Build an NCBI Gene Package RefSeq Annotation and Semantic Kernel Indexer
Extract gene metadata and RefSeq accession catalogs from NCBI Datasets archive packages. Build an index of functional annotations and link them to FHIR DiagnosticReport resources.
What you are building
The core problem, expected build, and operating context for this challenge.
Extract gene metadata and RefSeq accession catalogs from NCBI Datasets archive packages. Build an index of functional annotations and link them to FHIR DiagnosticReport resources.
Genomics Research Engineer
Extract gene data packages containing gene, RNA, and protein accessions.
Parse accession mappings across eukaryotic transcript isoforms.
Index functional definitions using Semantic Kernel connectors.
Export FHIR R5 DiagnosticReport resources summarizing transcript catalog status.
Console-based search and export tool producing FHIR DiagnosticReport packages.
Fetch reference gene metadata via NCBI Datasets CLI using command 'datasets download gene gene-id 1 2 3'. Starter examples below are synthetic. They are not downloaded records.
NCBI Datasets gene download Uses NCBI Datasets accession arguments (RefSeq nucleotide and protein accessions) to extract transcript structures.
semantic-kernel, biopython, pydantic. Semantic Kernel enables structured plugin skills to orchestrate multi-step data transformation and search indexing. Hosted Claude or OpenAI model through Semantic Kernel native connector.
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.
Successfully parses NCBI Datasets data package reports into accession tables.
Semantic Kernel skills accurately categorize RefSeq NM_ and NP_ identifiers.
Generates FHIR DiagnosticReport objects linked to specific gene IDs.
```json [ { "input": { "gene_id": "2", "symbol": "A2M", "transcripts": [ "NM_000014.6" ], "proteins": [ "NP_000005.3" ] }, "expected_output": { "report_id": "REP-GENE-2", "matched_accessions": 2, "indexing_status": "INDEXED", "transcript_count": 1, "protein_count": 1 } }, { "input": { "gene_id": "999999", "symbol": "UNKNOWN", "transcripts": [], "proteins": [] }, "expected_output": { "report_id": "REP-GENE-999999", "matched_accessions": 0, "indexing_status": "EMPTY_CATALOG", "transcript_count": 0, "protein_count": 0 } } ] ```
Designed solely for reference genome sequence indexing without clinical diagnosis or therapeutic intent. Use mock external writes. Require human review before any real deployment.
Participation guide
Designed solely for reference genome sequence indexing without clinical diagnosis or therapeutic intent. Use mock external writes and human review.
How work is evaluated
Successfully parses NCBI Datasets data package reports into accession tables. Semantic Kernel skills accurately categorize RefSeq NM_ and NP_ identifiers. Generates FHIR DiagnosticReport objects linked to specific gene IDs.
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
Extract gene data packages containing gene, RNA, and protein accessions. Parse accession mappings across eukaryotic transcript isoforms. Index functional definitions using Semantic Kernel connectors. Export FHIR R5 DiagnosticReport resources summarizing transcript catalog status.
Missing or incorrect.
Partly complete, with documented gaps.
Complete, with reproducible evidence.
Correctness and evidence
Successfully parses NCBI Datasets data package reports into accession tables. Semantic Kernel skills accurately categorize RefSeq NM_ and NP_ identifiers. Generates FHIR DiagnosticReport objects linked to specific gene IDs.
Missing or incorrect.
Partly complete, with documented gaps.
Complete, with reproducible evidence.
Review interface
Console-based search and export tool producing FHIR DiagnosticReport packages.
Missing or incorrect.
Partly complete, with documented gaps.
Complete, with reproducible evidence.
Safe execution
Designed solely for reference genome sequence indexing without clinical diagnosis or therapeutic intent.
This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.
What you should walk away with
Extract gene data packages containing gene, RNA, and protein accessions.
Parse accession mappings across eukaryotic transcript isoforms.
Index functional definitions using Semantic Kernel connectors.
Export FHIR R5 DiagnosticReport resources summarizing transcript catalog status.
Reference links and supporting material
Fetch reference gene metadata via NCBI Datasets CLI using command 'datasets download gene gene-id 1 2 3'. Supplied starter examples are synthetic, not source extracts.
Challenge setup
Configuration summary for this challenge.
Challenge input
Input details are not configured.
Semantic Kernel
Agent Systems · Agent Frameworks
Evaluated output
No output checks are configured.
- Extract gene data packages containing gene, RNA, and protein accessions. Parse accession mappings across eu...
- Successfully parses NCBI Datasets data package reports into accession tables. Semantic Kernel skills accura...
- Console-based search and export tool producing FHIR DiagnosticReport packages.
- 2 public reference cases
- 1 configured tool
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
- Semantic Kernel · 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.