Hugging Face's logo

Datasets:
ncbi
/
pubmed

Tasks:
Text Generation
Fill-Mask
Text Classification
Sub-tasks:
language-modeling
masked-language-modeling
text-scoring
Languages:
English
Size:
10M<n<100M
Tags:
citation-estimation
License:
Dataset card Files Community
12
pubmed / README.md
albertvillanova's picture
albertvillanova HF staff
Update 2024 annual baseline data URLs (#11)
8263182 verified
preview code
|
raw
history blame
12.5 kB
metadata
annotations_creators:
  - crowdsourced
language_creators:
  - crowdsourced
language:
  - en
license:
  - other
multilinguality:
  - monolingual
size_categories:
  - 10M<n<100M
source_datasets:
  - original
task_categories:
  - text-generation
  - fill-mask
  - text-classification
task_ids:
  - language-modeling
  - masked-language-modeling
  - text-scoring
  - topic-classification
paperswithcode_id: pubmed
pretty_name: PubMed
tags:
  - citation-estimation
dataset_info:
  - config_name: '2024'
    features:
      - name: MedlineCitation
        struct:
          - name: PMID
            dtype: int32
          - name: DateCompleted
            struct:
              - name: Year
                dtype: int32
              - name: Month
                dtype: int32
              - name: Day
                dtype: int32
          - name: NumberOfReferences
            dtype: int32
          - name: DateRevised
            struct:
              - name: Year
                dtype: int32
              - name: Month
                dtype: int32
              - name: Day
                dtype: int32
          - name: Article
            struct:
              - name: Abstract
                struct:
                  - name: AbstractText
                    dtype: string
              - name: ArticleTitle
                dtype: string
              - name: AuthorList
                struct:
                  - name: Author
                    sequence:
                      - name: LastName
                        dtype: string
                      - name: ForeName
                        dtype: string
                      - name: Initials
                        dtype: string
                      - name: CollectiveName
                        dtype: string
              - name: Language
                dtype: string
              - name: GrantList
                struct:
                  - name: Grant
                    sequence:
                      - name: GrantID
                        dtype: string
                      - name: Agency
                        dtype: string
                      - name: Country
                        dtype: string
              - name: PublicationTypeList
                struct:
                  - name: PublicationType
                    sequence: string
          - name: MedlineJournalInfo
            struct:
              - name: Country
                dtype: string
          - name: ChemicalList
            struct:
              - name: Chemical
                sequence:
                  - name: RegistryNumber
                    dtype: string
                  - name: NameOfSubstance
                    dtype: string
          - name: CitationSubset
            dtype: string
          - name: MeshHeadingList
            struct:
              - name: MeshHeading
                sequence:
                  - name: DescriptorName
                    dtype: string
                  - name: QualifierName
                    dtype: string
      - name: PubmedData
        struct:
          - name: ArticleIdList
            sequence:
              - name: ArticleId
                sequence: string
          - name: PublicationStatus
            dtype: string
          - name: History
            struct:
              - name: PubMedPubDate
                sequence:
                  - name: Year
                    dtype: int32
                  - name: Month
                    dtype: int32
                  - name: Day
                    dtype: int32
          - name: ReferenceList
            sequence:
              - name: Citation
                dtype: string
              - name: CitationId
                dtype: int32
    splits:
      - name: train
        num_bytes: 54723097181
        num_examples: 36555430
    download_size: 45202943276
    dataset_size: 54723097181

Dataset Card for PubMed

Table of Contents

Dataset Description

Dataset Summary

PubMed comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

NLM produces a baseline set of PubMed citation records in XML format for download on an annual basis. The annual baseline is released in December of each year.

  • Last Updated December 15, 2023

Each day, NLM produces update files that include new, revised, and deleted citations.

Source: https://ftp.ncbi.nlm.nih.gov/pubmed/README.txt

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

The use of "Medline" in an element name does not mean the record represents a citation from a MEDLINE-selected journal. When the NLM DTDs and XML elements were first created, MEDLINE records were the only data exported. Now NLM exports citations other than MEDLINE records. To minimize unnecessary disruption to users of the data, NLM has retained the original element names (e.g., MedlineCitation, MedlineJournalInfo, MedlineTA).

Policies affecting data creation have evolved over the years. Some PubMed records are added or revised well after the cited article was first published. In these cases, on occasion an element that had not yet been created when the article was published may appear on the record. For example, the Abstract element was not created until 1975, but some records published before 1975 but added to PubMed after 1975 contain . It is also possible that an element may be treated differently from the way it would have been treated had the record been created or maintained near the time the article was published. For example, the number of occurrences can diverge from the policies stated in the NLM author indexing policy (https://pubmed.ncbi.nlm.nih.gov/help/#author-indexing-policy). Lastly, as of October 2016, the publisher of the original article has the capability to edit the PubMed record’s citation data, with the exception of MeSH data, using the PubMed Data Management system. PubMed record data for older citations, therefore, may contain data for elements that didn’t exist when the citation was created.

Source Data

Initial Data Collection and Normalization

[More Information Needed]

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

National Library of Medicine Terms and Conditions

Downloading PubMed data from the National Library of Medicine FTP servers indicates your acceptance of the following Terms and Conditions. No charges, usage fees or royalties are paid to NLM for these data.

PubMed Specific Terms:

NLM freely provides PubMed data. Please note some abstracts may be protected by copyright.

General Terms and Conditions

Users of the data agree to:

  • acknowledge NLM as the source of the data in a clear and conspicuous manner,
  • NOT use the PubMed wordmark or the PubMed logo in association or in connection with user's or any other party's product or service.
  • NOT adopt, use, or seek to register any mark or trade name confusingly similar to or suggestive of the PubMed wordmark or PubMed logo
  • NOT to indicate or imply that NLM/NIH/HHS has endorsed its products/services/applications.

Users who republish or redistribute the data (services, products or raw data) agree to:

  • maintain the most current version of all distributed data, or
  • make known in a clear and conspicuous manner that the products/services/applications do not reflect the most current/accurate data available from NLM.

These data are produced with a reasonable standard of care, but NLM makes no warranties express or implied, including no warranty of merchantability or fitness for particular purpose, regarding the accuracy or completeness of the data. Users agree to hold NLM and the U.S. Government harmless from any liability resulting from errors in the data. NLM disclaims any liability for any consequences due to use, misuse, or interpretation of information contained or not contained in the data.

NLM does not provide legal advice regarding copyright, fair use, or other aspects of intellectual property rights. See the NLM Copyright page: https://www.nlm.nih.gov/web_policies.html#copyright

NLM reserves the right to change the type and format of its machine-readable data. NLM will take reasonable steps to inform users of any changes to the format of the data before the data are distributed via the announcement section or subscription to email and RSS updates.

The PubMed wordmark and the PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

Citation Information

Courtesy of the U.S. National Library of Medicine.

Contributions

Thanks to @Narsil for adding this dataset.