Create README.md
Browse files
README.md
ADDED
@@ -0,0 +1,25 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
---
|
2 |
+
language:
|
3 |
+
- en
|
4 |
+
pipeline_tag: token-classification
|
5 |
+
---
|
6 |
+
|
7 |
+
Named Entity Recognition (NER) model to recognize chemical entities.
|
8 |
+
|
9 |
+
[PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:
|
10 |
+
|
11 |
+
- [Chemdner patents CEMP corpus](https://biocreative.bioinformatics.udel.edu/resources/corpora/chemdner-patents-cemp-corpus/) (train, dev, test sets)
|
12 |
+
- [DDI corpus](https://github.com/isegura/DDICorpus) (train, dev, test sets): entity types "GROUP", "DRUG", "DRUG_N"
|
13 |
+
- [GREC Corpus](http://www.nactem.ac.uk/GREC/standoff.php) (train, dev, test sets): entity type "organic_compounds"
|
14 |
+
- [MLEE](http://nactem.ac.uk/MLEE/) (train, dev, test sets): entity type "Drug or compound"
|
15 |
+
- [NLM-CHEM](https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem/) (train, dev, test sets)
|
16 |
+
- [CHEMDNER](https://biocreative.bioinformatics.udel.edu/resources/) (train, dev, test sets)
|
17 |
+
- [Chebi Corpus](http://www.nactem.ac.uk/chebi/) (train, dev, test sets): entity types "Metabolite", "Chemical"
|
18 |
+
- [PHAEDRA](http://www.nactem.ac.uk/PHAEDRA/) (train, dev, test sets): entity type "Pharmalogical_substance"
|
19 |
+
- [Chemprot](https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vi/track-5/) (train, dev, test sets)
|
20 |
+
- [PGx Corpus](https://github.com/practikpharma/PGxCorpus) (train, dev, test sets): entity type "Chemical"
|
21 |
+
- [BioNLP11ID](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11ID-chem-IOB) (train, dev, test sets): entity type "Chemical"
|
22 |
+
- [BioNLP13CG]() (train, dev, test sets): entity type "Chemical"
|
23 |
+
- [BC4CHEMD](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BC4CHEMD) (train, dev, test sets)
|
24 |
+
- [CRAFT corpus](https://github.com/UCDenver-ccp/CRAFT/tree/master/concept-annotation) (train, dev, test sets): entity type "ChEBI"
|
25 |
+
- [BC5CDR]() (train, dev, test sets): entity type "Chemical"
|