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).

• Functional classification using phylogenomic inference.

  PMID 16846248 · PMC1484587 · PLoS computational biology · 2006 · 8 claims · 1 setups

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  Functional annotation via top-hit database search transfer is used far more often in practice than phylogenomic inference, despite phylogenomic inference being more accurate.

  uniprot database

• 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