| Blocking issue | Why it matters | Evidence of issue in this run | Required input to unblock | Expected output after unblocking |
|---|---|---|---|---|
| No retrievable literature documents | Without retrieved documents, no disease-specific claims can be grounded in source text | `paper_search` returned no retrievable papers across multiple EDN3/EDNRB/Waardenburg-Shah/Hirschsprung queries | Provide retrievable PubMed papers, PDFs, DOIs, or direct links for core EDN3/EDNRB Waardenburg–Shah references | PMID-cited disease overview, etiology, phenotype, mechanism, and recent-literature synthesis |
| No citable context IDs generated | The system requires context IDs to produce verifiable citations, quotes, URLs, and dates | Multiple tool outputs explicitly showed `Context IDs that may be cited: []` | Ingest at least one authoritative source so context IDs can be created | Properly cited report sections with source-linked claims and abstract quotations |
| OpenTargets disease-target lookup failed | Disease-target association evidence could not be incorporated into genetics/mechanism sections | `open_targets_search` failed after retries during queries for Waardenburg syndrome/Hirschsprung disease with EDNRB/EDN3/SOX10 | Restore OpenTargets access or provide equivalent disease-target source material | Target-disease association summary and pathway-oriented interpretation |
| No clinical trial records retrieved | Treatment and experimental-therapy sections cannot include trial-based evidence | `clinical_trials_search` returned zero trials for Waardenburg syndrome type IV, EDNRB, EDN3, and Hirschsprung-related queries | Provide NCT IDs or retrievable trial registry pages if relevant | Trial/activity summary for experimental or observational management evidence |
| Answer submission blocked by evidence-grounding requirement | Even a limitation report cannot be submitted through the grounded-answer path without evidence contexts | `answer` call raised `EmptyContextsError` because no citable contexts were available | Seed the run with OMIM/Orphanet/GeneReviews/PubMed sources before synthesis | Full structured report with citations, URLs, publication dates, ontology mappings, and evidence-backed tables |


*Table: This table summarizes the main blockers encountered in the session, why each prevented completion of the requested cited disease report, and what specific inputs are needed to enable a successful follow-up run.*