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.
September 2024 Our paper "Overview of BioNNE Task on Biomedical Nested Named Entity Recognition at BioASQ 2024" has been published at CLEF 2024.
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},
}
Our papers on entity linking annotations and BioNNE shared task:
@CONFERENCE{Loukachevitch20242383,
author = {Loukachevitch, Natalia and Sakhovskiy, Andrey and Tutubalina, Elena},
title = {Biomedical Concept Normalization over Nested Entities with Partial UMLS Terminology in Russian},
year = {2024},
journal = {2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation, LREC-COLING 2024 - Main Conference Proceedings},
pages = {2383 – 2389},
}
@CONFERENCE{Davydova202428,
author = {Davydova, Vera and Loukachevitch, Natalia and Tutubalina, Elena},
title = {Overview of BioNNE Task on Biomedical Nested Named Entity Recognition at BioASQ 2024},
year = {2024},
journal = {CEUR Workshop Proceedings},
volume = {3740},
pages = {28 – 34}
}
@ARTICLE{Nentidis2024490,
author = {Nentidis, Anastasios and Krithara, Anastasia and Paliouras, Georgios and Krallinger, Martin and Sanchez, Luis Gasco and Lima, Salvador and Farre, Eulalia and Loukachevitch, Natalia and Davydova, Vera and Tutubalina, Elena},
title = {BioASQ at CLEF2024: The Twelfth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge},
year = {2024},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
volume = {14612 LNCS},
pages = {490 – 497},
doi = {10.1007/978-3-031-56069-9_67}
}