This project presents NEREL-BIO -- an annotation scheme and corpus of PubMed abstracts in Russian and in English. NEREL-BIO extends the general domain dataset NEREL. NEREL-BIO annotation scheme covers both general and biomedical domains making it suitable for domain transfer experiments.
March 2024 Our paper about nested entity linking has been accepted to COLING 2024. For more information and new annotations, please visit https://github.com/nerel-ds/NEREL-BIO/tree/master/nested-mcn
Ferbuary 2024 NEREL-BIO is being used as dataset for the BioNNE shared task on nested NER in English and Russian (BioASQ workshop, CLEF 2024). For more information, please visit https://github.com/nerel-ds/NEREL-BIO/tree/master/bio-nne
November 2023 
for a quick sampling of contexts with most subject-object relation mentions with just single script into
JSONL/CSV/SqLiteincluding (optional) language transfering 🔥 [Learn more ...]
April 2023 NEREL-BIO has been published in Bioinformatics.
| No. | Entity type | No. | Entity type | No. | Entity type |
|---|---|---|---|---|---|
| 1. | ACTIVITY | 14. | MEDPROC | 27. | MONEY |
| 2. | ADMINISTRATION_ROUTE | 15. | MENTALPROC | 28. | NATIONALITY |
| 3. | ANATOMY | 16. | PHYS | 29. | NUMBER |
| 4. | CHEM | 17. | SCIPROC | 30. | ORDINAL |
| 5. | DEVICE | 18. | AGE | 31. | ORGANIZATION |
| 6. | DISO | 19. | CITY | 32. | PERCENT |
| 7. | FINDING | 20. | COUNTRY | 33. | PERSON |
| 8. | FOOD | 21. | DATE | 34. | PRODUCT |
| 9. | GENE | 22. | DISTRICT | 35. | PROFESSION |
| 10. | INJURY_POISONING | 23. | EVENT | 36. | STATE_OR_PROVINCE |
| 11. | HEALTH_CARE_ACTIVITY | 24. | FAMILY | 37. | TIME |
| 12. | LABPROC | 25. | FACILITY | ||
| 13. | LIVB | 26. | LOCATION |
We release entity normalization (entity linking) annotation over nested entities, see.
Loukachevitch N., Manandhar S., Baral E., Rozhkov I., Braslavski P., Ivanov V., Batura T., Tutubalina E. NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities. Bioinformatics. 2023. Volume 39, Issue 4, btad161. https://doi.org/10.1093/bioinformatics/btad161
@article{NERELBIO,
author = {Loukachevitch, Natalia and Manandhar, Suresh and Baral, Elina and Rozhkov, Igor and Braslavski, Pavel and Ivanov, Vladimir and Batura, Tatiana and Tutubalina, Elena},
title = "{NEREL-BIO: A Dataset of Biomedical Abstracts Annotated with Nested Named Entities}",
journal = {Bioinformatics},
year = {2023},
month = {04},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btad161},
url = {https://doi.org/10.1093/bioinformatics/btad161},
note = {btad161},
}