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).

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

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

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

  Full-text index only

  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

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

  PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

  pubmed ucsc laser-captured literature genome comparative

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

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

  Full-text index only

  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

• WebGestalt: an integrated system for exploring gene sets in various biological contexts.

  PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

  genes gene est-based enrichment kegg

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

  Full-text index only

  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence