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Datasets:
ATLASBIOINFO
/
pubmed_embedding

Tasks:
Text Generation
Languages:
English
Size:
100M<n<1B
Tags:
pubmed embedding
License:
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The dataset viewer is not available for this dataset.
Cannot get the config names for the dataset.
Error code:   ConfigNamesError
Exception:    DataFilesNotFoundError
Message:      No (supported) data files found in ATLASBIOINFO/pubmed_embedding
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 73, in compute_config_names_response
                  config_names = get_dataset_config_names(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 347, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1904, in dataset_module_factory
                  raise e1 from None
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1885, in dataset_module_factory
                  return HubDatasetModuleFactoryWithoutScript(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1270, in get_module
                  module_name, default_builder_kwargs = infer_module_for_data_files(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 597, in infer_module_for_data_files
                  raise DataFilesNotFoundError("No (supported) data files found" + (f" in {path}" if path else ""))
              datasets.exceptions.DataFilesNotFoundError: No (supported) data files found in ATLASBIOINFO/pubmed_embedding

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PubMed Embeddings Dataset

This dataset contains embeddings generated from the PubMed dataset, which can be found at https://huggingface.co/datasets/ncbi/pubmed. The embeddings were created using the NeuML/pubmedbert-base-embedding model.

Dataset Structure

Each line in the dataset represents a single embedding in the form of a list. The format for each entry is defined as follows:

node.id_ = f"node-{tpubmed}-{idx}"
node.metadata["title"] = ttitle
node.metadata["author"] = firstAuthor
node.metadata["pubmed"] = tpubmed
node.metadata["date"] = tdate
node.metadata["key"] = tpubmed
node.metadata["source"] = "Pubmed"
  • node.id_: A unique identifier for each node, formatted as node-{tpubmed}-{idx}, where tpubmed is the PubMed ID and idx is the index of the entry.
  • node.metadata["title"]: The title of the PubMed article.
  • node.metadata["author"]: The first author of the PubMed article.
  • node.metadata["pubmed"]: The PubMed ID of the article.
  • node.metadata["date"]: The publication date of the article.
  • node.metadata["key"]: The PubMed ID of the article (same as node.metadata["pubmed"]).
  • node.metadata["source"]: The source of the data, which is always "Pubmed".

Usage

To use this dataset, you can load it into your preferred data processing library or tool. Each line in the dataset represents a single embedding, and the metadata associated with each embedding can be accessed using the keys defined in the format above.

Original Data Source

The original data used to create these embeddings can be found at https://huggingface.co/datasets/ncbi/pubmed. Please refer to the documentation and license of the original dataset for more information on its contents and usage.

Embedding Model

The embeddings in this dataset were generated using the NeuML/pubmedbert-base-embedding model. For more information on the model and its performance, please refer to the model's documentation.

This dataset card aims to be a base template for new datasets. It has been generated using this raw template.

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