DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36655766", "kind": "science-record", "revision": 2, "content_hash": "sha256:784d4d26034727b3f274459cd913ef286abb5f731e687250f8b4a8833c23ccd6", "created_at": "2026-11-01T19:01:12Z", "updated_at": "2026-11-01T21:29:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity.", "doi": "10.1093/bioinformatics/btad039", "pmid": "36655766", "authors": ["Xiangning Xue", "Wei Zong", "Zhiguang Huo", "Kyle D Ketchesin", "Madeline R Scott", "Kaitlyn A Petersen", "Ryan W Logan", "Marianne L Seney", "Colleen McClung", "George Tseng"], "journal": "Bioinformatics (Oxford, England)", "year": 2023, "abstract": "SUMMARY: Circadian oscillations of gene expression regulate daily physiological processes, and their disruption is linked to many diseases. Circadian rhythms can be disrupted in a variety of ways, including differential phase, amplitude and rhythm fitness. Although many differential circadian biomarker detection methods have been proposed, a workflow for systematic detection of multifaceted differential circadian characteristics with accurate false positive control is not currently available. We propose a comprehensive and interactive pipeline to capture the multifaceted characteristics of differentially rhythmic biomarkers. Analysis outputs are accompanied by informative visualization and interactive exploration. The workflow is demonstrated in multiple case studies and is extensible to general omics applications.\nAVAILABILITY AND IMPLEMENTATION: R package, Shiny app and source code are available in GitHub (https://github.com/DiffCircaPipeline) and Zenodo (https://doi.org/10.5281/zenodo.7507989).\nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.", "claims": [{"id": "claim-method", "statement": "A SSMS procedure (G’Sell et al., 2016) is applied to categorize biomarkers into four TORs: (i) rhythmic only in Group I (RhyI); (ii) rhythmic only in Group II (RhyII); (iii) rhythmic in both groups (RhyBoth); and (iv) arrhythmic in both groups (Arrhy).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36655766", "locator": "sections[2] \"2 Results\" paragraph 2", "quote": "A SSMS procedure (G’Sell et al., 2016) is applied to categorize biomarkers into four TORs: (i) rhythmic only in Group I (RhyI); (ii) rhythmic only in Group II (RhyII); (iii) rhythmic in both groups (RhyBoth); and (iv) arrhythmic in both groups (Arrhy)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:36655766"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36655766", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/bioinformatics/btad039", "sha256": "sha256:c49d19455943503fa3a87b96c7d298628d1daeae878652aed19e9e0090539c0e", "bytes": 17371, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/bioinformatics/btad039", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9889843", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "cosinor model fitting, selective sequential model selection (SSMS), likelihood ratio test for differential rhythm fitness, and two-stage global and post hoc tests for differential rhythm parameters", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A SSMS procedure (G’Sell et al., 2016) is applied to categorize biomarkers into four TORs: (i) rhythmic only in Group I (RhyI); (ii) rhythmic only in Group II (RhyII); (iii) rhythmic in both groups (RhyBoth); and (iv) arrhythmic in both groups (Arrhy)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (cosinor model fitting, selective sequential model selection (SSMS), likelihood ratio test for differential rhythm fitness, and two-stage global and post hoc tests for differential rhythm parameters), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36655766"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:23:33Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 5759, "completion_tokens": 1132, "cached_tokens": 0}}, "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:36655766", "type": "paper", "label": "pmid:36655766"}, {"id": "source:pmid:36655766", "type": "manuscript", "label": "PMID 36655766 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36655766", "type": "paper", "label": "pmid:36655766"}, {"id": "source:pmid:36655766", "type": "manuscript", "label": "PMID 36655766 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36655766", "type": "extraction", "used": ["source:pmid:36655766"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:36655766", "parent_hash": "sha256:383e286f8261267c466b07e8e1a0531e952edb7f539a87e1f02aec94555cd8cd", "fork_of": null, "generation": 1}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}