ArticleFrontiers in research metrics and analytics2021
Discovering and Summarizing Relationships Between Chemicals, Genes, Proteins, and Diseases in PubChem.
Article in Frontiers in research metrics and analytics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled 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.
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
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-ancestry analyses of Chinese and European populations reveal insights into the genetic architecture and disease implication of metabolites.Cell genomics · 2025Pooled it
- Summarizing relationships between chemicals, genes, proteins, and diseases in PubChem using analysis of their co-occurrences in patents.Journal of cheminformatics · 2025Article
- A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF.Journal of cheminformatics · 2025Article
- Database resources of the National Center for Biotechnology Information in 2025.Nucleic acids research · 2025Article
- Network pharmacology to explore the mechanism of traditional Chinese medicine in the treatment of ground glass nodules.Journal of thoracic disease · 2024Article
- Can Small Molecules Provide Clues on Disease Progression in Cerebrospinal Fluid from Mild Cognitive Impairment and Alzheimer's Disease Patients?Environmental science & technology · 2024Article
- The IUPHAR/BPS Guide to PHARMACOLOGY in 2024.Nucleic acids research · 2024Article
- The application of natural language processing for the extraction of mechanistic information in toxicology.Frontiers in toxicology · 2024Article
- Expression signature of ten small nuclear RNAs serves as novel biomarker for prognosis prediction of acute myeloid leukemia.Scientific reports · 2023Article
- Cluster-based text mining for extracting drug candidates for the prevention of COVID-19 from the biomedical literature.Journal of Taibah University Medical Sciences · 2023Article
- Osteoarthritis related epigenetic variations in miRNA expression and DNA methylation.BMC medical genomics · 2023Article
- PubChem 2023 update.Nucleic acids research · 2023Article
- Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study.Analytical and bioanalytical chemistry · 2022Article
- Molecular mechanisms defining penetrance ofMedizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2022Article
- The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials.Nucleic acids research · 2022Article
- Epigenetic Biomarkers Screening of Non-Coding RNA and DNA Methylation Based on Peripheral Blood Monocytes in Smokers.Frontiers in genetics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
The literature knowledge panels developed and implemented in PubChem are described. These help to uncover and summarize important relationships between chemicals, genes, proteins, and diseases by analyzing co-occurrences of terms in biomedical literature abstracts. Named entities in PubMed records are matched with chemical names in PubChem, disease names in Medical Subject Headings (MeSH), and gene/protein names in popular gene/protein information resources, and the most closely related entities are identified using statistical analysis and relevance-based sampling. Knowledge panels for the co-occurrence of chemical, disease, and gene/protein entities are included in PubChem Compound, Protein, and Gene pages, summarizing these in a compact form. Statistical methods for removing redundancy and estimating relevance scores are discussed, along with benefits and pitfalls of relying on automated (i.e., not human-curated) methods operating on data from multiple heterogeneous sources.
Indexed as
Identifiers
What 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.