Dataset Card for [Dataset Name]

Dataset Summary

NLM produces a baseline set of MEDLINE/PubMed citation records in XML format for download on an annual basis. The annual baseline is released in December of each year. Each day, NLM produces update files that include new, revised and deleted citations. See our documentation page for more information.

Supported Tasks and Leaderboards

[More Information Needed]

Languages

  • English

Dataset Structure

Bear in mind the data comes from XML that have various tags that are hard to reflect in a concise JSON format. Tags and list are kind of non "natural" to XML documents leading this library to make some choices regarding data. "Journal" info was dropped altogether as it would have led to many fields being empty all the time.

The hierarchy is also a bit unnatural but the choice was made to keep as close as possible to the original data for future releases that may change schema from NLM's side.

Author has been kept and contains either "ForeName", "LastName", "Initials", or "CollectiveName". (All the fields will be present all the time, but only some will be filled)

Data Instances

{
    "MedlineCitation": {
        "PMID": 0,
        "DateCompleted": {"Year": 0, "Month": 0, "Day": 0},
        "NumberOfReferences": 0,
        "DateRevised": {"Year": 0, "Month": 0, "Day": 0},
        "Article": {
            "Abstract": {"AbstractText": "Some abstract (can be missing)" },
            "ArticleTitle": "Article title",
            "AuthorList": {"Author": [
                {"FirstName": "John", "ForeName": "Doe", "Initials": "JD", "CollectiveName": ""}
                {"CollectiveName": "The Manhattan Project", "FirstName": "", "ForeName": "", "Initials": ""}
            ]},
            "Language": "en",
            "GrantList": {
                "Grant": [],
            },
            "PublicationTypeList": {"PublicationType": []},
        },
        "MedlineJournalInfo": {"Country": "France"},
        "ChemicalList": {"Chemical": [{
            "RegistryNumber": "XX",
            "NameOfSubstance": "Methanol"
        }]},
        "CitationSubset": "AIM",
        "MeshHeadingList": {
            "MeshHeading": [],
        },
    },
    "PubmedData": {
        "ArticleIdList": {"ArticleId": "10.1002/bjs.1800650203"},
        "PublicationStatus": "ppublish",
        "History": {"PubMedPubDate": [{"Year": 0, "Month": 0, "Day": 0}]},
        "ReferenceList": [{"Citation": "Somejournal", "CitationId": 01}],
    },
}

Data Fields

Main Fields will probably interest people are:

  • "MedlineCitation" > "Article" > "AuthorList" > "Author"
  • "MedlineCitation" > "Article" > "Abstract" > "AbstractText"
  • "MedlineCitation" > "Article" > "Article Title"
  • "MedlineCitation" > "ChemicalList" > "Chemical"
  • "MedlineCitation" > "NumberOfReferences"

Data Splits

There are no splits in this dataset. It is given as is.

Dataset Creation

Curation Rationale

[More Information Needed]

Source Data

Initial Data Collection and Normalization

https://www.nlm.nih.gov/databases/download/pubmed_medline_faq.html

Who are the source language producers?

[More Information Needed]

Annotations

Annotation process

[More Information Needed]

Who are the annotators?

[More Information Needed]

Personal and Sensitive Information

[More Information Needed]

Considerations for Using the Data

Social Impact of Dataset

[More Information Needed]

Discussion of Biases

[More Information Needed]

Other Known Limitations

[More Information Needed]

Additional Information

Dataset Curators

[More Information Needed]

Licensing Information

https://www.nlm.nih.gov/databases/download/terms_and_conditions.html

Citation Information

[More Information Needed]

Contributions

Thanks to @Narsil for adding this dataset.

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Homepage:
https://www.nlm.nih.gov/databases/download/pubmed_medline.html
Documentation:
https://www.nlm.nih.gov/databases/download/pubmed_medline_documentation.html
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Models trained or fine-tuned on pubmed