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).

• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

  PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

  huge pdgene snps3d dbsnp curated comparative snp

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

  PMID 16034025 · PMC1179732 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Partial EC numbers are semantically ambiguous, and databases that assign a gene to all reactions sharing the same partial EC number make a faulty inference, causing systematic misannotation.

  e.coli biocyc vimss specific database comparative manual

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.

  PMID 41282419 · PMC12636342 · Computational and structural biotechnology journal · 2025 · 6 claims · 4 setups

  Has reproduction · 83

  POE is a web platform that semantically links GEO datasets and ENA records through their associated PubMed publications for literature-informed dataset retrieval

  pubmed natural-language representative semantic comparative qualitative

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

  PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

  ligand gpcr glida principal sequence gene