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).

• LMPD: LIPID MAPS proteome database.

  PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.

  uniprot kegg in-house oracle9i kegg database enzyme

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• 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

• Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 8 claims · 8 setups

  Has reproduction · 83

  Metabolite-centric reporter pathway analysis (RPAm) computes reporter metabolites and reporter pathways from transcriptome P-values by aggregating Z-scores of neighboring genes in a genome-scale metabolic network

  arabidopsis gene-metabolite-pathway tripartite microarray metabolite-centric reporter

• DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

  PMID 17576678 · PMC1933169 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  The DAVID Gene Concept uses a single-linkage method to agglomerate tens of millions of gene/protein identifiers from NCBI, PIR, UniProt and other resources into unified DAVID genes.

  gene example gene single-linkage functional