{"id":"htan-the-cellular-geography-of-therapeutic-resistance-in-cancer","title":"The Cellular Geography of Therapeutic Resistance in Cancer","short_title":"HTA5","aliases":["HTA5"],"summary":"Of the fourteen HTAN atlases, this is the one whose stated purpose is resistance: mapping where in a tumor resistant cells survive treatment. It carries 20,350 files across multiplexed tissue imaging, single-cell RNA sequencing and bulk DNA, and it is the only atlas in the network carrying the extended clinical data tier alongside therapy, follow-up, exposure, family history and molecular test components.\nIt is also the clearest case in this corpus of a resource that is well built and apparently unused. HTAN maintains its own publication manifest, and this atlas has no entry in it - unlike most atlases, which record three to five publications. The combination of a resistance-focused design, unusually complete clinical annotation and no recorded downstream use makes it the strongest reuse opportunity we identified.","one_liner":"An HTAN atlas built explicitly around therapeutic resistance, with multiplexed imaging, single-cell RNA sequencing and the richest clinical annotation of any atlas here - and no publications recorded in the network's own manifest.","identifiers":[{"scheme":"accession_other","value":"HTA5","url":"https://humantumoratlas.org/explore?selectedFilters=%5B%7B%22value%22%3A%22HTA5%22%7D%5D","is_primary":true,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn39259236","url":"https://www.synapse.org/#!Synapse:syn39259236","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn39259256","url":"https://www.synapse.org/#!Synapse:syn39259256","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn39259280","url":"https://www.synapse.org/#!Synapse:syn39259280","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn39259513","url":"https://www.synapse.org/#!Synapse:syn39259513","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn39259855","url":"https://www.synapse.org/#!Synapse:syn39259855","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn50549510","url":"https://www.synapse.org/#!Synapse:syn50549510","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn51185203","url":"https://www.synapse.org/#!Synapse:syn51185203","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn51218193","url":"https://www.synapse.org/#!Synapse:syn51218193","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn51218570","url":"https://www.synapse.org/#!Synapse:syn51218570","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn51360919","url":"https://www.synapse.org/#!Synapse:syn51360919","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn51360962","url":"https://www.synapse.org/#!Synapse:syn51360962","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"synapse_id","value":"syn51364711","url":"https://www.synapse.org/#!Synapse:syn51364711","is_primary":false,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"atlas HTA5","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"Human Tumor Atlas Network (data hosted in Synapse)","short_name":"HTAN","url":"https://humantumoratlas.org","is_nci_crdc_node":false,"is_nih_repository":true},"additional_repositories":[],"program_name":"Human Tumor Atlas Network","program_url":"https://humantumoratlas.org","nci_program":"HTAN","generating_institutions":["Dana-Farber Cancer Institute, Broad Institute"],"data_generation_funding_role":"generation","version":null,"release_date":null,"last_upstream_update":null,"retrieved_at":"2026-09-18T02:46:11.906526Z","landing_page_url":"https://humantumoratlas.org/explore","cancer_types":[],"primary_sites":[],"subject":{"scope":"title_derived","tissues":[],"evidence":[{"method":"derived","source_url":null,"source_label":"Dataset title","retrieved_at":null,"snippet":null,"locator":"title: The Cellular Geography of Therapeutic Resistance in Cancer","confidence":"low","reviewer":null,"reviewed_at":null,"note":"Subject derived from the title because the repository did not state one. It is available for browsing but cannot admit this record to a topic shortlist."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":156,"n_samples":null,"n_aliquots":null,"n_files":20350,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[]},"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"participants counted as Demographics records (156)","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"spatial_proteomics","label":"Multiplexed tissue imaging","platform":null,"n_cases":null,"n_samples":null,"n_files":16811,"data_levels":["level 2","level 3","level 4"],"access_tier":"mixed","evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"components: ImagingLevel2, ImagingLevel3, ImagingLevel4","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"scrna_seq","label":"Single-cell / single-nucleus RNA sequencing","platform":null,"n_cases":null,"n_samples":null,"n_files":408,"data_levels":["level 1","level 2","level 3","level 4"],"access_tier":"mixed","evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"components: ScRNA-seqLevel1, ScRNA-seqLevel2, ScRNA-seqLevel3, ScRNA-seqLevel4","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"bulk_dna","label":"Bulk DNA sequencing","platform":null,"n_cases":null,"n_samples":null,"n_files":341,"data_levels":["level 2","level 3"],"access_tier":"mixed","evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"components: BulkDNALevel2, BulkDNALevel3","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"htan:ClinicalDataTier2","harmonized_name":null,"label":"Extended clinical data (tier 2)","category":"other","n_nonmissing":167,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":100.0,"is_repeated":true,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"167 ClinicalDataTier2 records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:Demographics","harmonized_name":null,"label":"Demographics","category":"demographic","n_nonmissing":156,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":100.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"156 Demographics records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:Diagnosis","harmonized_name":null,"label":"Diagnosis","category":"diagnosis","n_nonmissing":212,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":100.0,"is_repeated":true,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"212 Diagnosis records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:Exposure","harmonized_name":null,"label":"Exposure history","category":"exposure","n_nonmissing":100,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":64.1,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"100 Exposure records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:FamilyHistory","harmonized_name":null,"label":"Family history","category":"other","n_nonmissing":185,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":100.0,"is_repeated":true,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"185 FamilyHistory records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:FollowUp","harmonized_name":null,"label":"Follow-up","category":"followup","n_nonmissing":291,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":100.0,"is_repeated":true,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"291 FollowUp records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:MolecularTest","harmonized_name":null,"label":"Clinical molecular test","category":"molecular_marker","n_nonmissing":64,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":41.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"64 MolecularTest records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"htan:Therapy","harmonized_name":null,"label":"Therapy","category":"treatment","n_nonmissing":704,"n_not_reported":null,"n_informative":null,"n_total":156,"coverage_pct":null,"populated_pct":100.0,"is_repeated":true,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"704 Therapy records across 1 manifest(s); 156 participants in the atlas","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":null,"survival_endpoints":[],"median_followup_months":null,"max_followup_months":null,"n_cases_with_followup":null,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":null,"response_criteria":[],"evidence":[{"method":"api","source_url":"https://raw.githubusercontent.com/ncihtan/htan-portal/master/data/syn_metadata.json","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":"presence of FollowUp/Therapy components","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"mixed","open_components":["level 3-4 derived data","most imaging"],"controlled_components":["level 1-2 sequencing (dbGaP)"],"mechanism":"Level 1-2 sequencing data are controlled through dbGaP; level 3-4 derived data and most imaging are downloadable from Synapse after registering and accepting the HTAN data use terms.","dua_url":"https://humantumoratlas.org/data-access","data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":true,"citation_requirement":"Cite the atlas publication and acknowledge HTAN per the network's publication policy.","license":"HTAN data use terms; CC BY 4.0 for many level 3-4 products","publication_policy_url":"https://humantumoratlas.org/data-access","evidence":[{"method":"api","source_url":"https://humantumoratlas.org/data-access","source_label":"HTAN portal metadata (ncihtan/htan-portal)","retrieved_at":"2026-09-18T02:46:11.906526Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[{"question":"Where within a tumor do cells that survive therapy actually reside?","rationale":"Multiplexed tissue imaging with single-cell RNA sequencing on the same specimens, in an atlas designed around this question, with therapy records available as a clinical component to define the treatment context.","required_fields":[],"required_modalities":["spatial_proteomics","scrna_seq","treatment"],"feasibility":"needs_access","approx_n":null,"statistical_note":"Spatial analyses are specimen-level; patient numbers are small and the appropriate unit of inference is the region or cell neighborhood, with patient as a random effect.","exemplar_pmid":null,"topics":["treatment-resistance","spatial-biology"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"question":"Do spatial niches associated with resistance recur across cancer types, or are they tissue-specific?","rationale":"Neighborhood definitions derived here can be tested against other HTAN atlases that share the multiplexed imaging component, giving cross-atlas comparison within a single access framework and a common data model.","required_fields":[],"required_modalities":["spatial_proteomics"],"feasibility":"needs_linkage","approx_n":null,"statistical_note":null,"exemplar_pmid":null,"topics":["spatial-biology","cross-cohort","treatment-resistance"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"question":"Can the extended clinical tier be used to relate spatial organization to real treatment sequences rather than to treatment as a single binary?","rationale":"This atlas carries the extended clinical data tier that most atlases lack, alongside therapy and follow-up. That is what allows spatial features to be related to what was actually given and what happened next.","required_fields":[],"required_modalities":["spatial_proteomics","treatment","clinical"],"feasibility":"needs_access","approx_n":null,"statistical_note":"Confirm the completeness of the extended clinical fields in Synapse before designing; the portal metadata records their presence but not their coverage.","exemplar_pmid":null,"topics":["treatment-response","spatial-biology","clinical-annotation"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]}],"limitations":[{"kind":"statistical_power","statement":"HTAN atlases profile few patients deeply. 20,350 files does not mean many participants, and participant counts are not exposed in the portal metadata.","severity":"blocking","affected_analyses":["Cohort-level association","Powered biomarker discovery"],"mitigation":"Obtain participant counts from Synapse first; design within-patient or region-level comparisons.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"annotation_quality","statement":"No publication is recorded for this atlas in HTAN's own manifest, so there is no marker paper to read for design details, quality caveats or the intended interpretation of the clinical fields.","severity":"major","affected_analyses":["Interpreting cohort design","Understanding sampling"],"mitigation":"Contact the atlas team through the HTAN portal before investing in an analysis. The absence of a marker paper is the main practical barrier to reusing this resource.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"access_constraint","statement":"Level 1 and 2 sequencing is controlled through dbGaP; derived data and imaging need a Synapse account and acceptance of the HTAN terms.","severity":"major","affected_analyses":["Raw sequence analysis"],"mitigation":"Start with the Synapse tier.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"harmonization","statement":"Assay coverage varies by specimen across the three modalities.","severity":"major","affected_analyses":["Multimodal integration"],"mitigation":"Build the specimen intersection from Synapse manifests.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]}],"inappropriate_uses":[{"statement":"Cohort-level statistical inference.","reason":"Deep sampling of few patients; the design does not support it.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"statement":"Assuming clinical field completeness from their presence in the metadata.","reason":"The portal metadata records which clinical components exist, not how completely they are populated. Verify in Synapse.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]}],"primary_publications":[],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{},"n_by_tier_raw":{},"accession_precision":null,"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":false,"n_verified_reuse":null,"n_reuse_examined":0,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":null,"latest_reuse_year":null,"years_since_release":null,"expected_reuse":null,"reuse_gap_index":null,"reuse_gap_percentile":null,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-21T02:11:08.404148Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-21T02:11:08.404148Z","snippet":null,"locator":null,"confidence":"low","reviewer":null,"reviewed_at":null,"note":"This dataset has no accession specific enough to search for in the literature, so citation-based reuse cannot be measured. 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Not machine-generated."}]},{"order":3,"action":"Verify participant counts and clinical field coverage before designing","detail":null,"url":null,"requires":[],"est_time":"2-3 hours","cli_snippet":null,"audience":"human","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908811Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"order":4,"action":"Give an agent a Synapse token, not a password","detail":"Unauthenticated calls return metadata and no files, so an agent should report the credential requirement explicitly.","url":"https://help.synapse.org/docs/Getting-Started.2055471150.html","requires":["SYNAPSE_AUTH_TOKEN"],"est_time":null,"cli_snippet":"export SYNAPSE_AUTH_TOKEN=...\nsynapse get syn39259236","audience":"agent","evidence":[{"method":"derived","source_url":"https://help.synapse.org/docs/Getting-Started.2055471150.html","source_label":"HTAN access documentation","retrieved_at":"2026-09-21T12:30:59.432583Z","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":[{"level":"advanced","title":"Select a dataset the way an agent should","question":"Given a research goal, which dataset should an agent choose, and what must it refuse to do with it?","problem":"Ranking by size or fame can select a large dataset that cannot answer the question.","lesson":"Filter on measured capability, rank on fit, and carry blocking limitations into the analysis brief.","figure":"Horizontal bars of the fit score for each shortlisted dataset, with the selected cohort highlighted, showing whether the ranking is decided by overall fit or by one dominant term.","featured":false,"inputs":["The CD2S structured export","pandas"],"outputs":["Contrast between a size-ranked and a capability-ranked selection","A transparent fit score favoring under-used resources","Blocking limitations read before committing","A machine-readable task brief for the next step","A chart of the ranked fit scores with the selected cohort highlighted"],"steps":["Load the structured index","Show what a naive size-ranked selection returns","Filter on measured capability rather than description","Rank on fit, rewarding under-used datasets","Read blocking limitations from the full record","Emit a task brief including what the agent must not do"],"findings":["A size-ranked agent picks msk_ch_2023 and its 42,714 cases, which record neither treatment response nor a survival endpoint.","Only 51 of 602 datasets record both, measured from field coverage rather than description.","Ranking on fit selects MP2PRT-ALL - 1,510 cases, 100 months of follow-up - and carries its 4 major limitations into the brief."],"contributor":null,"contributor_url":null,"language":"python","est_runtime":"under a minute","est_compute":null,"workbook_path":"workbooks/python/06_agent_dataset_selection.py","workbook_url":null,"notebook_download_url":"/data/notebooks/06_agent_dataset_selection.ipynb","notebook_preview_url":"/data/notebooks/06_agent_dataset_selection.png","notebook_preview_width":1021,"notebook_preview_height":685,"colab_url":null,"binder_url":null,"receipt":{"executed":true,"executed_at":"2026-09-21T00:43:02.488936Z","runtime_seconds":1.19,"executor":"nbclient / python 3.12.13 / Darwin 25.5.0 arm64","package_versions":{"python":"3.12.13","pandas":"3.0.6","numpy":"2.5.3","matplotlib":"3.11.2","lifelines":"0.30.0","scipy":"1.18.1","requests":"2.34.2","httpx":"0.28.1"},"n_cells":8,"n_cells_executed":8,"output_hash":"dc49bfd688a5ab7ef77292e914fdd645","data_retrieved_at":null,"error":null},"template_source":"06_agent_dataset_selection","evidence":[{"method":"curated","source_url":null,"source_label":"CD2S workbook","retrieved_at":"2026-09-21T12:30:59.450387Z","snippet":null,"locator":"workbooks/python/06_agent_dataset_selection.py","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Executed end to end against the live public APIs; the receipt records when, with which package versions and how long it took."}]}],"agent_package":{"json_url":"/data/datasets/htan-the-cellular-geography-of-therapeutic-resistance-in-cancer.json","jsonld_url":"/data/jsonld/htan-the-cellular-geography-of-therapeutic-resistance-in-cancer.jsonld","croissant_url":"/data/croissant/htan-the-cellular-geography-of-therapeutic-resistance-in-cancer.json","instructions_url":"/data/agent/htan-the-cellular-geography-of-therapeutic-resistance-in-cancer.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"project_curated","reviewer":"CD2S project curation","reviewer_affiliation":null,"reviewed_at":"2026-09-18","sections_reviewed":["useful_for","limitations","inappropriate_uses","access_steps"],"open_questions":["This atlas has no entry in the HTAN publication manifest, so we cannot identify its marker publication or confirm whether one exists yet. Confirm with the atlas team.","Participant counts are not exposed in the portal metadata; obtain them from Synapse."],"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":true,"completeness_score":78.6,"tags":["htan","no-recorded-publications","rare-modality","single-cell","spatial","treatment-linked","treatment-resistance","underexplored-candidate"],"search_text":null}