Python client for OmicsDI Restful API
Project description
ddipy
An Python package to obtain data from the Omics Discovery Index (OmicsDI. It uses the RESTful Web Services at OmicsDI WS for that purpose.
Installation
we need to install ddipy
:
pip install ddipy
Examples
This example shows how retrieve details of one dataset by using the Python package ddipy.
from ddipy.dataset_client import DatasetClient
if __name__ == '__main__':
client = DatasetClient()
res = client.get_dataset_details("pride", "PXD000210", False)
This example shows a search for all the datasets for human.
from ddipy.dataset_client import DatasetClient
if __name__ == '__main__':
client = DatasetClient()
res = client.search("cancer human", "publication_date", "ascending")
This example shows a search for all the datasets for cancer human and loop over the pagination
from ddipy.dataset_client import DatasetClient
if __name__ == '__main__':
client = DatasetClient()
res = client.search("cancer human", "publication_date", "ascending", 1200, 30, 20)
This example is a query to retrieve all the datasets that reported the UniProt protein P21399 as identified.
from ddipy.dataset_client import DatasetClient
if __name__ == '__main__':
client = DatasetClient()
res = client.search("UNIPROT:P21399")
This example is a query to find all the datasets where the gene ENSG00000147251 is reported as differentially expressed.
from ddipy.dataset_client import DatasetClient
if __name__ == '__main__':
client = DatasetClient()
res = client.search("ENSEMBL:ENSG00000147251")
This example is a query to retrieve all databases recorded in OmicsDI
from ddipy.dataset_client import DatabaseClient
if __name__ == '__main__':
client = DatabaseClient()
res = client.get_database_all()
This example is retriveing JSON+LD for dataset page
from ddipy.dataset_client import SeoClient
if __name__ == '__main__':
client = SeoClient()
res = client.get_seo_dataset("pride", "PXD000210")
This example is retriveing JSON+LD for home page
from ddipy.dataset_client import SeoClient
if __name__ == '__main__':
client = SeoClient()
res = client.get_seo_home()
This example is a query for statistics about the number of datasets per Tissue
from ddipy.dataset_client import StatisticsClient
if __name__ == '__main__':
client = StatisticsClient()
res = client.get_statistics_tissues(20)
This example is a query for statistics about the number of datasets per dieases
from ddipy.dataset_client import StatisticsClient
if __name__ == '__main__':
client = StatisticsClient()
res = client.get_statistics_diseases(20)
This example for searching dictionary terms
from ddipy.dataset_client import TermClient
if __name__ == '__main__':
client = TermClient()
res = client.get_term_by_pattern("hom", 10)
This example for retrieving frequently terms from the repo
from ddipy.dataset_client import TermClient
if __name__ == '__main__':
client = TermClient()
res = client.get_term_by_pattern("pride", "description", 20)
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