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).

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

  Full-text index only

  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

  Full-text index only

  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

  PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

  kegg 8192x8192 user-submitted species pathway zoomable sequence

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna