Data · dataset · 2022
MedMentions
Listed in Hugging Face Datasets
MedMentions is a new manually annotated resource for the recognition of biomedical concepts.
Description
What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. Corpus: The MedMentions corpus consists of 4,392 papers (Titles and Abstracts) randomly selected from among papers released on PubMed in 2016, that were in the biomedical field, published in the English language, and had both a Title and an Abstract.
Annotators: We recruited a team of professional annotators with rich experience in biomedical content curation to exhaustively annotate all UMLS® (2017AA full version) entity mentions in these papers. Annotation quality: We did not collect stringent IAA (Inter-annotator agreement) data. To gain insight on the annotation quality of MedMentions, we randomly selected eight papers from the annotated corpus, containing a total of 469 concepts.
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Two biologists ('Reviewer') who did not participate in the annotation task then each reviewed four papers. The agreement between Reviewers and Annotators, an estimate of the Precision of the annotations, was 97.3%.
Links
Where it is published
- Hugging Face dataset page huggingface.co/datasets/bigbio/medmentions ↗
landing page · from Hugging Face
Documentation and papers
- arXiv:1902.09476 arxiv.org/abs/1902.09476 ↗
publication · from Hugging Face
Catalogue records · 1
- Hub API huggingface.co/api/datasets/bigbio/medmentions ↗
metadata API · from Hugging Face
Topics
- From keywords
- Computer Science & AI
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Hugging Face Datasets | bigbio/medmentions | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · Hugging Face | connector:huggingface@1.0.0 | /gated |
| concepts[field].local:field:computer-science-ai | mapping · Hugging Face | connector:huggingface@1.0.0 | |
| created_date | source · Hugging Face | connector:huggingface@1.0.0 | |
| description | source · Hugging Face | connector:huggingface@1.0.0 | /description |
| license | source · Hugging Face | connector:huggingface@1.0.0 | /tags[license:*] |
| publication_date | source · Hugging Face | connector:huggingface@1.0.0 | |
| title | source · Hugging Face | connector:huggingface@1.0.0 | /id |
| updated_date | source · Hugging Face | connector:huggingface@1.0.0 |