{"id":"pdc-prospective-colon-pnnl-phosphoproteome-lumos","title":"Prospective Colon PNNL Phosphoproteome Lumos","short_title":"PDC000117","aliases":["Prospective Colon PNNL Phosphoproteome Lumos"],"summary":null,"one_liner":null,"identifiers":[{"scheme":"pdc_study_id","value":"PDC000117","url":"https://pdc.cancer.gov/pdc/study/PDC000117","is_primary":true,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"1 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"NCI Proteomic Data Commons","short_name":"PDC","url":"https://pdc.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"Clinical Proteomic Tumor Analysis Consortium","program_url":"https://pdc.cancer.gov/pdc/browse","nci_program":"Clinical Proteomic Tumor Analysis Consortium","generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":"2023-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:36:15.354973Z","landing_page_url":"https://pdc.cancer.gov/pdc/study/PDC000117","cancer_types":[{"label":"Colon Adenocarcinoma","ontology":null,"code":null,"url":null}],"primary_sites":["Colon"],"subject":{"scope":"single","tissues":["BOWEL"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Colon Adenocarcinoma; primary_sites: Colon","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Repository disease labels or primary sites mapped to pinned tissues."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":102,"n_samples":null,"n_aliquots":198,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"female":58,"male":42,"not reported":2},"race":{"white":74,"asian":16,"black or african american":7,"not reported":4,"american indian or alaska native":1},"ethnicity":{"not hispanic or latino":92,"not reported":3,"hispanic or latino":7},"age_at_diagnosis_years":{},"vital_status":{"Not Reported":100},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy demographic fields","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"1 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"phosphoproteome","label":"Phosphoproteome mass spectrometry (TMT10 / DDA)","platform":"TMT10","n_cases":102,"n_samples":198,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"1 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"pdc:vital_status","harmonized_name":"demographic.vital_status","label":"Vital status","category":"outcome","n_nonmissing":100,"n_not_reported":100,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":98.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field vital_status over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:cause_of_death","harmonized_name":"demographic.cause_of_death","label":"Cause of death","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field cause_of_death over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:race","harmonized_name":"demographic.race","label":"Race","category":"demographic","n_nonmissing":102,"n_not_reported":4,"n_informative":98,"n_total":102,"coverage_pct":96.1,"populated_pct":100.0,"is_repeated":false,"example_values":["white","asian","black or african american","not reported","american indian or alaska native"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field race over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ethnicity","harmonized_name":"demographic.ethnicity","label":"Ethnicity","category":"demographic","n_nonmissing":102,"n_not_reported":3,"n_informative":99,"n_total":102,"coverage_pct":97.1,"populated_pct":100.0,"is_repeated":false,"example_values":["not hispanic or latino","hispanic or latino","not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field ethnicity over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:gender","harmonized_name":"demographic.sex_at_birth","label":"Sex at birth (gender)","category":"demographic","n_nonmissing":102,"n_not_reported":2,"n_informative":100,"n_total":102,"coverage_pct":98.0,"populated_pct":100.0,"is_repeated":false,"example_values":["female","male","not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field gender over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:morphology","harmonized_name":"diagnoses.morphology","label":"Morphology (ICD-O)","category":"pathology","n_nonmissing":102,"n_not_reported":2,"n_informative":100,"n_total":102,"coverage_pct":98.0,"populated_pct":100.0,"is_repeated":false,"example_values":["8140/3","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field morphology over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:primary_diagnosis","harmonized_name":"diagnoses.primary_diagnosis","label":"Primary diagnosis","category":"diagnosis","n_nonmissing":102,"n_not_reported":1,"n_informative":101,"n_total":102,"coverage_pct":99.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Adenocarcinoma, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field primary_diagnosis over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tissue_or_organ_of_origin","harmonized_name":"diagnoses.tissue_or_organ_of_origin","label":"Tissue or organ of origin","category":"diagnosis","n_nonmissing":102,"n_not_reported":1,"n_informative":101,"n_total":102,"coverage_pct":99.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Colon, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field tissue_or_organ_of_origin over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tumor_grade","harmonized_name":"diagnoses.tumor_grade","label":"Tumor grade","category":"pathology","n_nonmissing":102,"n_not_reported":102,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field tumor_grade over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ajcc_pathologic_stage","harmonized_name":"diagnoses.ajcc_pathologic_stage","label":"AJCC pathologic stage","category":"staging","n_nonmissing":102,"n_not_reported":2,"n_informative":100,"n_total":102,"coverage_pct":98.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Stage IIA","Stage IIIB","Stage I","Stage IIIC","Stage IVA","Stage IIB"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field ajcc_pathologic_stage over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ajcc_clinical_stage","harmonized_name":"diagnoses.ajcc_clinical_stage","label":"AJCC clinical stage","category":"staging","n_nonmissing":102,"n_not_reported":102,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field ajcc_clinical_stage over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tumor_stage","harmonized_name":"diagnoses.ajcc_pathologic_stage","label":"AJCC pathologic stage (tumor_stage)","category":"staging","n_nonmissing":102,"n_not_reported":1,"n_informative":101,"n_total":102,"coverage_pct":99.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Stage IIA","Stage IIIB","Stage1","Stage IIIC","Stage IVA","Stage IIB"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field tumor_stage over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:progression_or_recurrence","harmonized_name":"diagnoses.progression_or_recurrence","label":"Progression or recurrence","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field progression_or_recurrence over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:last_known_disease_status","harmonized_name":"diagnoses.last_known_disease_status","label":"Last known disease status","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field last_known_disease_status over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:prior_treatment","harmonized_name":"diagnoses.prior_treatment","label":"Prior treatment","category":"treatment","n_nonmissing":102,"n_not_reported":102,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field prior_treatment over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:prior_malignancy","harmonized_name":"diagnoses.prior_malignancy","label":"Prior malignancy","category":"diagnosis","n_nonmissing":102,"n_not_reported":1,"n_informative":101,"n_total":102,"coverage_pct":99.0,"populated_pct":100.0,"is_repeated":false,"example_values":["no","yes","not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field prior_malignancy over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:synchronous_malignancy","harmonized_name":"diagnoses.synchronous_malignancy","label":"Synchronous malignancy","category":"diagnosis","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field synchronous_malignancy over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:classification_of_tumor","harmonized_name":"diagnoses.classification_of_tumor","label":"Classification of tumor","category":"pathology","n_nonmissing":100,"n_not_reported":100,"n_informative":0,"n_total":102,"coverage_pct":0.0,"populated_pct":98.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field classification_of_tumor over 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:age_at_diagnosis","harmonized_name":"diagnoses.age_at_diagnosis","label":"Age at diagnosis","category":"demographic","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field age_at_diagnosis; a value for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_death","harmonized_name":"demographic.days_to_death","label":"Days to death","category":"outcome","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field days_to_death; a value for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_last_follow_up","harmonized_name":"diagnoses.days_to_last_follow_up","label":"Days to last follow-up","category":"followup","n_nonmissing":1,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":1.0,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field days_to_last_follow_up; a value for 1 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_recurrence","harmonized_name":"diagnoses.days_to_recurrence","label":"Days to recurrence","category":"outcome","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: clinicalPerStudy, field days_to_recurrence; a value for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_type","harmonized_name":"diagnoses.treatments.treatment_type","label":"Treatment type","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:37.480944Z","snippet":null,"locator":"PDC000117: paginatedCaseTreatmentsPerStudy, field treatment_type; informative for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.therapeutic_agents","harmonized_name":"diagnoses.treatments.therapeutic_agents","label":"Therapeutic agents","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:37.480944Z","snippet":null,"locator":"PDC000117: paginatedCaseTreatmentsPerStudy, field therapeutic_agents; informative for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_outcome","harmonized_name":"diagnoses.treatments.treatment_outcome","label":"Treatment outcome","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:37.480944Z","snippet":null,"locator":"PDC000117: paginatedCaseTreatmentsPerStudy, field treatment_outcome; informative for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.regimen_or_line_of_therapy","harmonized_name":"diagnoses.treatments.regimen_or_line_of_therapy","label":"Regimen or line of therapy","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:37.480944Z","snippet":null,"locator":"PDC000117: paginatedCaseTreatmentsPerStudy, field regimen_or_line_of_therapy; informative for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_or_therapy","harmonized_name":"diagnoses.treatments.treatment_or_therapy","label":"Treatment given","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":102,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:37.480944Z","snippet":null,"locator":"PDC000117: paginatedCaseTreatmentsPerStudy, field treatment_or_therapy; informative for 0 of 102 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":false,"survival_endpoints":[],"median_followup_months":0.0,"max_followup_months":0.0,"n_cases_with_followup":1,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":false,"response_criteria":[],"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:05.725697Z","snippet":null,"locator":"PDC000117: computed from 102 cases: 0 deaths, 1 with a follow-up time, progression informative for 0","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"open","open_components":["1 analytical fraction studies"],"controlled_components":[],"mechanism":"Direct download from the PDC portal or its API; no account required","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the PDC study identifier and the study's primary publication; PDC asks that the consortium be acknowledged.","license":"Open access under the PDC data use terms","publication_policy_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"1 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[],"inappropriate_uses":[],"primary_publications":[{"pmid":"38724493","pmcid":"PMC11082183","doi":"10.1038/s41467-024-47957-3","title":"Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.","journal":"Nature communications","year":2024,"authors_short":"Rosenberger et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38724493/","is_open_access":true,"citation_count":16,"evidence":[{"method":"derived","source_url":null,"source_label":"Candidate primary publication (machine-inferred)","retrieved_at":"2026-09-20T18:15:55.021429Z","snippet":null,"locator":"earliest highly cited article analyzing PDC000117 (published 2024)","confidence":"low","reviewer":null,"reviewed_at":null,"note":"Inferred, not authoritative. The source repository does not publish a marker-paper link for this dataset, so we nominate the earliest heavily cited article that analyzed it. Flagged for expert review before being relied on."}]}],"reuse":[{"publication":{"pmid":"36688801","pmcid":"PMC9903327","doi":"10.1021/acs.jproteome.2c00614","title":"MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data.","journal":"Journal of proteome research","year":2023,"authors_short":"Canderan et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36688801/","is_open_access":true,"citation_count":3,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["canderan j","stamboulian m"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000117\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:13.716236Z","snippet":null,"locator":"accession \"PDC000117\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"40276932","pmcid":"PMC12045569","doi":"10.1080/15476286.2025.2498203","title":"The implication of non-AUG-initiated N-terminally extended proteoforms in cancer.","journal":"RNA biology","year":2025,"authors_short":"Pancsa et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/40276932/","is_open_access":true,"citation_count":1,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["andreev d","dean k","pancsa r"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000117\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:13.716236Z","snippet":null,"locator":"accession \"PDC000117\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"41822325","pmcid":"PMC12978393","doi":"10.14740/wjon2695","title":"TP53 Loss Fuels mTORC1 Activation and Autophagy Suppression to Drive Immune-Cold Colorectal Cancer.","journal":"World journal of oncology","year":2026,"authors_short":"Lee et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41822325/","is_open_access":true,"citation_count":0,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"RESULTS","author_keys":["al-assi d","joy a","lee e","paul s","rivera-rueda r"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=RESULTS:\"PDC000117\"","source_label":"Europe PMC section search (RESULTS)","retrieved_at":"2026-09-18T03:29:13.716236Z","snippet":null,"locator":"accession \"PDC000117\" indexed in RESULTS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]}],"reuse_metrics":{"n_candidates_screened":2,"n_by_tier":{"t3_analyzed":2,"t2_declared":1,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":2,"t2_declared":1,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000117","query":"METHODS:\"PDC000117\"","strategy_id":"epmc-literal-precision-v1","needs_correction":false,"precision":1.0,"precision_low":1.0,"precision_high":1.0,"n_sampled":0,"n_checked":0,"n_literal":0,"note":"This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":true,"n_verified_reuse":2,"n_reuse_examined":4,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":2023,"latest_reuse_year":2026,"years_since_release":3.72,"expected_reuse":2.43,"reuse_gap_index":-0.192,"reuse_gap_percentile":43.9,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.902571Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC section-scoped hit counts","retrieved_at":"2026-09-20T18:07:48.902571Z","snippet":null,"locator":"tokens: PDC000117; queries: METHODS:\"PDC000117\"; DATA_AVAILABILITY:\"PDC000117\"; ACCESSION_ID:\"PDC000117\"; REF:\"PDC000117\"","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Index strategy epmc-index-v3. Every dataset is measured with the same single section field per tier, so the counts are comparable; the per-tier value is the largest across the dataset's own accessions, excluding any accession shared with other datasets in the corpus. This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC first-reference dating","retrieved_at":"2026-09-20T18:15:55.021429Z","snippet":null,"locator":"first referenced in 2023 (METHODS section)","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Availability dated from the literature (epmc-first-reference-v2) rather than from repository file timestamps, which record re-harmonization. This is a lower bound on availability."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index -0.19)."],"index_value":-0.192,"percentile":43.9,"comparator_set":"132 datasets in this corpus with a citable accession and sufficient metadata","evidence":[{"method":"derived","source_url":null,"source_label":"Reuse Gap Index (rgi-huber-v2)","retrieved_at":"2026-09-21T02:11:22.976067Z","snippet":null,"locator":"Huber robust regression of log2(analyzing articles + 1) on cohort size, years available, modality breadth and access tier","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Model, covariates and coefficients are published with the dataset export so the label can be recomputed or contested."}]},"grants":[],"access_steps":[{"order":1,"action":"Open the study in the PDC portal","detail":"Proteomic data are released open; the portal's use guidelines still apply.","url":"https://pdc.cancer.gov/pdc/study/PDC000117","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000117","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434859Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":2,"action":"Accept the data use guidelines and download","detail":"The portal asks for acknowledgement and citation, not a data access request.","url":"https://pdc.cancer.gov/pdc/data-use-guidelines","requires":[],"est_time":"minutes to hours, by study size","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434861Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000117: called with the pdc_study_id it returns the right number of rows with every column null. Resolve the UUID first and pass the terms acknowledgement.","url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nimport requests\nAPI = \"https://proteomic.datacommons.cancer.gov/graphql\"\n\ndef gql(query, **variables):\n    r = requests.post(API, json={\"query\": query, \"variables\": variables}, timeout=180)\n    r.raise_for_status()\n    body = r.json()\n    if body.get(\"errors\"):\n        raise RuntimeError(body[\"errors\"][0][\"message\"])\n    return body[\"data\"]\n\nstudy = gql('query($id:String!){ study(pdc_study_id:$id acceptDUA:true){ study_id } }',\n            id=\"PDC000117\")[\"study\"][0]\nfiles = gql('query($sid:String!){ filesPerStudy(study_id:$sid acceptDUA:true)'\n            '{ file_id file_name file_size } }', sid=study[\"study_id\"])[\"filesPerStudy\"]\nprint(len(files), \"files\")\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434863Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[],"agent_package":{"json_url":"/data/datasets/pdc-prospective-colon-pnnl-phosphoproteome-lumos.json","jsonld_url":"/data/jsonld/pdc-prospective-colon-pnnl-phosphoproteome-lumos.jsonld","croissant_url":"/data/croissant/pdc-prospective-colon-pnnl-phosphoproteome-lumos.json","instructions_url":"/data/agent/pdc-prospective-colon-pnnl-phosphoproteome-lumos.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"open_questions":[],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":false,"completeness_score":32.1,"tags":["pdc","proteogenomics"],"search_text":null}