Protocols (recipe cards)

One row per paper: the extracted protocol header. grounding_rate is the fraction of signaling factors whose evidence quote is a verbatim substring of the source text.

Data license: MIT · Data source: PMC Open Access + author-manuscript corpus (per-row license in the data)

4 rows where gold_candidate = "yes" and license = "CC-BY" sorted by grounding_rate descending

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Suggested facets: species, base_media, year, n_figure_confirmed, grounding_rate

organoid_type 3

source_cell_type 2

license 1

  • CC-BY · 4 ✖

gold_candidate 1

pmcid doi organoid_type species source_cell_type matrix base_media base_media_reporting first_author year journal license gold_candidate n_signaling_factors n_supplements n_figure_confirmed reagents_grounded reagents_total grounding_rate ▲ extractor passaging timeline assay_endpoints
PMC6376275 10.15252/embj.2018100300 lung Mus musculus adult_stem_cell BME Advanced DMEM/F12 reported Sachs 2019 EMBO J CC-BY yes 3 10 0 3 3 1.0 tier1_local::gemma3:12b mechanical shearing · 1:1–1:6 · 14d   luminescence
PMC6906116 10.1038/s41586-019-1289-x cerebral human iPSC Geltrex mTESR1 reported Velasco 2019 Nature CC-BY yes 4 14 0 4 4 1.0 tier1_local::gemma3:12b     single-cell RNA-seq · IHC
PMC4620584 10.1038/ncomms9715 kidney human iPSC GelTrex mTeSR1 reported Freedman 2015 Nat Commun CC-BY yes 8 9 2 6 8 0.75 tier1_local::gemma3:12b Accutase or TrypLE   KIM-1 expression · TEER · permeability
PMC4370217 10.7554/eLife.05098 lung human iPSC Matrigel mTeSR1 reported Dye 2015 eLife CC-BY yes 11 6 5 5 11 0.455 tier1_local::gemma3:12b     NKX2.1 expression · PAX8 expression

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CREATE TABLE protocols (
    pmcid TEXT PRIMARY KEY,
    doi TEXT,
    organoid_type TEXT,
    species TEXT,
    source_cell_type TEXT,
    matrix TEXT,
    base_media TEXT,
    base_media_reporting TEXT,
    first_author TEXT,
    year TEXT,
    journal TEXT,
    license TEXT,
    gold_candidate TEXT,
    n_signaling_factors INTEGER,
    n_supplements INTEGER,
    n_figure_confirmed INTEGER,
    reagents_grounded INTEGER,
    reagents_total INTEGER,
    grounding_rate REAL,
    extractor TEXT,
    passaging TEXT,
    timeline TEXT,
    assay_endpoints TEXT
);
CREATE INDEX idx_protocols_type ON protocols(organoid_type);