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).

• MatchMiner: a tool for batch navigation among gene and gene product identifiers.

  PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

  Full-text index only

  MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

  nci-60 fish-mapped random batch fish-mapped cross-validation

• 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

  Full-text index only

  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

• Recent additions and improvements to the Onto-Tools.

  PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

  Full-text index only

  The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

  homo example mus functional pathway cross-database

• taxize: taxonomic search and retrieval in R.

  PMID 24555091 · PMC3901538 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 30

  taxize is an open-source R package (on CRAN) giving simple programmatic access to taxonomic data from 13 web data sources.

  package session name identifier upstream

• g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

  PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

  input 1000-bp microarray organisms functional transcription gene