Build a Gene Functional Evidence Publication Matcher

Extract gene symbols and RefSeq accessions from NCBI Datasets packages to retrieve literature abstracts. Synthesize structured evidence matrices linked to FHIR DiagnosticReport payloads.

Functional Biocurator

Extract canonical gene symbols and RefSeq accessions from NCBI Datasets gene data packages.

Retrieve indexed open scientific abstracts matching gene accession queries using Haystack.

Synthesize functional evidence statements summarizing protein molecular functions and pathways.

Link extracted evidence statements to FHIR DiagnosticReport resources with narrative sections.

Curator desktop web app displaying paper citations alongside proposed FHIR narrative snippets.

Download open access scientific summary corpora and synthetic NCBI gene packages for human BRCA1 (gene-id: 672). Starter examples below are synthetic. They are not downloaded records.

NCBI Datasets gene download Uses NCBI Datasets gene-id syntax 'datasets download gene gene-id 672 --include gene,protein' to seed literature queries.

haystack, biopython, qdrant. Orchestrates retriever-reader pipelines over biomedical abstracts to match gene accessions with published evidence. High-capability reasoning model with 32k context for comprehensive document synthesis.

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.

Indexes and searches biomedical literature text using canonical NCBI gene identifiers.

Produces synthesized evidence summaries containing verified document accession citations.

Outputs FHIR DiagnosticReport JSON containing a compliant human-readable narrative div.

```json [ { "input": { "gene_id": 672, "symbol": "BRCA1", "abstract_text": "BRCA1 plays a critical role in DNA repair through homologous recombination, interacting directly with BARD1." }, "expected_output": { "gene_symbol": "BRCA1", "functional_summary": "Involved in DNA repair via homologous recombination and forms complexes with BARD1.", "citations_found": 1, "fhir_narrative_generated": true } }, { "input": { "gene_id": 99999, "symbol": "C9orf000", "abstract_text": "Uncharacterized open reading frame with unknown biological function and no documented protein interactions." }, "expected_output": { "gene_symbol": "C9orf000", "functional_summary": "Uncharacterized locus with no documented molecular function.", "citations_found": 0, "fhir_narrative_generated": true } } ] ```

Research evidence synthesis only; non-diagnostic and not for patient therapy selection. Use mock external writes. Require human review before any real deployment.