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)

Find out about us in our GitHub profiles:

Yasset Perez-Riverol
Pan Xu