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).

• pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

  PMID 31114675 · PMC6505635 · F1000Research · 2019 · 6 claims · 7 setups

  Has reproduction · 90

  pysradb provides a simple, user-friendly command-line interface for querying metadata and downloading datasets from SRA without requiring knowledge of a programming language.

  sra geo metadata assay-type accession

• poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

  PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data

  porecov sars-cov-2 nanopore fastq gisaid workflow real-world

• GeMI: interactive interface for transformer-based Genomic Metadata Integration.

  PMID 35657113 · PMC9216561 · Database : the journal of biological databases and curation · 2022 · 8 claims · 5 setups

  Has reproduction · 64

  GeMI is a web tool that uses a fine-tuned GPT2 model to extract 15 structured key-value attributes from free-text GEO sample metadata.

  cistrome encode geo fine-tuned manual batch transformer-based

• The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

  PMID 19914934 · PMC2808860 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  GOLD is a comprehensive, centralized resource for tracking genome and metagenome sequencing projects and their associated metadata worldwide.

  bacteria archaea eukarya environmental genome metagenome metadata

• StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

  PMID 24627795 · PMC3938176 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 43

  StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, backed by an SQL (MySQL) database with Perl and Java APIs.

  fastq mysql perl java fastqc relational programmatic

• A metadata approach for clinical data management in translational genomics studies in breast cancer.

  PMID 19948017 · PMC3225860 · BMC medical genomics · 2009 · 8 claims · 5 setups

  Full-text index only

  A metadata/CDE-based approach using CancerGrid's semantic web tools enables automatic integration of heterogeneous clinical datasets without loss of original detail

  clinical breast metadata estrogen her2

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• All of gene expression (AOE): An integrated index for public gene expression databases.

  PMID 31978081 · PMC6980531 · PloS one · 2020 · 8 claims · 5 setups

  Has reproduction

  AOE integrates publicly available gene expression data from GEO, ArrayExpress, and GEA into a single searchable index.

  ebi ncbi sequence arrayexpress metadata cross-database visualization

• The archives are half-empty: an assessment of the availability of microbial community sequencing data.

  PMID 32859925 · PMC7455719 · Communications biology · 2020 · 8 claims · 5 setups

  Has reproduction · 95

  More than half of surveyed amplicon sequencing studies were affected by lack of data deposition, improper file formatting, or inconsistent labeling that impede reuse.

  microbiology randomly insdc v3-v4 literature manual repository

• The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.

  PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups

  Has reproduction · 90

  The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application

  tuberculosis outlier whole-genome maximum-likelihood read

• Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.

  PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups

  Has reproduction · 91

  73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3

  monocytogenes isolate whole-genome core minimum

• TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

  PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 43

  TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

  mdr-tb paired-end raw bam whole-genome kraken raw

• Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.

  PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.

  rhizosphere nematode wtex wolbachia metagenomic pcr comparative

• A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

  PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids

  coli st58 novo draft whole-genome pan-genome-wide plasmid

• Current status of use of high throughput nucleotide sequencing in rheumatology.

  PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 4 setups

  Has reproduction · 83

  RNA-Seq is the most represented HTS assay in rheumatology research (n=457, 65%), used for biomarker identification in blood or synovial tissue

  pubmed sequence icd-11 sle semiautomated sequencing disease-name