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).

• PubMatrix: a tool for multiplex literature mining.

  PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups

  Full-text index only

  PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts

  pubmed ovarian genome literature cdna

• Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).

  PMID 32463383 · PMC7734503 · Journal of integrative bioinformatics · 2020 · 7 claims · 4 setups

  Has reproduction · 78

  Public fungal metabarcoding raw DNA data and their associated environmental metadata in sequence archives are heterogeneously annotated and lack a uniform processing pipeline, preventing large-scale biodiversity/distribution assessments.

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• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

  Full-text index only

  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

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

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

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  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

• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

  PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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  Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

  pubmed genes same randomly geneseeker evoc disease

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature

• KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.

  PMID 36430895 · PMC9694301 · International journal of molecular sciences · 2022 · 8 claims · 6 setups

  Has reproduction · 57

  KARAJ automates end-to-end querying and downloading of genomic/transcriptomic sequence data from a list of PMCIDs, URLs, or accession numbers

  fastq gse126379 research sequence download parallel literature

• Linking disease-associated genes to regulatory networks via promoter organization.

  PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

  orthologous eukaryotic genomatix pubmed promoter model additional

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based

• Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.

  PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue

  eoc analysis overlapping pubmed microarray kegg protein-protein

• Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

  PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups

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  Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins

  riken medline sequence manual semi-automated

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

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• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

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