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).

• Representing and querying disease networks using graph databases.

  PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups

  Has reproduction · 77

  Graph databases are well suited for representing biological information because it is typically highly connected, semi-structured and unpredictable, unlike relational databases which require rigid schemas.

  uniprot proteins tissues asthma all-vs-all protein-protein metabolic

• Inparanoid: a comprehensive database of eukaryotic orthologs.

  PMID 15608241 · PMC540061 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  The Inparanoid algorithm identifies true ortholog clusters by seeding on reciprocal best-matching pairs, gathering inparalogs (post-speciation duplicates) while excluding outparalogs (pre-speciation duplicates)

  eukaryotic pairwise uniprot sequences whole-genome inparanoid redundancy

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

  sequences animal treefam-b lamin phylogenetic homology sequence

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• The Vertebrate Genome Annotation (Vega) database.

  PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.

  chromosomes genomic manual sequence initio

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in regions of increased calcite spicule formation in S. ciliatum, including known sclerocyte-specific biomineralization genes.

  sycon ciliatum cnidarian sponges differential go-term blastp

• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

  PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

  Full-text index only

  Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

  private disease uniprot snps database controlled sequence

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

  Full-text index only

  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding