Evidence map›Paper›PMID 35953524›Full record

ArticleScientific data2022

The Leaf Clinical Trials Corpus: a new resource for query generation from clinical trial eligibility criteria.

Nicholas J Dobbins, Tony Mullen, Özlem Uzuner, Meliha Yetisgen

Abstract readDataset
In one paragraph

Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. LeafAI: query generator for clinical cohort discovery rivaling a human programmer.Journal of the American Medical Informatics Association : JAMIA · 2023
    Article
  8. Review
  9. Named Entity Recognition and Normalization for Alzheimer's Disease Eligibility Criteria.Proceedings. IEEE International Conference on Healthcare Informatics · 2023
    Article
  10. Text Classification of Cancer Clinical Trial Eligibility Criteria.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2023
    Article
  11. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Nicholas J DobbinsDepartment of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA, USA. ndobb@uw.edu.ORCID 0000-0002-3598-8747
Tony MullenKhoury College of Computer Science, Northeastern University, Seattle, WA, USA.ORCID 0000-0002-3717-1810
Özlem UzunerDepartment of Information Sciences and Technology, George Mason University, Fairfax, VA, USA.
Meliha YetisgenDepartment of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA, USA.

Funding

Transform Dissemination and Implementation Science in CTSA ProgramsUL1TR002319 · NCATS · UNIVERSITY OF WASHINGTON · PI John K. Amory · 2017 to 2026
$100.0M
Leveraging Unlabeled and Pseudo Data for Clinical Information ExtractionR15LM013209 · NLM · GEORGE MASON UNIVERSITY · PI UZUNER, OZLEM · 2019 to 2022
$840k
NCATS NIH HHS UL1 TR002319NLM NIH HHS R15 LM013209
6 · The paper itself

Abstract

Identifying cohorts of patients based on eligibility criteria such as medical conditions, procedures, and medication use is critical to recruitment for clinical trials. Such criteria are often most naturally described in free-text, using language familiar to clinicians and researchers. In order to identify potential participants at scale, these criteria must first be translated into queries on clinical databases, which can be labor-intensive and error-prone. Natural language processing (NLP) methods offer a potential means of such conversion into database queries automatically. However they must first be trained and evaluated using corpora which capture clinical trials criteria in sufficient detail. In this paper, we introduce the Leaf Clinical Trials (LCT) corpus, a human-annotated corpus of over 1,000 clinical trial eligibility criteria descriptions using highly granular structured labels capturing a range of biomedical phenomena. We provide details of our schema, annotation process, corpus quality, and statistics. Additionally, we present baseline information extraction results on this corpus as benchmarks for future work.

Indexed as

Clinical Trials as TopicNatural Language ProcessingPatient SelectionDatabases, FactualHumansInformation Storage and Retrieval

Identifiers

PMID35953524
PMCPMC9372145

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.