Gene–Disease Evidence, Dosage and Actionability¶

See the FAQ for dependencies and return conventions.

1) Retrieve ClinGen gene dosage sensitivity curations¶

Purpose: Retrieve ClinGen gene dosage sensitivity curations.
Method: Use ClinGenDosage to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_dosage_by_gene(*, gene=None, gene_symbol=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a list of records; each record includes symbol, hgnc_id, location, grch37 and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_dosage_by_gene(
    gene='BRCA1',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "symbol": "<string>",
    "hgnc_id": "<string>",
    "location": "<string>",
    "grch37": "<string>",
    "grch38": "<string>",
    "haplo_assertion": "<integer>",
    "triplo_assertion": "<integer>",
    "pli": "<number>"
  }
]

Full parameters and usage notes

2) Search ClinGen dosage sensitivity by genomic interval¶

Purpose: Search ClinGen dosage sensitivity by genomic interval.
Method: Use ClinGenDosage to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_dosage_region_search(*, chromosome, start, end, assembly=None, verbose=True)
Input: Provide chromosome, start, end.
Output: Returns a list of records; each record includes symbol, hgnc_id, type, location and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_dosage_region_search(
    chromosome='17',
    start=43044295,
    end=43125370,
    assembly='GRCh38',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "symbol": "<string>",
    "hgnc_id": "<string>",
    "type": "<integer>",
    "location": "<string>",
    "grch37": "<string>",
    "grch38": "<string>",
    "haplo_assertion": "<integer>",
    "triplo_assertion": "<integer>"
  }
]

Full parameters and usage notes

3) Retrieve adult clinical actionability curations¶

Purpose: Retrieve adult clinical actionability curations.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_get_actionability_adult(*, gene=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a list of records; each record includes docId, topicIri, curationType, latestSearchDate and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_get_actionability_adult(
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "docId": "<string>",
    "topicIri": "<string>",
    "curationType": "<string>",
    "latestSearchDate": "<string>",
    "lastUpdated": "<string>",
    "lastAuthor": "<string>",
    "context": "<string>",
    "contextIri": "<string>"
  }
]

Full parameters and usage notes

4) Retrieve pediatric clinical actionability curations¶

Purpose: Retrieve pediatric clinical actionability curations.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_get_actionability_pediatric(*, gene=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a list of records; each record includes docId, topicIri, curationType, latestSearchDate and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_get_actionability_pediatric(
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "docId": "<string>",
    "topicIri": "<string>",
    "curationType": "<string>",
    "latestSearchDate": "<string>",
    "lastUpdated": "<string>",
    "lastAuthor": "<string>",
    "context": "<string>",
    "contextIri": "<string>"
  }
]

Full parameters and usage notes

5) Retrieve ClinGen dosage sensitivity records¶

Purpose: Retrieve ClinGen dosage sensitivity records.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_get_dosage_sensitivity(*, gene=None, include_regions=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a list for “Retrieve ClinGen dosage sensitivity records”; the item shape is shown below.
Example code:

import dnakit

result = dnakit.databases.clin_gen_get_dosage_sensitivity(
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  "<object>"
]

Full parameters and usage notes

6) Retrieve ClinGen gene–disease validity curations¶

Purpose: Retrieve ClinGen gene–disease validity curations.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_get_gene_validity(*, gene=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a list for “Retrieve ClinGen gene–disease validity curations”; the item shape is shown below.
Example code:

import dnakit

result = dnakit.databases.clin_gen_get_gene_validity(
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  "<object>"
]

Full parameters and usage notes

7) Retrieve ClinGen variant classifications¶

Purpose: Retrieve ClinGen variant classifications.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_get_variant_classifications(*, gene=None, variant=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a list of records; each record includes Variation, ClinVar Variation Id, HGNC Gene Symbol, Disease and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_get_variant_classifications(
    gene='BRCA1',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "Variation": "<string>",
    "ClinVar Variation Id": "<string>",
    "HGNC Gene Symbol": "<string>",
    "Disease": "<string>",
    "Mondo Id": "<string>",
    "Assertion": "<string>",
    "Expert Panel": "<string>"
  }
]

Full parameters and usage notes

8) Search gene actionability across adult and pediatric contexts¶

Purpose: Search gene actionability across adult and pediatric contexts.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_search_actionability(*, gene, verbose=True)
Input: Provide gene.
Output: Returns a mapping with data, gene_searched, adult_count, pediatric_count and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_search_actionability(
    gene='BRCA1',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "data": {
    "Adult": [
      "<value>"
    ],
    "Pediatric": [
      "<value>"
    ]
  },
  "gene_searched": "<string>",
  "adult_count": "<integer>",
  "pediatric_count": "<integer>",
  "failed_contexts": "<object>",
  "note": "<string>",
  "source": "<string>"
}

Full parameters and usage notes

9) Search dosage sensitivity scores by gene symbol¶

Purpose: Search dosage sensitivity scores by gene symbol.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_search_dosage_sensitivity(*, gene, verbose=True)
Input: Provide gene.
Output: Returns a list of records; each record includes GENE SYMBOL, HGNC ID, HAPLOINSUFFICIENCY, TRIPLOSENSITIVITY and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_search_dosage_sensitivity(
    gene='MECP2',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "GENE SYMBOL": "<string>",
    "HGNC ID": "<string>",
    "HAPLOINSUFFICIENCY": "<string>",
    "TRIPLOSENSITIVITY": "<string>",
    "ONLINE REPORT": "<string>",
    "DATE": "<string>"
  }
]

Full parameters and usage notes

10) Search gene–disease validity by gene symbol¶

Purpose: Search gene–disease validity by gene symbol.
Method: Use ClinGen to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_gen_search_gene_validity(*, gene, verbose=True)
Input: Provide gene.
Output: Returns a list of records; each record includes GENE SYMBOL, GENE ID (HGNC), DISEASE LABEL, DISEASE ID (MONDO) and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_gen_search_gene_validity(
    gene='BRCA1',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "GENE SYMBOL": "<string>",
    "GENE ID (HGNC)": "<string>",
    "DISEASE LABEL": "<string>",
    "DISEASE ID (MONDO)": "<string>",
    "CLASSIFICATION": "<string>",
    "MOI": "<string>",
    "SOP": "<string>",
    "GCEP": "<string>"
  }
]

Full parameters and usage notes