Abstract
We present a manually annotated new corpus, Species-Species Interaction (SSI), for extracting meaningful binary relations between species, in biomedical texts, at sentence level, with a focus on the gut microbiota. The corpus leverages PubTator to annotate species in full-text articles after evaluating different NER species taggers. Our first results are promising for extracting relations between species using BERT and its biomedical variants.- Anthology ID:
- 2023.bionlp-1.21
- Volume:
- The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks
- Month:
- July
- Year:
- 2023
- Address:
- Toronto, Canada
- Editors:
- Dina Demner-fushman, Sophia Ananiadou, Kevin Cohen
- Venue:
- BioNLP
- SIG:
- Publisher:
- Association for Computational Linguistics
- Note:
- Pages:
- 248–254
- Language:
- URL:
- https://aclanthology.org/2023.bionlp-1.21
- DOI:
- 10.18653/v1/2023.bionlp-1.21
- Cite (ACL):
- Oumaima El Khettari, Solen Quiniou, and Samuel Chaffron. 2023. Building a Corpus for Biomedical Relation Extraction of Species Mentions. In The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 248–254, Toronto, Canada. Association for Computational Linguistics.
- Cite (Informal):
- Building a Corpus for Biomedical Relation Extraction of Species Mentions (El Khettari et al., BioNLP 2023)
- PDF:
- https://preview.aclanthology.org/add_acl24_videos/2023.bionlp-1.21.pdf