ArticleThe Plant cell2025
PlantConnectome: A knowledge graph database encompassing >71,000 plant articles.
Article in The Plant cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Cross-species transcriptomics uncovers shared responses to water deficiency in plants.The plant genome · 2026Article
- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Sustainable bioenergy manufacturing in plants.Plant communications · 2026Review
- PharaohFUN: phylogenomic analysis for plant protein history and function elucidation.Molecular biology and evolution · 2026Article
- Precision breeding in a changing climate: unlocking resilience through omics and gene editing.Functional & integrative genomics · 2026Review
- Growing connections: PlantConnectome maps molecular networks in Arabidopsis.The Plant cell · 2025Article
- Arabidopsis research in 2030: Translating the computable plant.The Plant journal : for cell and molecular biology · 2025Review
- 20 years of the Bio-Analytic Resource for Plant Biology.Nucleic acids research · 2025Article
- From text to traits: exploring the role of large language models in plant breeding.Frontiers in plant science · 2025Review
- Harnessing full-text publications for deep insights into C. elegans and Drosophila biomaps.BMC genomics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
One of the main quests in plant biology is understanding how gene products and metabolites work together to form complex networks that drive plant development and responses to environmental stimuli. However, the ever-growing volume and diversity of scientific literature make it increasingly challenging to stay current with the latest advances in functional genetics studies. Here, we tackled this challenge by deploying the text-mining capacities of large language models to process over 71,000 plant biology abstracts. Our approach presents nearly 5 million functional relationships between 2.4 million biological entities-genes or gene products, metabolites, tissues, and others-with a high accuracy of over 85%. We encapsulated these findings in the user-friendly database PlantConnectome and demonstrated its diverse utility by providing insights into gene regulatory networks, protein-protein interactions, and stress responses. We believe this innovative use of artificial intelligence (AI) in the life sciences will allow plant scientists to keep up to date with the rapidly growing corpus of scientific literature. PlantConnectome is available at https://plant.connectome.tools/.
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.