ClinVar Annotations
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. It facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. It provides access to a broader set of clinical interpretations that can be incorporated into genomics workflows and applications.
For more information on the data, see the Data Dictionary and FAQ.
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 ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/
Data volumes and update frequency
This dataset contains approximately 56 GB of data and is updated daily.
Storage location
This dataset is stored in the West US 2 and West Central US Azure regions. Allocating compute resources in West US 2 or West Central US is recommended for affinity.
Data Access
West US 2: 'https://datasetclinvar.blob.core.windows.net/dataset'
West Central US: 'https://datasetclinvar-secondary.blob.core.windows.net/dataset'
SAS Token: sv=2019-02-02&se=2050-01-01T08%3A00%3A00Z&si=prod&sr=c&sig=qFPPwPba1RmBvaffkzkLuzabYU5dZstSTgMwxuLNME8%3D
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
Getting the ClinVar data from Azure Open Dataset
Several public genomics data has been uploaded as an Azure Open Dataset here. We create a blob service linked to this open dataset. You can find examples of data calling procedure from Azure Open Dataset for ClinVar
dataset in below:
Users can call and download the following path with this notebook: 'https://datasetclinvar.blob.core.windows.net/dataset/ClinVarFullRelease_00-latest.xml.gz.md5'
Note
Users needs to log-in their Azure Account via Azure CLI for viewing the data with Azure ML SDK. On the other hand, they do not need do any actions for downloading the data.
For more information on installing the Azure CLI, see Install the Azure CLI
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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