Build a Gene Catalog Nomenclature Drift Detector

Evaluate gene symbol synonym catalogs from NCBI Datasets gene reports against FHIR terminology standards. Detect naming conflicts across multi-species registries and record migration actions.

Genomic Terminology Curator

Extract gene symbols and synonym lists from downloaded NCBI gene metadata reports.

Audit extracted nomenclatures against FHIR CodeSystem and ConceptMap structures.

Detect ambiguous multi-symbol collisions or deprecated HGNC nomenclature strings.

Produce standardized FHIR ConceptMap entries detailing recommended term mappings.

Web interface showing nomenclature conflict alerts, symbol mapping graphs, and approved synonym dictionaries.

Ingest public human gene metadata reports via NCBI Datasets command for symbols ACRV1 and A2M. Starter examples below are synthetic. They are not downloaded records.

NCBI Datasets gene download Extracts gene symbols and synonyms from NCBI Datasets gene report metadata formats.

crewai, pydantic, duckdb. crewai coordinates distinct curation sub-tasks including terminology validation, synonym parsing, and conflict auditing. Hosted or local model via OpenAI-compatible endpoints with structured JSON emission capabilities.

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.

Extract all reported gene synonyms from NCBI metadata JSON files.

Produce a valid FHIR ConceptMap element with equivalence mapping fields.

Flag cases where one symbol maps to multiple distinct NCBI Gene IDs.

```json [ { "input": { "gene_id": "2", "symbol": "A2M", "synonyms": [ "A2MD", "CPAMD5", "FWP007" ], "hgnc_approved": "A2M" }, "expected_output": { "resourceType": "ConceptMap", "status": "active", "group": [ { "source": "http://ncbi.nlm.nih.gov/gene", "target": "http://www.genenames.org", "element": [ { "code": "A2M", "target": [ { "code": "HGNC:7", "equivalence": "equivalent" } ] } ] } ], "collision_detected": false } }, { "input": { "gene_id": "99999", "symbol": "OCT4", "synonyms": [ "POU5F1", "OCT3" ], "hgnc_approved": "POU5F1" }, "expected_output": { "resourceType": "ConceptMap", "status": "draft", "group": [ { "source": "http://ncbi.nlm.nih.gov/gene", "target": "http://www.genenames.org", "element": [ { "code": "OCT4", "target": [ { "code": "HGNC:9221", "equivalence": "wider" } ] } ] } ], "collision_detected": true } } ] ```

Performs lexical terminology validation only. Synthetic records used without patient identifiers or diagnostic impact. Use mock external writes. Require human review before any real deployment.