ClinVar Annotations

Article
10/18/2024

Note

Important Update 9/19/2024: All URLs are changing. We are enabling public access to all Genomics Data Lake containers. The existing “signed URLs” (shared access signatures) will be retired at: 2024-11-04T00:00:00Z. After this time, the URLs without a query string will continue to work, however the “signed URLs” will no longer work and will return a 403 HTTP status code. Please plan accordingly to access the public URLs without a query string after this date (remove the ‘?’ and trailing characters).

The ClinVar resource is a freely accessible, public archive of reports - with supporting evidence - about the relationships among human variations and phenotypes. It facilitates access to and communication about the claimed relationships between human variation and observed health status, and about the history of that interpretation. It provides access to a broader set of clinical interpretations that researchers can incorporate into genomics workflows and applications.

Visit the Data Dictionary and the FAQ resource for more information about the data.

Note

Microsoft provides Azure Open Datasets on an “as is” basis. Microsoft makes no warranties, express or implied, guarantees or conditions with respect to your use of the datasets. To the extent permitted under your local law, Microsoft disclaims all liability for any damages or losses, including direct, consequential, special, indirect, incidental or punitive, resulting from your use of the datasets.

This dataset is provided under the original terms that Microsoft received source data. The dataset may include data sourced from Microsoft.

Data source

This dataset is a mirror of the National Library of Medicine ClinVar FTP resource.

Data update frequency

This dataset receives daily updates.

Data Access

FTP resource

FTP Overview

Use Terms

Data is available without restrictions. More information and citation details, see Accessing and using data in ClinVar.

Contact

For any questions or feedback about this dataset, contact clinvar@ncbi.nlm.nih.gov.

Data access

Azure Notebooks

azure-storage

Getting the ClinVar data from Azure Open Dataset

Several public genomics data resources were uploaded as Azure Open Dataset at this resource.

Calling the data from 'ClinVar Data Set'

import azureml.core
print("Azure ML SDK Version: ", azureml.core.VERSION)

from azureml.core import  Dataset
reference_dataset = Dataset.File.from_files('https://datasetclinvar.blob.core.windows.net/dataset')
mount = reference_dataset.mount()

import os

REF_DIR = '/dataset'
path = mount.mount_point + REF_DIR

with mount:
    print(os.listdir(path))

import pandas as pd

# create mount context
mount.start()

# specify path to README file
REF_DIR = '/dataset'
metadata_filename = '{}/{}/{}'.format(mount.mount_point, REF_DIR, '_README')

# read README file
metadata = pd.read_table(metadata_filename)
metadata

Download the specific file

import os
import uuid
import sys
from azure.storage.blob import BlockBlobService, PublicAccess

blob_service_client = BlockBlobService(account_name='datasetclinvar', sas_token='sv=2019-02-02&se=2050-01-01T08%3A00%3A00Z&si=prod&sr=c&sig=qFPPwPba1RmBvaffkzkLuzabYU5dZstSTgMwxuLNME8%3D')     
blob_service_client.get_blob_to_path('dataset', 'ClinVarFullRelease_00-latest.xml.gz.md5', './ClinVarFullRelease_00-latest.xml.gz.md5')

Next steps

View the rest of the datasets in the Open Datasets catalog.

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