retrieving expression data via the API

[Han Jo]

Dear *,

I am banging my head against the API and cannot find the right way to retrieve expression data. I am in particular interested in the study ccle_broad_2019.

Could anyone point me towards the right API call? I found the molecular profiles, e.g. ccle_broad_2019_protein_quantification and ccle_broad_2019_rna_seq_mrna but all I get is some meta information via the API.

I want to retrieve (ideally) all the matching RNA seq and protein expression samples from the study.

Here is snippet of what I have so far ...

Any help is greatly appreciated!

"""

from bravado.client import SwaggerClient

cbioportal = SwaggerClient.from_url('https://www.cbioportal.org/api/api-docs',
config={"validate_requests": False, "validate_responses": False,
"validate_swagger_spec": False})


studyid = "ccle_broad_2019"
ccl_study = cbioportal.Studies.getStudyUsingGET(studyId=studyid).result()
samples = cbioportal.Samples.getAllSamplesInStudyUsingGET(studyId=studyid).result()
print(len(samples))
profiles = cbioportal.Molecular_Profiles.getAllMolecularProfilesInStudyUsingGET(studyId=studyid, projection="DETAILED"
).result()
for i in profiles:
print(i.molecularProfileId)

data = cbioportal.Molecular_Data.getAllMolecularDataInMolecularProfileUsingGET(
entrezGeneId=2, molecularProfileId="ccle_broad_2019_protein_quantification",
sampleListId="ccle_broad_2019_all").result()
print(len(data))
for i in data[0]:
print(i, data[0])

"""

[Gaofei Zhao]

Hi Han,

You are doing it in a right way, you already get related protein related data.

To make your result more clear, you could change your last line from "print(i, data[0])" to "print(i, data[0][i])"

Then you will see something like this:

entrezGeneId ENTREZ_GENE_ID gene GENE molecularProfileId MOLECULAR_PROFILE_ID patientId PATIENT_ID sampleId SAMPLE_ID studyId STUDY_ID uniquePatientKey UNIQUE_PATIENT_KEY uniqueSampleKey UNIQUE_SAMPLE_KEY value EXPRESSION_DATA

The expression data is located in the value field (the last one).

[Sasha Dagayev]

Hi Han, 

I wrote a package for some of these issues here: https://pypistats.org/packages/cbio-py. 

If the endpoint that you're looking for isn't covered. I wrote this helper function to help transform the return objects from the Swagger client into a standard dictionary here: 

def return_to_dict_converter(return_type,return_list):
if type(return_list) == list:
if return_type == 'dict':
return_list_dict = []
for return_item in return_list:
return_item_dict = {}
for att in dir(return_item):
return_item_dict[att] = getattr(return_item, att)
return_list_dict.append(return_item_dict)
return return_list_dict
elif return_type == 'native':
return return_list

Hope this helps!

[Han Jo]

Thanks for the input!

@Gaofei Zhao Yes, true! Sorry, I didnt specify my problem precise enough. I just wasnt able to conveniently get ALL the protein/RNA data from "a single query". So I thought my approach was wrong or suboptimal at the least.

@Sasha thanks for the hint!

I will need to fiddle around a bit but might come back to you if my solution is too clumsy.

Cheers,

Sven

[debr...@mskcc.org]

Hi Sven,

 

The API is optimized for slicing data. That is pulling a subset of cases and a subset of genes. If you are looking to download all the data, it might be better to download the data files for the entire study from our datahub. See e.g.:

 

https://github.com/cBioPortal/datahub/tree/master/public/ccle_broad_2019

 

Hope that helps!

 

Best wishes,

Ino

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