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Nova: Medical Text Understanding Framework
📑 Paper | 🌐 Project Page | 💾 Released Resources | 📦 Repo
We release the raw data for our processed MedNotes dataset, adopted from the PubMed abstracts dataset from NCBI/NLM.
The data format for each line in the pubmed_abstracts_filtered.jsonl is as follows:
{
"abstract_text": <the original abstract text>,
"mesh_terms": <MeSH terms associated with the abstract>,
"publication_type": <type of publication>,
"pmid": <PubMed ID>,
"entities": [
{
"text": <entity text>,
"type": <entity type: DISEASE, DRUG, GENE, etc.>
},
...
],
"source": <the source of the raw data>,
"meta": <meta information about this sample>
}
Some entity annotations may be incomplete due to the automatic NER pipeline limitations.
*Note: This dataset is derived from PubMed abstracts made available by the National Library of Medicine.
License
The license for this dataset is other.
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