minor fixes suggested by coderabbitai

Author: stolpeo

data/acmg_sf/3.3/acmg_sf.spec.yaml

@@ -7,7 +7,7 @@ dc.description: >
   and then translated to ENSEMBL and Entrez/NCBI gene ID with the
   HGNC BioMart
 dc.date: 2026-02-09
-dc.creator: American Collect of Medical Genetics
+dc.creator: American College of Medical Genetics
 dc.contributor:
   - VarFish Developer Team
 dc.source:
@@ -30,12 +30,12 @@ tsv.columns:
   - name: disease_phenotype
     description: Name of the relevant disorder(s).
   - name: disorder_mim
-    description: MIM code of the relevant disorder(s).s
+    description: MIM code of the relevant disorder(s).
   - name: phenotype_category
     description: Phenotype category.
   - name: inheritance
     description: Mode(s) of inheritance.
   - name: sf_list_version
     description: ACMG SF list version that this gene first appeared in.
   - name: variants_to_report
-    description: comment on which variants are to be reported.
+    description: Comment on which variants are to be reported.

scripts/enrich_acmg_sf.py

@@ -44,7 +44,7 @@ def fetch_gene_info_from_hgnc(gene_symbol: str) -> Optional[Dict[str, str]]:
             return {
                 "hgnc_id": doc.get("hgnc_id", ""),
                 "ensembl_gene_id": doc.get("ensembl_gene_id", ""),
-                "ncbi_gene_id": doc.get("entrez_id", ""),
+                "ncbi_gene_id": str(doc.get("entrez_id", "")),
                 "gene_symbol": doc.get("symbol", gene_symbol),
             }
         else:
@@ -117,7 +117,6 @@ def process_acmg_sf_file(input_file: str, output_file: str, delay: float = 0.2):
                 gene_info = fetch_gene_info_from_hgnc(gene_symbol)
                 if gene_info:
                     gene_cache[gene_symbol] = gene_info
-                    time.sleep(delay)  # Be respectful to the API
                 else:
                     # Create empty entry if not found
                     gene_cache[gene_symbol] = {
@@ -126,6 +125,7 @@ def process_acmg_sf_file(input_file: str, output_file: str, delay: float = 0.2):
                         "ncbi_gene_id": "",
                         "gene_symbol": gene_symbol,
                     }
+                time.sleep(delay)  # Be respectful to the API
 
             gene_info = gene_cache[gene_symbol]