{"as_of":"2026-09-04","atlas_id":"pmmr-mucinous-colon","count_definitions":{"distinct_experimental_pdb_entries":"Unique RCSB PDB accessions in structures.json; derived compatibility records that reuse an accession do not increase this count.","duplicate_records":"Duplicate PubMed query memberships removed when producing the unique literature index.","known_compound_measured_records":"Normalized measured ChEMBL or BindingDB protein-target activity rows from the bounded Structure-A query pass; these rows are not site-localized.","preprint_normalized_unique_dois":"Unique DOI identities across hydrated 10.1101 records and non-10.1101 preprint discovery metadata.","raw_records":"Emitted PubMed query memberships before cross-query deduplication; heterogeneous source rows are reported in their own named count fields and are not summed."},"counts":{"canonical_sequence_targets":185,"canonical_sequence_unresolved_targets":0,"canonical_topology_targets":185,"cbioportal_expression_measurements":107566,"cbioportal_mapped_targets":184,"cbioportal_unresolved_targets":1,"clinical_trial_intervention_entries":1335,"clinical_trial_studies":495,"derived_structure_records":1,"distinct_experimental_pdb_entries":15,"duplicate_records":46,"excluded_from_surface_universe":334,"hpa_represented_targets":184,"hpa_unresolved_targets":1,"intervention_target_assignments":140,"known_compound_bounded_queries":73,"known_compound_complete_queries":65,"known_compound_failed_queries":8,"known_compound_measured_records":57,"known_compound_structure_a_targets":10,"literature_missing_or_merged_pmids":24,"literature_requested_records":2640,"literature_unique_records":2570,"molecular_library_records":44,"normalized_discovered_entities":601,"normalized_intervention_candidates":766,"open_targets_associated_targets":558,"preprint_completed_queries":40,"preprint_hydrated_records":6,"preprint_normalized_unique_dois":13,"preprint_raw_query_memberships":20,"preprint_registered_queries":40,"preprint_truncated_queries":0,"preprint_unique_10_1101_dois":6,"preprint_unique_other_dois":7,"preprint_unresolved_records":0,"query_seed_additions":43,"raw_records":2616,"resolved_molecular_identities":43,"reviewed_uniprot_matches":592,"structure_records":16,"surface_targets":185,"tcsa_coad_specific_records":22,"tcsa_global_surface_records":3567,"tcsa_single_cell_gene_records":899,"unresolved_molecular_identities":1,"unresolved_records":82},"coverage_state":"complete_within_recorded_scope","limitations":["The searched-in-scope census is complete for the recorded public-source snapshot and reconciliation policy; 82 discovered entities remain explicitly unresolved rather than silently excluded.","The HPA and cBioPortal overlays preserve one unresolved target mapping each and remain expression context rather than patient-specific surface abundance or safety evidence.","Canonical sequences cover every retained target; target-specific isoform and proteoform reconciliation remains incomplete. Preprint discovery is bounded to 40 registered concepts and 100 records per concept.","The measured ChEMBL/BindingDB pass is bounded to ten Structure-A targets and is not site-localized. Prospective screening and de novo binder design remain computational hypothesis lanes."],"planned_source_classes":["literature-and-preprints","cancer-genomics-and-expression","surface-and-proteome-studies","single-cell-and-spatial-context","normal-tissue-and-cell-context","sequence-topology-and-proteoforms","interventions-and-trials","structures-and-complexes"],"schema_version":"codex-surface-search-ledger/v0.1","sources":[{"limitation":"Three PubMed query families yielded 2,570 unique records from 2,616 query memberships; 24 requested PMIDs were missing or merged. The source snapshot is bounded to the registered query families.","query_id":"Q-LIT-001","record_count":2570,"record_unit":"unique PubMed records","retrieved_at":"2026-09-04","source_class":"literature-and-preprints","status":"partial"},{"artifact":{"bytes":157776,"format":"json","sha256":"dba49f42ee8450c01d13d3b406c9136dbc5a0fe321c55f16198834b6366f3ff3","storage":"atlas-workspace"},"limitation":"All 40 registered concepts completed at a hard 100-record-per-concept cutoff; 0 reached the cutoff. 6 unique 10.1101 records were hydrated; 7 other DOI records remain discovery metadata rather than bioRxiv/medRxiv hydrations.","query_id":"Q-PREPRINT-001","record_count":13,"record_unit":"unique preprint DOI records","retrieved_at":"2026-09-04","source_class":"literature-and-preprints","status":"complete"},{"query_id":"Q-CANCER-001","record_count":601,"record_unit":"normalized disease-linked entities","retrieved_at":"2026-09-04","source_class":"cancer-genomics-and-expression","status":"complete"},{"artifact":{"bytes":361923,"format":"json","sha256":"32175b4de01ff8b2dcb5fcc6981a8bbc86bf83956e489090340e65b763579544","storage":"atlas-workspace"},"collection_schema":"codex-surface-cbioportal-phenotype-overlay/v0.1","limitation":"Mapped 184 of 185 retained targets and retained 107,566 transcript-expression measurements. Unresolved: T-ENSG00000130202 (PVRL2). This is a public-cohort MSS proxy, not patient-specific protein or surface abundance.","query_id":"Q-CBIO-001","record_count":184,"record_unit":"retained targets mapped to the declared cBioPortal cohort","retrieved_at":"2026-09-04","source_class":"cancer-genomics-and-expression","status":"partial","unresolved_target_ids":["T-ENSG00000130202"]},{"query_id":"Q-PROTEOME-001","record_count":3567,"record_unit":"global Cancer Surfaceome Atlas GESP records","retrieved_at":"2026-09-04","source_class":"surface-and-proteome-studies","status":"complete"},{"limitation":"The snapshot includes the published COAD single-cell expression matrix; it does not include a patient-specific single-cell or spatial dataset.","query_id":"Q-CELL-001","record_count":899,"record_unit":"Cancer Surfaceome Atlas single-cell gene rows","retrieved_at":"2026-09-04","source_class":"single-cell-and-spatial-context","status":"partial"},{"artifact":{"bytes":654039,"format":"json","sha256":"eea1865692a579a31ede2a43eae56ab31a001cfbb148d1d0904acf9bf676ac00","storage":"atlas-workspace"},"collection_schema":"codex-surface-hpa-normal-tissue-overlay/v0.1","limitation":"Human Protein Atlas normal-tissue summaries represent 184 of 185 retained targets. Unresolved: T-NECTIN4 (NECTIN4). The overlay is expression context, not accessible surface density or a therapeutic-index model.","query_id":"Q-NORMAL-001","record_count":184,"record_unit":"retained targets represented in the HPA normal-tissue overlay","retrieved_at":"2026-09-04","source_class":"normal-tissue-and-cell-context","status":"partial","unresolved_target_ids":["T-NECTIN4"]},{"artifact":{"bytes":1308203,"format":"json","sha256":"5072da13c060ee603b135dd781b7593cea6ae848c92a2408d1dd0ad8a12cd29b","storage":"atlas-workspace"},"limitation":"Canonical sequence and reviewed topology are present for 185 of 185 retained targets, with 0 unresolved canonical records. Target-specific isoform and proteoform reconciliation remains outside this collection.","query_id":"Q-SEQ-001","record_count":185,"record_unit":"retained targets with canonical protein sequence and reviewed topology","retrieved_at":"2026-09-05","source_class":"sequence-topology-and-proteoforms","status":"partial"},{"limitation":"ClinicalTrials.gov yielded 766 normalized intervention candidates and 140 target assignments. Bounded measured activity evidence for Structure-A targets is recorded separately under Q-ACTIVITY-001; neither lane is an exhaustive intervention review.","query_id":"Q-THERAPY-001","record_count":495,"record_unit":"unique ClinicalTrials.gov studies","retrieved_at":"2026-09-04","source_class":"interventions-and-trials","status":"partial"},{"artifact":{"bytes":240108,"format":"json","sha256":"26aaa2e132443759fd200931f372de154e56b370d6ecd291299684383a3ce627","storage":"atlas-workspace"},"collection_schema":"codex-surface-known-compound-interaction-collection/v0.1","limitation":"The bounded Structure-A pass ran 73 registered queries for 10 targets and retained 57 measured records: 31 from ChEMBL and 26 from BindingDB. 8 PDB-indexed BindingDB queries failed. All records remain target-level or PDB-indexed target matches without extracellular-site localization; none establishes action, selectivity, safety, or efficacy.","query_id":"Q-ACTIVITY-001","record_count":57,"record_unit":"measured ChEMBL or BindingDB protein-target activity records","retrieved_at":"2026-09-05","source_class":"interventions-and-trials","status":"partial"},{"artifact":{"bytes":228650,"format":"json","sha256":"42015660cf5e51fb59cf5159077b29a3daae6012fca9fde8307e9487815ab72d","storage":"atlas-workspace"},"collection_schema":"codex-surface-structure-collection/v0.1","limitation":"The library contains 15 distinct experimental PDB entries and 16 total records, including 1 target-only compatibility record. Accession-level deposited complex searches are not complete for every retained target.","query_id":"Q-STRUCTURE-001","record_count":15,"record_unit":"distinct verified experimental RCSB PDB entries","retrieved_at":"2026-09-04","source_class":"structures-and-complexes","status":"partial"}]}