Datasets:
Dr. Jorge Abreu Vicente commited on
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Update README.md
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README.md
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## Dataset Description
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- **Homepage: https://microsoft.github.io/BLURB/index.html
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- **Paper: [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://arxiv.org/pdf/2007.15779.pdf)
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- **Leaderboard: https://microsoft.github.io/BLURB/leaderboard.html
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- **Point of Contact:**
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### Dataset Summary
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As before, the training set consists of a set of sentences,
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and for each sentence a set of gene mentions
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(GENE annotations).
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- **Homepage:
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- **Repository:** [NER GitHub repo by @GamalC](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/raw/master/data/)
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- **Paper:
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#### NCBI Disease
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The NCBI disease corpus is fully annotated at the mention
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and concept level to serve as a research resource for the biomedical natural
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language processing community.
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Corpus Characteristics
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* 793 PubMed abstracts
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* 6,892 disease mentions
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* 790 unique disease concepts
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* Medical Subject Headings (MeSH®)
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* Online Mendelian Inheritance in Man (OMIM®)
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* 91% of the mentions map to a single disease concept
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Corpus Annotation
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* Fourteen annotators
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* Two-annotators per document (randomly paired)
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* Three annotation phases
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* Checked for corpus-wide consistency of annotations
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- **Homepage: ** https://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/
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- **Repository:** [NER GitHub repo by @GamalC](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/raw/master/data/)
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- **Paper:
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#### JNLPBA
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The BioNLP / JNLPBA Shared Task 2004 involves the identification
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- **Paper: ** [Introduction to the Bio-entity Recognition Task at JNLPBA](https://aclanthology.org/W04-1213)
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#### EBM PICO
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- **Homepage:
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- **Repository:**
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- **Paper:
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- **Leaderboard:
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#### ChemProt
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- **Homepage:
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- **Repository:**
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- **Paper:
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#### DDI
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- **Homepage:
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- **Repository:**
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- **Paper:
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#### GAD
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- **Homepage:
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- **Repository:**
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- **Paper:
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#### BIOSSES
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- **Point of Contact:** [Gizem Soğancıoğlu](gizemsogancioglu@gmail.com) and [Arzucan Özgür](gizemsogancioglu@gmail.com)
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#### HoC
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- **Homepage:
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- **Repository:**
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- **Paper:
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- **Leaderboard:
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- **Point of Contact:**
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#### PubMedQA
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- **Homepage:
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- **Repository:**
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- **Paper:
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- **Leaderboard:
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- **Point of Contact:**
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#### BioASQ
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- **Homepage:
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- **Repository:**
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- **Paper:
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- **Leaderboard:
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- **Point of Contact:**
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### Supported Tasks and Leaderboards
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## Dataset Description
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+
- **Homepage:** https://microsoft.github.io/BLURB/index.html
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| 63 |
+
- **Paper:** [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://arxiv.org/pdf/2007.15779.pdf)
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+
- **Leaderboard:** https://microsoft.github.io/BLURB/leaderboard.html
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- **Point of Contact:**
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### Dataset Summary
|
|
|
|
| 108 |
As before, the training set consists of a set of sentences,
|
| 109 |
and for each sentence a set of gene mentions
|
| 110 |
(GENE annotations).
|
| 111 |
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- **Homepage:** https://biocreative.bioinformatics.udel.edu/tasks/biocreative-ii/task-1a-gene-mention-tagging/
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- **Repository:** [NER GitHub repo by @GamalC](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/raw/master/data/)
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- **Paper:** [verview of BioCreative II gene mention recognition](https://link.springer.com/article/10.1186/gb-2008-9-s2-s2)
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#### NCBI Disease
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|
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The NCBI disease corpus is fully annotated at the mention
|
| 118 |
and concept level to serve as a research resource for the biomedical natural
|
| 119 |
language processing community.
|
| 120 |
+
Corpus Characteristics
|
| 121 |
+
----------------------
|
| 122 |
+
* 793 PubMed abstracts
|
| 123 |
+
* 6,892 disease mentions
|
| 124 |
+
* 790 unique disease concepts
|
| 125 |
+
* Medical Subject Headings (MeSH®)
|
| 126 |
+
* Online Mendelian Inheritance in Man (OMIM®)
|
| 127 |
+
* 91% of the mentions map to a single disease concept
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+
**divided into training, developing and testing sets.
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+
Corpus Annotation
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+
* Fourteen annotators
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| 131 |
+
* Two-annotators per document (randomly paired)
|
| 132 |
+
* Three annotation phases
|
| 133 |
+
* Checked for corpus-wide consistency of annotations
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| 134 |
+
- **Homepage:** https://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/
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- **Repository:** [NER GitHub repo by @GamalC](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/raw/master/data/)
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- **Paper:** [NCBI disease corpus: a resource for disease name recognition and concept normalization](https://pubmed.ncbi.nlm.nih.gov/24393765/)
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#### JNLPBA
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The BioNLP / JNLPBA Shared Task 2004 involves the identification
|
|
|
|
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- **Paper: ** [Introduction to the Bio-entity Recognition Task at JNLPBA](https://aclanthology.org/W04-1213)
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| 149 |
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#### EBM PICO
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+
- **Homepage:**
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- **Repository:**
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| 153 |
+
- **Paper:**
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+
- **Leaderboard:**
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#### ChemProt
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+
- **Homepage:**
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- **Repository:**
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+
- **Paper:**
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#### DDI
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+
- **Homepage:**
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- **Repository:**
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+
- **Paper:**
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#### GAD
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+
- **Homepage:**
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- **Repository:**
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+
- **Paper:**
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#### BIOSSES
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- **Point of Contact:** [Gizem Soğancıoğlu](gizemsogancioglu@gmail.com) and [Arzucan Özgür](gizemsogancioglu@gmail.com)
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#### HoC
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+
- **Homepage:**
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| 188 |
- **Repository:**
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| 189 |
+
- **Paper:**
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| 190 |
+
- **Leaderboard:**
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| 191 |
- **Point of Contact:**
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#### PubMedQA
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+
- **Homepage:**
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- **Repository:**
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+
- **Paper:**
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| 198 |
+
- **Leaderboard:**
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- **Point of Contact:**
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#### BioASQ
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+
- **Homepage:**
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| 203 |
- **Repository:**
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| 204 |
+
- **Paper:**
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| 205 |
+
- **Leaderboard:**
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| 206 |
- **Point of Contact:**
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### Supported Tasks and Leaderboards
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