Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 9

System / cell line: selected ✕ Assay: text-mining ✕ Clear

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

biomedical refseq training independent text-mining data-mining candidate
CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

PMID 15796777 · PMC1274267 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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CGMIM is a Perl program that text-mines OMIM entries to identify cancer-gene associations and genetically-related cancer type pairs.

omim automated manual
The archives are half-empty: an assessment of the availability of microbial community sequencing data.

PMID 32859925 · PMC7455719 · Communications biology · 2020 · 8 claims · 5 setups

Has reproduction · 95

More than half of surveyed amplicon sequencing studies were affected by lack of data deposition, improper file formatting, or inconsistent labeling that impede reuse.

microbiology randomly insdc v3-v4 literature manual repository
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

PMID 17202167 · PMC1899097 · Nucleic acids research · 2007 · 7 claims · 6 setups

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BRENDA is the largest publicly available enzyme information system worldwide, manually curated from primary literature and covering all identified enzymes regardless of source.

pubmed randomly enzyme full text-mining manual transmembrane
Extraction of human kinase mutations from literature, databases and genotyping studies.

PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

pubmed large labeled swissprot literature supervised comparative
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

pubmed genes same randomly geneseeker evoc disease
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

The archives are half-empty: an assessment of the availability of microbial community sequencing data.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

Extraction of human kinase mutations from literature, databases and genotyping studies.

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.