ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2020
PGxMine: Text mining for curation of PharmGKB.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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.
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.
Who cites it
14 citing papers in PubMed, 16 citations in OpenAlex.
- An agentic AI system for automated pharmacogenomic recommendation generation.NPJ digital medicine · 2026Article
- Pharmacotherapy Risks in Rare Genetic Diseases: Cross-Referencing ACMG Secondary Findings v3.2 List With Clinical Databases.Clinical and translational science · 2026Article
- Artificial intelligence coupled to pharmacometrics modelling to tailor malaria and tuberculosis treatment in Africa.Nature communications · 2025Article
- Pharmacogenomics Tools for Precision Public Health and Lessons for Low- and Middle-Income Countries: A Scoping Review.Pharmacogenomics and personalized medicine · 2025Review
- Genetic polymorphisms of pharmacogenomic VIP variants in the Hui population from Ningxia Province of China.Functional & integrative genomics · 2023Article
- Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study.Cell reports. Medicine · 2022Article
- Knowledge bases and software support for variant interpretation in precision oncology.Briefings in bioinformatics · 2021Article
- An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine.Clinical pharmacology and therapeutics · 2021Article
- PharmGKB, an Integrated Resource of Pharmacogenomic Knowledge.Current protocols · 2021Article
- LitSuggest: a web-based system for literature recommendation and curation using machine learning.Nucleic acids research · 2021Article
- Identifying naloxone administrations in electronic health record data using a text-mining tool.Substance abuse · 2021Article
- PharmGKB Tutorial for Pharmacogenomics of Drugs Potentially Used in the Context of COVID-19.Clinical pharmacology and therapeutics · 2021Article
- Extending TextAE for annotation of non-contiguous entities.Genomics & informatics · 2020Article
- A Novel Text-Mining Approach for Retrieving Pharmacogenomics Associations From the Literature.Frontiers in pharmacology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Precision medicine tailors treatment to individuals personal data including differences in their genome. The Pharmacogenomics Knowledgebase (PharmGKB) provides highly curated information on the effect of genetic variation on drug response and side effects for a wide range of drugs. PharmGKB's scientific curators triage, review and annotate a large number of papers each year but the task is challenging. We present the PGxMine resource, a text-mined resource of pharmacogenomic associations from all accessible published literature to assist in the curation of PharmGKB. We developed a supervised machine learning pipeline to extract associations between a variant (DNA and protein changes, star alleles and dbSNP identifiers) and a chemical. PGxMine covers 452 chemicals and 2,426 variants and contains 19,930 mentions of pharmacogenomic associations across 7,170 papers. An evaluation by PharmGKB curators found that 57 of the top 100 associations not found in PharmGKB led to 83 curatable papers and a further 24 associations would likely lead to curatable papers through citations. The results can be viewed at https://pgxmine.pharmgkb.org/ and code can be downloaded at https://github.com/jakelever/pgxmine.
Indexed as
Identifiers
31797632PMC6917032W2991516389What OpenQuestion holds
Registered trials
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.