Datasets:
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:
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
config_name: '2021'
splits:
- name: train
num_bytes: 46372156591
num_examples: 31850051
download_size: 32882348650
dataset_size: 46372156591
Dataset Card for PubMed
Table of Contents
- Dataset Description
- Dataset Structure
- Dataset Creation
- Considerations for Using the Data
- Additional Information
Dataset Description
- Homepage: : https://www.nlm.nih.gov/databases/download/pubmed_medline.html
- Documentation: : https://www.nlm.nih.gov/databases/download/pubmed_medline_documentation.html
- Repository:
- Paper:
- Leaderboard:
- Point of Contact:
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
Courtesy of the U.S. National Library of Medicine.
Contributions
Thanks to @Narsil for adding this dataset.