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).

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• Using prototyping to choose a bioinformatics workflow management system.

  PMID 33630841 · PMC7906312 · PLoS computational biology · 2021 · 7 claims · 6 setups

  Has reproduction

  Prototyping a subset of the RiboViz workflow in each candidate system gives more insight into suitability, ease of use, and documentation quality than reading documentation or working through developer tutorials alone

  workflow snakemake cwltool toil web repository prototype

• Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

  PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

  Has reproduction · 92

  Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

  post-mortem adra immunohistochemistry protein-protein pathway

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

  Full-text index only

  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

  Full-text index only

  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

  PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

  Full-text index only

  Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

  huge pdgene snps3d dbsnp curated comparative snp

• Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

  PMID 18782832 · PMC2686584 · Nucleic acids research · 2009 · 8 claims · 5 setups

  Full-text index only

  CTD is a manually curated knowledgebase that integrates chemical-gene interactions, chemical-disease relationships, and gene-disease relationships into a chemical-gene-disease triad

  pubmed ctd manual computational case-study

• SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

  PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

  scientific pubmed cyp-drug cyp text mutation manual

• Blazing a trail: a public health research agenda in genomics and chronic disease.

  PMID 15888215 · PMC1327698 · Preventing chronic disease · 2005 · 8 claims · 1 setups

  Full-text index only

  Public health scientists must be trailblazers in genomics research now, rather than waiting and being relegated to translators of technologies poorly suited to populations

  articles bibliometric

• COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

  PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

  cancer tumour manual semi-automated candidate

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• The asthma consultative process: a collaborative approach to integrating genomics into public health practice.

  PMID 15888238 · PMC1327721 · Preventing chronic disease · 2005 · 6 claims · 4 setups

  Full-text index only

  A collaborative process combining literature review, expert working group input, and professional/community consultations can synthesize asthma genomics knowledge for public health practice.

  professionals community scientific key group literature

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

  PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

  Full-text index only

  mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

  nonredundant database high-throughput homology

• INTERFEROME: the database of interferon regulated genes.

  PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

  Full-text index only

  INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

  chimp ifn-treated tissues irg microarray in-house basal

• BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

  PMID 17202167 · PMC1899097 · Nucleic acids research · 2007 · 7 claims · 6 setups

  Full-text index only

  BRENDA is the largest publicly available enzyme information system worldwide, manually curated from primary literature and covering all identified enzymes regardless of source.

  pubmed randomly enzyme full text-mining manual transmembrane

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

  Full-text index only

  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

  PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

  Full-text index only

  SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

  msi-h aggregated genome mnr sigmoid genome-wide

• 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

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive