Build an NCBI Gene Package Splice Form Curation Agent
Ingest gene packages downloaded via NCBI Datasets to evaluate eukaryotic transcript sequences. Validate coding coordinates and structure curated transcript metrics into FHIR DiagnosticReport payloads.
What you are building
The core problem, expected build, and operating context for this challenge.
Ingest gene packages downloaded via NCBI Datasets to evaluate eukaryotic transcript sequences. Validate coding coordinates and structure curated transcript metrics into FHIR DiagnosticReport payloads.
Biocurator
Download gene data packages containing transcript and protein FASTA using NCBI Datasets CLI arguments.
Parse multi-FASTA headers and sequence strings with Biopython to extract open reading frames.
Format transcript boundary evaluations and translation lengths into structured validation records.
Map transcript findings into FHIR DiagnosticReport and Observation resources for biocuration review.
Terminal command runner with browser-based split-view table displaying transcript alignments and FHIR JSON.
Download human gene package 672 via NCBI Datasets CLI sandbox using mock ZIP archives locally. Starter examples below are synthetic. They are not downloaded records.
NCBI Datasets gene download Uses NCBI Datasets CLI command options '--include gene,rna,cds,protein' to download multi-sequence zip archives.
pydantic-ai, biopython, fastapi. Validates structured schema objects representing transcript models before generating standard FHIR JSON payloads. Hosted LLM API with structured function calling support or local open model via Ollama.
Submit runnable source, pinned dependencies, setup commands, a working interface, example outputs, and a recorded end-to-end demo. Include tests and an action log.
Parses multi-sequence transcript FASTA files using Biopython without unhandled exception flags.
Emits valid JSON strictly matching FHIR R5 DiagnosticReport and Observation resource shapes.
Flags coding sequences missing valid ATG start codons or proper stop triplets.
```json [ { "input": { "gene_id": 672, "symbol": "BRCA1", "fasta_record": ">NM_007294.4 Homo sapiens BRCA1 transcript variant 1\nATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTGAAGAGCTATTGAAAATCATTTGTGCTTTTCAGCTTGACACAGGTTTGGAGTATGCAAACAGCTATAATTTTGCAAAAAAGGAAAATAACTCTCCTGAACATCTAAAAGATGAAGTTTCTATCATCCAAAGTATGGGCTACAGAAACCGTGCCAAAAGACTTCTTACAGAAAGTGAACCCAAAATCCTCATTTGA" }, "expected_output": { "curation_status": "valid", "transcript_id": "NM_007294.4", "cds_length_bp": 348, "start_codon": "ATG", "stop_codon": "TGA", "in_frame": true, "fhir_resource": "DiagnosticReport" } }, { "input": { "gene_id": 672, "symbol": "BRCA1", "fasta_record": ">NM_truncated Homo sapiens BRCA1 incomplete\nCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGC" }, "expected_output": { "curation_status": "flagged", "transcript_id": "NM_truncated", "cds_length_bp": 60, "start_codon": "CCA", "stop_codon": "TGC", "in_frame": false, "fhir_resource": "DiagnosticReport" } } ] ```
Synthetic and de-identified NCBI public reference data only; non-diagnostic curation sandbox without patient health identifiers. Use mock external writes. Require human review before any real deployment.
Participation guide
Synthetic and de-identified NCBI public reference data only; non-diagnostic curation sandbox without patient health identifiers. Use mock external writes and human review.
How work is evaluated
Parses multi-sequence transcript FASTA files using Biopython without unhandled exception flags. Emits valid JSON strictly matching FHIR R5 DiagnosticReport and Observation resource shapes. Flags coding sequences missing valid ATG start codons or proper stop triplets.
Runnable source, pinned dependencies, setup commands, working interface, example outputs, recorded demo, tests, and action logs.
Challenge datasets
Public datasets, plus the private datasets you have access to.
How submissions are scored
These dimensions define what the evaluator checks and which criteria separate a passable run from a strong one.
Complete workflow
Download gene data packages containing transcript and protein FASTA using NCBI Datasets CLI arguments. Parse multi-FASTA headers and sequence strings with Biopython to extract open reading frames. Format transcript boundary evaluations and translation lengths into structured validation records. Map transcript findings into FHIR DiagnosticReport and Observation resources for biocuration review.
Missing or incorrect.
Partly complete, with documented gaps.
Complete, with reproducible evidence.
Correctness and evidence
Parses multi-sequence transcript FASTA files using Biopython without unhandled exception flags. Emits valid JSON strictly matching FHIR R5 DiagnosticReport and Observation resource shapes. Flags coding sequences missing valid ATG start codons or proper stop triplets.
Missing or incorrect.
Partly complete, with documented gaps.
Complete, with reproducible evidence.
Review interface
Terminal command runner with browser-based split-view table displaying transcript alignments and FHIR JSON.
Missing or incorrect.
Partly complete, with documented gaps.
Complete, with reproducible evidence.
Safe execution
Synthetic and de-identified NCBI public reference data only; non-diagnostic curation sandbox without patient health identifiers.
This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.
What you should walk away with
Download gene data packages containing transcript and protein FASTA using NCBI Datasets CLI arguments.
Parse multi-FASTA headers and sequence strings with Biopython to extract open reading frames.
Format transcript boundary evaluations and translation lengths into structured validation records.
Map transcript findings into FHIR DiagnosticReport and Observation resources for biocuration review.
Reference links and supporting material
Download human gene package 672 via NCBI Datasets CLI sandbox using mock ZIP archives locally. Supplied starter examples are synthetic, not source extracts.
Challenge setup
Configuration summary for this challenge.
Challenge input
Input details are not configured.
Pydantic AI
Typed Python agent framework.
Evaluated output
No output checks are configured.
- Download gene data packages containing transcript and protein FASTA using NCBI Datasets CLI arguments. Pars...
- Parses multi-sequence transcript FASTA files using Biopython without unhandled exception flags. Emits valid...
- Terminal command runner with browser-based split-view table displaying transcript alignments and FHIR JSON.
- 2 public reference cases
- 2 configured tools
Summary shows the first task, up to three tools, and up to three evidence items. Open the technical recipe to view all configured items.
View technical recipe
Configured tools
- Pydantic AI · Optional
- Pydantic AI · Optional
Evaluation contract
- Complete workflow · Weight 40
- Correctness and evidence · Weight 30
- Review interface · Weight 20
- Safe execution · Weight 10
Reference cases
- 2 public reference cases
Workflow tasks
No workflow tasks are configured.
Recipe freeze marker
No recipe freeze time is recorded.