: Add BioInfer
e1a1aa3
mariosaenger pushed a commit that referenced this issue Apr 6, 2020
GH-1513: Add JNLPBA
feec3bc
leonweber added a commit that referenced this issue Apr 7, 2020
@leonweber
GH-1513: Add CellFinder
3d34e94
mariosaenger pushed a commit that referenced this issue Apr 7, 2020
GH-1513: Refactor JNLPBA corpus integration
7f45fa7
mariosaenger pushed a commit that referenced this issue Apr 7, 2020
GH-1513: Add handling of nested and overlapping entities
825b2d9
mariosaenger pushed a commit that referenced this issue Apr 7, 2020
GH-1513: Add miRNA
180dfcd
mariosaenger pushed a commit that referenced this issue Apr 8, 2020
GH-1513: Add CLL
585b9e3
leonweber added a commit that referenced this issue Apr 8, 2020
@leonweber
GH-1513: Use linear instead of quadratic check for entity-token overlap
515ef30
mariosaenger pushed a commit that referenced this issue Apr 8, 2020
GH-1513: Add Gellus
ebd7023
mariosaenger pushed a commit that referenced this issue Apr 8, 2020
Merge branch 'GH-1513-huner' of github.com:flairNLP/flair into GH-1513-…
5123659 
…huner
mariosaenger pushed a commit that referenced this issue Apr 9, 2020
GH-1513: Add LocText and fix CoNLLWriter
35c2772
leonweber added a commit that referenced this issue Apr 9, 2020
@leonweber
GH-1513: Map corpora-specific tags to canonical tags
46714d0
leonweber added a commit that referenced this issue Apr 10, 2020
@leonweber
GH-1513: Add CHEMDNER
7e2655e
leonweber added a commit that referenced this issue Apr 10, 2020
@leonweber
GH-1513: Add IEPA
98f5a3a
leonweber added a commit that referenced this issue Apr 10, 2020
@leonweber
GH-1513: Rename protein to gene for consistency with HUNER paper
77ecdb3
mariosaenger pushed a commit that referenced this issue Apr 11, 2020
GH-1513: Add LINNEAUS
04271cb
leonweber added a commit that referenced this issue Apr 11, 2020
@leonweber
GH-1513: Add CDR
fbdaf5d
leonweber added a commit that referenced this issue Apr 11, 2020
@leonweber
Merge remote-tracking branch 'origin/GH-1513-huner' into GH-1513-huner
9d1637e 
# Conflicts:
#	flair/datasets/biomedical.py
leonweber added a commit that referenced this issue Apr 11, 2020
@leonweber
GH-1513: Add Variome
0708523
leonweber added a commit that referenced this issue Apr 11, 2020
@leonweber
GH-1513: Add Progress bars for biocreative reading and conll writing
8ea1346
mariosaenger pushed a commit that referenced this issue Apr 13, 2020
GH-1513: Add NCBI disease
a58f805
mariosaenger pushed a commit that referenced this issue Apr 14, 2020
GH-1513: Add OSIRIS
cfad680
leonweber added a commit that referenced this issue Apr 14, 2020
@leonweber
GH-1513: Add S800
bb6dfdd
leonweber added a commit that referenced this issue Apr 15, 2020
@leonweber
GH-1513: Split entities spanning sentence boundaries
42893bb
mariosaenger pushed a commit that referenced this issue Apr 16, 2020
GH-1513: Add GPRO
8cef031
mariosaenger pushed a commit that referenced this issue Apr 16, 2020
GH-1513: Add DECA
d9e611e
mariosaenger pushed a commit that referenced this issue Jul 13, 2020
GH-1513: Fix imports
3120b31
mariosaenger pushed a commit that referenced this issue Jul 13, 2020
GH-1513: Clean up BIONLP13 corpora implementation
a17b511
mariosaenger pushed a commit that referenced this issue Jul 13, 2020
GH-1513: Fix imports within test_datasets_biomedical.py
f14ae9e
mariosaenger pushed a commit that referenced this issue Jul 15, 2020
GH-1513: Remove default default tokenizer of SpacySentenceSplitter to…
ce59f69 
… constructor body
mariosaenger pushed a commit that referenced this issue Jul 15, 2020
GH-1513: Revise sentence splitter api (rename classes, add SegtokSent…
e9e386a 
…ence Splitter, add tests)
mariosaenger pushed a commit that referenced this issue Jul 15, 2020
GH-1513: Add comments to the BioBERT corpora
a7e3b5b
mariosaenger pushed a commit that referenced this issue Jul 16, 2020
GH-1513: Revise sentence splitting API and add start_pos attribute to…
2b1bf1e 
… Sentence class
mariosaenger pushed a commit that referenced this issue Jul 16, 2020
GH-1513: Expose all biomedical data sets
be945a1
mariosaenger pushed a commit that referenced this issue Aug 3, 2020
GH-1513: Add convenience classes to access all HUNER corpora for a sp…
3152b1b 
…ecific entity type
mariosaenger pushed a commit that referenced this issue Aug 3, 2020
GH-1513: Add first version of documentation
d34e3a5
leonweber added a commit that referenced this issue Aug 3, 2020
@leonweber
GH-1513: Add HunFlair models to model map
6fb7aca
leonweber added a commit that referenced this issue Aug 3, 2020
@leonweber
Merge remote-tracking branch 'origin/GH-1513-huner' into GH-1513-huner
8c99163
leonweber added a commit that referenced this issue Aug 3, 2020
@leonweber
Merge branch 'master' into GH-1513-huner
889e086 
# Conflicts:
#	flair/models/sequence_tagger_model.py
alanakbik added a commit that referenced this issue Aug 4, 2020
@alanakbik
Merge branch 'master' into GH-1513-huner
a4deb81
mariosaenger pushed a commit that referenced this issue Aug 4, 2020
GH-1513: Fix documentation
de38dd2
mariosaenger pushed a commit that referenced this issue Aug 4, 2020
Merge branch 'GH-1513-huner' of github.com:flairNLP/flair into GH-1513-…
a519e7f 
…huner
leonweber added a commit that referenced this issue Aug 5, 2020
@leonweber
GH-1513: Update HUNER_* Corpora
1d6ecc4
mariosaenger pushed a commit that referenced this issue Aug 5, 2020
GH-1513: Support custom sentence splitters for HUNER_* corpora and ad…
5b1c0d6 
…d warning if spacy isn't loaded while using HunFlair
mariosaenger pushed a commit that referenced this issue Aug 5, 2020
Merge branch 'GH-1513-huner' of github.com:flairNLP/flair into GH-1513-…
49528f5 
…huner
mariosaenger pushed a commit that referenced this issue Aug 5, 2020
GH-1513: Revise error message if scispacy isn't installed.
8bbcd30
mariosaenger pushed a commit that referenced this issue Aug 6, 2020
GH-1513: Enable users to set different tokenizers for an sentence spl…
ddc7f95 
…itter
leonweber added a commit that referenced this issue Aug 10, 2020
@leonweber
GH-1513: Fix wrong tag for HUNER_SPECIES_CRAFT_V4
c608aab
leonweber added a commit that referenced this issue Aug 10, 2020
@leonweber
Merge remote-tracking branch 'origin/GH-1513-huner' into GH-1513-huner
55b25a3
alanakbik added a commit that referenced this issue Aug 12, 2020
@alanakbik
GH-1513: add full biomed models
6cb8fca
alanakbik added a commit that referenced this issue Aug 12, 2020
@alanakbik
GH-1513: add full biomed models
87565f9
alanakbik added a commit that referenced this issue Aug 12, 2020
@alanakbik
Merge pull request #1790 from flairNLP/GH-1513-huner
e0b3320 
Gh 1513 huner
@alanakbik
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Biomedical datasets and models added in #1790 - thanks @mariosaenger and @leonweber!

leonweber added a commit that referenced this issue Aug 17, 2020
@leonweber
GH-1513: Add page on how to reproduce paper results
b5fb757
leonweber added a commit that referenced this issue Aug 17, 2020
@leonweber
GH-1513: Use uploaded versions of embeddings
11b8453
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@leonweber @yetinam @alanakbik @mariosaenger