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).

• MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

  PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

  Has reproduction · 50

  MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

  bovine simulated cami trimming decontamination assembly

• Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

  PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

  Full-text index only

  Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

  animals cdk encephalitozoon pfmrk comparative bayesian distance

• Bcipep: a database of B-cell epitopes.

  PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups

  Full-text index only

  Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases

  synthetic antigenic anti-peptide sequence

• Structural organization and interactions of transmembrane domains in tetraspanin proteins.

  PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

  Full-text index only

  TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

  tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence

• Information extraction from full text scientific articles: where are the keywords?

  PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

  Full-text index only

  The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

  corpus same articles keyword validation qualitative

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast