ArticleDatabase : the journal of biological databases and curation2019
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- Semantic alignment of the German Human Genome-Phenome Archive metadata model in Europe's genomics field.Scientific data · 2026Article
- Integrating network toxicology, machine learning, and molecular dynamics simulations to reveal tanshinone iia's dual mechanisms in TNBC and doxorubicin-induced cardiotoxicity.Scientific reports · 2026Article
- Article
- How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO.Briefings in bioinformatics · 2025Review
- CORESH: a gene signature-based search engine for public gene expression datasets.Nucleic acids research · 2025Article
- IL-1β and CXCR4 as Potential Therapeutic Targets for Alzheimer's Disease.Combinatorial chemistry & high throughput screening · 2025Article
- Novel perceptions of the involvement of CPZ in gastric cancer prognosis and immunomodulation.Frontiers in oncology · 2025Article
- Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.Computational and structural biotechnology journal · 2025Article
- RummaGEO: Automatic mining of human and mouse gene sets from GEO.Patterns (New York, N.Y.) · 2024Article
- RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO.bioRxiv : the preprint server for biology · 2024Article
- Identifying New Contributors to Brain Metastasis in Lung Adenocarcinoma: A Transcriptomic Meta-Analysis.Cancers · 2023Article
- Establishing a prediction model of severe acute mountain sickness using machine learning of support vector machine recursive feature elimination.Scientific reports · 2023Article
- GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.Bioinformatics (Oxford, England) · 2023Article
- Challenges to sharing sample metadata in computational genomics.Frontiers in genetics · 2023Article
- New Drug Development and Clinical Trial Design by Applying Genomic Information Management.Pharmaceutics · 2022Review
- GeMI: interactive interface for transformer-based Genomic Metadata Integration.Database : the journal of biological databases and curation · 2022Article
- Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis.Scientific reports · 2021Article
- The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins.BMC genomics · 2021Article
- A Novel miRNA-mRNA Axis Involves in Regulating Transcriptional Disorders in Pancreatic Adenocarcinoma.Cancer management and research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Motivation: Gene Expression Omnibus (GEO) and other publicly available data store their metadata in the format of unstructured English text, which is very difficult for automated reuse. Results: We employed text mining techniques to analyze the metadata of GEO and developed Restructured GEO database (ReGEO). ReGEO reorganizes and categorizes GEO series and makes them searchable by two new attributes extracted automatically from each series' metadata. These attributes are the number of time points tested in the experiment and the disease being investigated. ReGEO also makes series searchable by other attributes available in GEO, such as platform organism, experiment type, associated PubMed ID as well as general keywords in the study's description. Our approach greatly expands the usability of GEO data, demonstrating a credible approach to improve the utility of vast amount of publicly available data in the era of Big Data research.
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.