{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31452765", "kind": "science-record", "revision": 8, "content_hash": "sha256:db09455fac5fd6ea8cfc06497951620f0d73160971a0d74dcdc0601258a0d235", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:44:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Long non-coding RNA LINC01627 is a prognostic risk factor for epithelial ovarian cancer.", "doi": "10.3892/ol.2019.10661", "pmid": "31452765", "authors": ["Xiaoqing Shen", "Weipei Zhu"], "journal": "Oncology letters", "year": 2019, "abstract": "Ovarian malignancies are commonly diagnosed cancers of the female reproductive system. Recent studies have revealed that long non-coding RNAs (lncRNAs) can regulate a variety of oncological processes. In the present study, ovarian cancer expression datasets were searched in the GEO database using the GPL570 platform. Differential lncRNA expression between normal ovarian tissues and ovarian tumors were analyzed using the R package 'limma', and patient prognosis was accessed using the package 'survival'. Four databases, GSE14001, GSE18520, GSE38666 and GSE40595, were used for the analysis. A total of 64 lncRNAs were highly expressed and 4 were downregulated within these four databases. Prognostic analysis of the 68 lncRNAs in the four databases was performed, and revealed that the expression of long intergenic non-protein coding RNA 1627 (LINC01627) was negatively associated with patient prognosis in GSE19829 and GSE62193; there was no association between LINC01627 expression and patient's prognosis in GSE18520 or GSE63885. To investigate the proposed association between LINC01627 and patient prognosis, meta-analysis revealed that the total hazard ratio was 1.38 and the 95% confidence interval was between 1.04 and 1.83. Subgroup analysis revealed that LINC01627 may predict patient prognosis in high-grade, advanced and serous epithelial ovarian cancer, which was a risk factor for prognosis. Further assessment was performed in clinical samples and ovarian cancer cells, where the knockdown of LINC01627 inhibited the proliferative and migratory capacities of HO8910 and HEY cells. Collectively, the present results suggested that lncRNA LINC01627 may serve an oncogenic role in the development of epithelial ovarian tumors.", "claims": [{"id": "claim-method", "statement": "Where P≥0.1 and I2≤50% indicated no heterogeneity between each study, meta-analysis was performed using the fixed effect model. Where P<0.1 and I2>50% suggested heterogeneity between each study, the random effects model was used for meta-analysis, and sub-analysis was conducted to determine the source of heterogeneity.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31452765", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "Where P≥0.1 and I2≤50% indicated no heterogeneity between each study, meta-analysis was performed using the fixed effect model. Where P<0.1 and I2>50% suggested heterogeneity between each study, the random effects model was used for meta-analysis, and sub-analysis was conducted to determine the source of heterogeneity."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31452765", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31452765"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE14001"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"i_squared": "d-effect model or, when heterogeneity was present, a random-e"}, "inputs": ["data:geo:GSE14001"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31452765", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2019.10661", "sha256": "sha256:d94029e1f76d8cafcace41186fff63e2bcfeef2e711d0100bb24511b32dfab90", "bytes": 19160, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ol.2019.10661", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6704277", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14001", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14001", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14001", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM349155", "GSM350579", "GSM350582", "GSM350584", "GSM350586", "GSM350588", "GSM350600", "GSM350603", "GSM350605", "GSM350606", "GSM350607", "GSM350609", "GSM350610", "GSM350612", "GSM350613", "GSM350614", "GSM350615", "GSM350616", "GSM350617", "GSM350618", "GSM350619", "GSM351318", "GSM351320"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "PAX2: A Potential Biomarker for Low Malignant Potential Ovarian Tumors and Low-Grade Serous Ovarian Carcinomas", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE18520", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18520", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM461348", "GSM461349", "GSM461350", "GSM461351", "GSM461352", "GSM461353", "GSM461354", "GSM461355", "GSM461356", "GSM461357", "GSM461358", "GSM461359", "GSM461360", "GSM461361", "GSM461362", "GSM461363", "GSM461364", "GSM461365", "GSM461366", "GSM461367", "GSM461368", "GSM461369", "GSM461370", "GSM461371", "GSM461372", "GSM461373", "GSM461374", "GSM461375", "GSM461376", "GSM461377", "GSM461378", "GSM461379", "GSM461380", "GSM461381", "GSM461382", "GSM461383", "GSM461384", "GSM461385", "GSM461386", "GSM461387", "GSM461388", "GSM461389", "GSM461390", "GSM461391", "GSM461392", "GSM461393", "GSM461394", "GSM461395", "GSM461396", "GSM461397", "GSM461398", "GSM461399", "GSM461400", "GSM462643", "GSM462644", "GSM462645", "GSM462646", "GSM462647", "GSM462648", "GSM462649", "GSM462650", "GSM462651", "GSM462652"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Whole-genome oligonucleotide expression analysis of papillary serous ovarian adenocarcinomas", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE19829", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19829", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19829", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM495139", "GSM495140", "GSM495141", "GSM495142", "GSM495143", "GSM495144", "GSM495145", "GSM495146", "GSM495147", "GSM495148", "GSM495149", "GSM495150", "GSM495151", "GSM495152", "GSM495153", "GSM495154", "GSM495155", "GSM495156", "GSM495157", "GSM495158", "GSM495159", "GSM495160", "GSM495161", "GSM495162", "GSM495163", "GSM495164", "GSM495165", "GSM495166", "GSM495167", "GSM495168", "GSM495169", "GSM495170", "GSM495171", "GSM495172", "GSM495173", "GSM495174", "GSM495175", "GSM495176", "GSM495177", "GSM495178", "GSM495179", "GSM495180", "GSM495181", "GSM495182", "GSM495183", "GSM495184", "GSM495185", "GSM495186", "GSM495187", "GSM495188", "GSM495189", "GSM495190", "GSM495191", "GSM495192", "GSM495193", "GSM495194", "GSM495195", "GSM495196", "GSM495197", "GSM495198", "GSM495199", "GSM495200", "GSM495201", "GSM495202", "GSM495203", "GSM495204", "GSM495205", "GSM495206", "GSM495207", "GSM495208"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "570;8300", "taxon": "Homo sapiens", "title": "A gene expression profile of BRCAness that is associated with outcome in ovarian cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26193", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26193", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26193", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM642933", "GSM642934", "GSM642935", "GSM642936", "GSM642937", "GSM642938", "GSM642939", "GSM642940", "GSM642941", "GSM642942", "GSM642943", "GSM642944", "GSM642945", "GSM642946", "GSM642947", "GSM642948", "GSM642949", "GSM642950", "GSM642951", "GSM642952", "GSM642953", "GSM642954", "GSM642955", "GSM642956", "GSM642957", "GSM642958", "GSM642959", "GSM642960", "GSM642961", "GSM642962", "GSM642963", "GSM642964", "GSM642965", "GSM642966", "GSM642967", "GSM642968", "GSM642969", "GSM642970", "GSM642971", "GSM642972", "GSM642973", "GSM642974", "GSM642975", "GSM642976", "GSM642977", "GSM642978", "GSM642979", "GSM642980", "GSM642981", "GSM642982", "GSM642983", "GSM642984", "GSM642985", "GSM642986", "GSM642987", "GSM642988", "GSM642989", "GSM642990", "GSM642991", "GSM642992", "GSM642993", "GSM642994", "GSM642995", "GSM642996", "GSM642997", "GSM642998", "GSM642999", "GSM643000", "GSM643001", "GSM643002", "GSM643003", "GSM643004", "GSM643005", "GSM643006", "GSM643007", "GSM643008", "GSM643009", "GSM643010", "GSM643011", "GSM643012", "GSM643013", "GSM643014", "GSM643015", "GSM643016", "GSM643017", "GSM643018", "GSM643019", "GSM643020", "GSM643021", "GSM643022", "GSM643023", "GSM643024", "GSM643025", "GSM643026", "GSM643027", "GSM643028", "GSM643029", "GSM643030", "GSM643031", "GSM643032", "GSM643033", "GSM643034", "GSM643035", "GSM643036", "GSM643037", "GSM643038", "GSM643039"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Control of oxidative stress by miRNA and impact on ovarian tumorigenesis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE38666", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38666", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38666", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM947269", "GSM947270", "GSM947271", "GSM947272", "GSM947273", "GSM947274", "GSM947275", "GSM947276", "GSM947277", "GSM947278", "GSM947279", "GSM947280", "GSM947281", "GSM947282", "GSM947283", "GSM947284", "GSM947285", "GSM947286", "GSM947287", "GSM947288", "GSM947289", "GSM947290", "GSM947291", "GSM947292", "GSM947293", "GSM947294", "GSM947295", "GSM947296", "GSM947297", "GSM947298", "GSM947299", "GSM947300", "GSM947301", "GSM947302", "GSM947303", "GSM947304", "GSM947305", "GSM947306", "GSM947307", "GSM947308", "GSM947309", "GSM947310", "GSM947311", "GSM947312", "GSM947313"], "sample_count": 45, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular Profiling provides evidence of the existence of two functionally distinct classes of ovarian cancer stroma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE40595", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40595", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40595", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM997591", "GSM997592", "GSM997593", "GSM997594", "GSM997595", "GSM997596", "GSM997597", "GSM997598", "GSM997599", "GSM997600", "GSM997601", "GSM997602", "GSM997603", "GSM997604", "GSM997605", "GSM997606", "GSM997607", "GSM997608", "GSM997609", "GSM997610", "GSM997611", "GSM997612", "GSM997613", "GSM997614", "GSM997615", "GSM997616", "GSM997617", "GSM997618", "GSM997619", "GSM997620", "GSM997621", "GSM997622", "GSM997623", "GSM997624", "GSM997625", "GSM997626", "GSM997627", "GSM997628", "GSM997629", "GSM997630", "GSM997631", "GSM997632", "GSM997633", "GSM997634", "GSM997635", "GSM997636", "GSM997637", "GSM997638", "GSM997639", "GSM997640", "GSM997641", "GSM997642", "GSM997643", "GSM997644", "GSM997645", "GSM997646", "GSM997647", "GSM997648", "GSM997649", "GSM997650", "GSM997651", "GSM997652", "GSM997653", "GSM997654", "GSM997655", "GSM997656", "GSM997657", "GSM997658", "GSM997659", "GSM997660", "GSM997661", "GSM997662", "GSM997663", "GSM997664", "GSM997665", "GSM997666", "GSM997667"], "sample_count": 77, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A cancer associated fibroblasts (CAFs) specific gene signature in high grade serous ovarian cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE62193", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62193", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62193", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1521721", "GSM1521722", "GSM1521723", "GSM1521724", "GSM1521725", "GSM1521726", "GSM1521727", "GSM1521728", "GSM1521729", "GSM1521730", "GSM1521731", "GSM1521732", "GSM1521733", "GSM1521734", "GSM1521735", "GSM1521736", "GSM1521737", "GSM1521738", "GSM1521739", "GSM1521740", "GSM1521741", "GSM1521742", "GSM1521743", "GSM1521744", "GSM1521745", "GSM1521746", "GSM1521747", "GSM1521748", "GSM1521749", "GSM1521750", "GSM1521751", "GSM1521752", "GSM1521753", "GSM1521754", "GSM1521755", "GSM1521756", "GSM1521757", "GSM1521758", "GSM1521759", "GSM1521760", "GSM1521761", "GSM1521762", "GSM1521763", "GSM1521764", "GSM1521765", "GSM1521766", "GSM1521767", "GSM1521768", "GSM1521769", "GSM1521770", "GSM1521771", "GSM1521772", "GSM1521773", "GSM1521774", "GSM1521775", "GSM1521776", "GSM1521777", "GSM1521778", "GSM1521779", "GSM1521780", "GSM1521781", "GSM1521782", "GSM1521783", "GSM1521784", "GSM1521785", "GSM1521786", "GSM1533983", "GSM1533984", "GSM1533985", "GSM1533986", "GSM1533987", "GSM1533988", "GSM1533989", "GSM1533990", "GSM1533991", "GSM1533992", "GSM1533993", "GSM1533994", "GSM1533995", "GSM1533996", "GSM1533997", "GSM1533998", "GSM1533999", "GSM1534000", "GSM1534001", "GSM1534002", "GSM1534003", "GSM1534004", "GSM1534005", "GSM1534006", "GSM1534007", "GSM1534008", "GSM1534009", "GSM1534010", "GSM1534011", "GSM1534012", "GSM1534013", "GSM1534014", "GSM1534015"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Dissecting neural differentiation regulatory networks through epigenetic footprinting", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63885", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63885", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63885", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1559299", "GSM1559300", "GSM1559301", "GSM1559302", "GSM1559303", "GSM1559304", "GSM1559305", "GSM1559306", "GSM1559307", "GSM1559308", "GSM1559309", "GSM1559310", "GSM1559311", "GSM1559312", "GSM1559313", "GSM1559314", "GSM1559315", "GSM1559316", "GSM1559317", "GSM1559318", "GSM1559319", "GSM1559320", "GSM1559321", "GSM1559322", "GSM1559323", "GSM1559324", "GSM1559325", "GSM1559326", "GSM1559327", "GSM1559328", "GSM1559329", "GSM1559330", "GSM1559331", "GSM1559332", "GSM1559333", "GSM1559334", "GSM1559335", "GSM1559336", "GSM1559337", "GSM1559338", "GSM1559339", "GSM1559340", "GSM1559341", "GSM1559342", "GSM1559343", "GSM1559344", "GSM1559345", "GSM1559346", "GSM1559347", "GSM1559348", "GSM1559349", "GSM1559350", "GSM1559351", "GSM1559352", "GSM1559353", "GSM1559354", "GSM1559355", "GSM1559356", "GSM1559357", "GSM1559358", "GSM1559359", "GSM1559360", "GSM1559361", "GSM1559362", "GSM1559363", "GSM1559364", "GSM1559365", "GSM1559366", "GSM1559367", "GSM1559368", "GSM1559369", "GSM1559370", "GSM1559371", "GSM1559372", "GSM1559373", "GSM1559374", "GSM1559375", "GSM1559376", "GSM1559377", "GSM1559378", "GSM1559379", "GSM1559380", "GSM1559381", "GSM1559382", "GSM1559383", "GSM1559384", "GSM1559385", "GSM1559386", "GSM1559387", "GSM1559388", "GSM1559389", "GSM1559390", "GSM1559391", "GSM1559392", "GSM1559393", "GSM1559394", "GSM1559395", "GSM1559396", "GSM1559397", "GSM1559398", "GSM1559399"], "sample_count": 101, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling in ovarian cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE14001 not downloaded", "asset:data:geo:GSE14001 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE19829 not downloaded", "asset:data:geo:GSE19829 licence not read", "asset:data:geo:GSE26193 not downloaded", "asset:data:geo:GSE26193 licence not read", "asset:data:geo:GSE38666 not downloaded", "asset:data:geo:GSE38666 licence not read", "asset:data:geo:GSE40595 not downloaded", "asset:data:geo:GSE40595 licence not read", "asset:data:geo:GSE62193 not downloaded", "asset:data:geo:GSE62193 licence not read", "asset:data:geo:GSE63885 not downloaded", "asset:data:geo:GSE63885 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": "random_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": ["random_effects_pool"], "missing_operations": [], "expressible": true, "parameters": {"i_squared": "d-effect model or, when heterogeneity was present, a random-e"}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Where P≥0.1 and I2≤50% indicated no heterogeneity between each study, meta-analysis was performed using the fixed effect model. Where P<0.1 and I2>50% suggested heterogeneity between each study, the random effects model was used for meta-analysis, and sub-analysis was conducted to determine the source of heterogeneity."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "The hazard ratio (HR) and 95% confidence", "confidence_interval": "zard ratio (HR) and 95% confidence interval (CI) were determined us"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-3", "family": "meta_analysis", "specific": "fixed_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": [], "missing_operations": ["fixed_effects_pool"], "expressible": false, "parameters": {"i_squared": "1 and I2≤50% indicated no heter"}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 0.8, "band": "high", "quote": "fixed effect"}}, {"id": "method-4", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["random_effects_pool"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_effects."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE18520", "GSE19829", "GSE26193", "GSE63885", "GSE14001", "GSE38666", "GSE40595", "GSE62193"], "resolved_accessions": ["GSE18520", "GSE19829", "GSE26193", "GSE63885", "GSE14001", "GSE38666", "GSE40595", "GSE62193"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE18520, GSE19829, GSE26193, GSE63885, GSE14001, GSE38666, GSE40595, GSE62193 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["random_effects_pool"], "assets": ["source:pmid:31452765", "data:geo:GSE14001"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14001"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:59Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 15799, "completion_tokens": 1793, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31452765", "type": "paper", "label": "pmid:31452765"}, {"id": "source:pmid:31452765", "type": "manuscript", "label": "PMID 31452765 full text"}, {"id": "data:geo:GSE14001", "type": "dataset", "label": "GEO GSE14001"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31452765", "type": "paper", "label": "pmid:31452765"}, {"id": "source:pmid:31452765", "type": "manuscript", "label": "PMID 31452765 full text"}, {"id": "data:geo:GSE14001", "type": "dataset", "label": "GEO GSE14001"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31452765", "type": "extraction", "used": ["source:pmid:31452765"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14001", "type": "accession_resolution", "used": ["data:geo:GSE14001"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31452765", "parent_hash": "sha256:a30e6f06d5d23342b844cc0106d52e4ffa64de7138dd62cb328501441142522d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE14001 licence not read", "asset:data:geo:GSE14001 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE19829 licence not read", "asset:data:geo:GSE19829 not downloaded", "asset:data:geo:GSE26193 licence not read", "asset:data:geo:GSE26193 not downloaded", "asset:data:geo:GSE38666 licence not read", "asset:data:geo:GSE38666 not downloaded", "asset:data:geo:GSE40595 licence not read", "asset:data:geo:GSE40595 not downloaded", "asset:data:geo:GSE62193 licence not read", "asset:data:geo:GSE62193 not downloaded", "asset:data:geo:GSE63885 licence not read", "asset:data:geo:GSE63885 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["samples and ovarian cancer cells, where the knockdown of LINC01627 inhibited the proliferative and", "r cells and tissue samples. Cell culture and transfection Ovarian cancer cell lines HO8910 and HEY wer", "and once reached 70% confluency, cells were transfected with 50nM negative control (NC) or LINC01627", "s 5′-UUCUCCGAACGUGUCACGUTT-3′. After 24 h of transfection, subsequent experiments were performed. Stat"], "order_basis": "paper_text_order:1545", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["varian cancer cell lines HO8910 and HEY were cultured in RPMI 1640 (Gibco; Thermo Fisher Scientific,"], "order_basis": "paper_text_order:4130", "id": "assay:2"}, {"role": "analysis", "definition_id": "meta_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["random_effects_pool"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Where P≥0.1 and I2≤50% indicated no heterogeneity between each study, meta-analysis was performed using the fixed effect model. Where P<0.1 and I2>50% suggested heterogeneity between each study, the random effects model was used for meta-analysis, and sub-analysis was conducted to determine the source of heterogeneity."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:34:26+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}