Multi-Tagger API
The Multi-Tagger API provides functionality to either retrieve publication type scores for
articles
from PubMed.gov by PMID, or to apply the models to articles by supplying a file
with article titles and abstracts.
Instructions for Accessing the API
This simplified web interface to the API may be used to apply the models to small sets of
articles or
to check the status of jobs:
Web
Interface to the Multi-Tagger API
Multi-Tagger File Download
We have processed all PubMed-indexed articles (written in English, containing an abstract, with at least 25 words in title+abstract). For each article, we have estimated the probability that it belongs to each of the 50 most important and the most clinically relevant publication types and study designs. Here, we provide a comprehensive dataset of PubMed articles and their predicted publication type/study design scores. (The Anne O'Tate tool's Publication Types button also allows users to view predicted publication types for articles retrieved by any query in PubMed.)
There are large files for all articles up through December 31, 2020, and yearly files going forward that are updated weekly.
All files are tab-delimited with a header row. Each row contains 50 columns, separated by tab
('\t',
ASCII 9). The first column is the PubMed article ID (PMID), followed by 49 columns for each
Publication Type and Study Design processed by our models.
Click here to download a
column
reference that includes the multi-tagger model names as well as their optimal F1
threshholds.
Model Score Files: These files contain scores between 0 and 1 for each Publication Type
and
Study Design for each article. Scores represent estimated probabilities that the article belongs
to
each of the Publication Types or Study Designs. Scores are displayed as floating point
numbers.
mt_modelscores_thru2020.tsv.gz
(all articles up to 12/31/2020, 1.4G compressed, 7.3G uncompressed)
mt_modelscores_2021-2025.tsv.gz
(full years 2021-2025, 498M compressed, 2.5G uncompressed)
mt_modelscores_2026.tsv.gz
(all articles currently available for 2026)
Model Indicator Files: These files are similar to those above, except that instead of
showing
estimated probability scores, we display 0 or 1 values.
A value of 1 indicates that the article's probability score was
above a threshold for considering the article to be each Publication Type or Study Design.
The threshold values were chosen separately for each Publication Type or Study Design,
by fixing the value that exhibited the highest F1 (balance of recall
and precision) on our training data (see Column Reference
above).
These predictions are employed in the Publication Types button in our
Anne
O'Tate search engine.
mt_modelindicators_thru2020.tsv.gz
(all articles up to 12/31/2020, 100M compressed, 2.3G uncompressed)
mt_modelindicators_2021-2025.tsv.gz
(full years 2021-2025, 33M compressed, 773M uncompressed)
mt_modelindicators_2026.tsv.gz
(all articles currently available for 2026)
Reference:
Cohen AM, Schneider J, Fu Y, McDonagh MS, Das P, Holt AW, Smalheiser NR. (2021) Fifty
Ways
to Tag your Pubtypes: Multi-Tagger, a Set of Probabilistic Publication Type and Study Design
Taggers to Support Biomedical Indexing and Evidence-Based Medicine. medRxiv. 2021 Jan 1.
2021.07.13.21260468v1.