Article

Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications

2023-10-05

Abstract excerpt

Every week thousands of biomedical research papers are published with a portion of them containing supporting tables with data about genes, transcripts, variants, and proteins. For example, supporting tables may contain differentially expressed genes and proteins from transcriptomics and proteomics assays, targets of transcription factors from ChIP-seq experiments, hits from genome-wide CRISPR screens, or genes id...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: e2c2e569-9ecd-531e-8ccd-91c56ea66ea4
DOI: 10.1101/2023.10.03.560783

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Rummagene: Mining Gene Sets from Supporting Materials of PMC PublicationsDOI 10.1101/2023.10.03.560783Read

RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEOSemantic proximity Read

BioLitMine: advanced mining of biomedical and biological literature about human genes and genes from major model organismsSemantic proximity Read

Finding Text-Supported Gene-to-Disease Co-appearances with MOPED-Digger.Semantic proximity Read

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text miningSemantic proximity Read

ReString – Automating Functional Enrichment Retrieval and Results AggregationSemantic proximity Read

PosMed: Ranking genes and bioresources based on Semantic Web Association Study.Semantic proximity Read

Capturing scientific knowledge in computable formSemantic proximity Read

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasetsSemantic proximity Read

DIAMOND2GO: A rapid Gene Ontology assignment and enrichment tool for functional genomicsSemantic proximity Read

Serial KinderMiner (SKiM) Discovers and Annotates Biomedical Knowledge Using Co-Occurrence and Transformer ModelsSemantic proximity Read

Matrisome AnalyzeR – a suite of tools to annotate and quantify ECM molecules in big datasets across organismsSemantic proximity Read

OnTheFly <sup>2.0</sup> : a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysisSemantic proximity Read