Generic Assay Data#

The module generic_assay_data provides functions related to Generic Assay Data section of cBioPortal Web Public API.

pybioportal.generic_assay_data.fetch_generic_assay_data(generic_assay_stable_ids=None, molecular_profile_ids=None, sample_molecular_identifiers=None, projection='SUMMARY')#

Fetch generic assay data from multiple molecular profiles in cBioPortal providing

List of Molecular Profile ID and Sample ID pairs or List of Molecular Profile IDs and Generic Assay IDs.

Parameters:

generic_assay_stable_ids (list of str) – List of Generic Assay IDs, e.g. [“TULP4_pS563”, “TEP1_pS397”]
molecular_profile_ids (list of str) – List of Molecular Profile IDs, e.g. [“brca_tcga_phosphoprotein_quantification”,”brain_cptac_2020_phosphoprotein”]
sample_molecular_identifiers – List of Molecular Profile ID and Sample IDs pairs.
projection (str) –
Level of detail of the response.

Possible values:
- ”DETAILED”: Detailed information.
- ”ID”: Information with only IDs.
- ”META”: Metadata information.
- ”SUMMARY”: Summary information (default).

Returns:

A DataFrame containing the fetched generic assay data.

Return type:

pandas.DataFrame

pybioportal.generic_assay_data.fetch_generic_assay_data_in_molecular_profile(molecular_profile_id, generic_assay_stable_ids=None, sample_ids=None, sample_list_id=None, projection='SUMMARY')#

Fetch generic assay data in a specific molecular profile from cBioPortal.

Parameters:

molecular_profile_id (str) – Molecular Profile ID (e.g., “brca_tcga_phosphoprotein_quantification”).
generic_assay_stable_ids (List of str) – List of Generic Assays IDs (e.g., [“TULP4_pS563”, “TEP1_pS397”]).
sample_ids (List of str) – List of Sample IDs (e.g., [“TCGA-C8-A130-01”, “TCGA-C8-A134-01”] and sample_list_id set to None).
sample_list_id (str) – Sample List ID (e.g., “brca_tcga_all” and sample_ids set to None).
projection (str) –
Level of detail of the response.

Possible values:
- ”DETAILED”: Detailed information.
- ”ID”: Information with only IDs.
- ”META”: Metadata information.
- ”SUMMARY”: Summary information (default).

Returns:

A DataFrame containing the fetched generic assay data in the specified molecular profile.

Return type:

pandas.DataFrame

pybioportal.generic_assay_data.get_generic_assay_data_in_molecular_profile(molecular_profile_id, generic_assay_stable_id, projection='SUMMARY')#

Get generic assay data in a molecular profile from cBioPortal.

Parameters:

molecular_profile_id (str) – Molecular Profile ID.
generic_assay_stable_id (str) – Generic Assay stable ID.
projection (str) –
Level of detail of the response.

Possible values:
- ”DETAILED”: Detailed information.
- ”ID”: Information with only IDs.
- ”META”: Metadata information.
- ”SUMMARY”: Summary information (default).

Returns:

A DataFrame containing the generic assay data in the specified molecular profile.

Return type:

pandas.DataFrame

Examples#

from pybioportal import generic_assay_data as gad

df1a = gad.fetch_generic_assay_data_in_molecular_profile(molecular_profile_id="brca_tcga_phosphoprotein_quantification",
                                                         generic_assay_stable_ids = ["TULP4_pS563", "TEP1_pS397"],
                                                         sample_ids = ["TCGA-C8-A130-01", "TCGA-C8-A134-01"])
df1a

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	value	genericAssayStableId	stableId
0	VENHQS1DOC1BMTMwLTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTMwOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A130-01	TCGA-C8-A130	brca_tcga	0.31374650000644216	TEP1_pS397	TEP1_pS397
1	VENHQS1DOC1BMTMwLTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTMwOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A130-01	TCGA-C8-A130	brca_tcga	1.8338606392734915	TULP4_pS563	TULP4_pS563
2	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.13629911078391418	TEP1_pS397	TEP1_pS397
3	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	-0.2314224260050513	TULP4_pS563	TULP4_pS563

df1b = gad.fetch_generic_assay_data_in_molecular_profile(molecular_profile_id="brca_tcga_phosphoprotein_quantification",
                                                         generic_assay_stable_ids = ["TULP4_pS563", "TEP1_pS397"],
                                                         sample_list_id = "brca_tcga_all")
df1b

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	value	genericAssayStableId	stableId
0	VENHQS1BMi1BMENNLTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMENNOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-A2-A0CM-01	TCGA-A2-A0CM	brca_tcga	0.3990168921075522	TEP1_pS397	TEP1_pS397
1	VENHQS1BMi1BMEQyLTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMEQyOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-A2-A0D2-01	TCGA-A2-A0D2	brca_tcga	-0.6936246814411646	TEP1_pS397	TEP1_pS397
2	VENHQS1BMi1BMEVRLTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMEVROmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-A2-A0EQ-01	TCGA-A2-A0EQ	brca_tcga	0.3121367021962257	TEP1_pS397	TEP1_pS397
3	VENHQS1BMi1BMEVWLTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMEVWOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-A2-A0EV-01	TCGA-A2-A0EV	brca_tcga	-1.14562097925631	TEP1_pS397	TEP1_pS397
4	VENHQS1BMi1BMEVYLTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMEVYOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-A2-A0EX-01	TCGA-A2-A0EX	brca_tcga	0.20418754958872287	TEP1_pS397	TEP1_pS397
...	...	...	...	...	...	...	...	...	...
65	VENHQS1DOC1BMTM4LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM4OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A138-01	TCGA-C8-A138	brca_tcga	0.6359899875778352	TEP1_pS397	TEP1_pS397
66	VENHQS1EOC1BMTQyLTAxOmJyY2FfdGNnYQ	VENHQS1EOC1BMTQyOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-D8-A142-01	TCGA-D8-A142	brca_tcga	-0.578947377398709	TEP1_pS397	TEP1_pS397
67	VENHQS1FMi1BMTU0LTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMTU0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-E2-A154-01	TCGA-E2-A154	brca_tcga	-0.3888088589350173	TEP1_pS397	TEP1_pS397
68	VENHQS1FMi1BMTU4LTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMTU4OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-E2-A158-01	TCGA-E2-A158	brca_tcga	-0.3037812098567177	TEP1_pS397	TEP1_pS397
69	VENHQS1FMi1BMTVBLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMTVBOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-E2-A15A-01	TCGA-E2-A15A	brca_tcga	-0.25129006810968774	TEP1_pS397	TEP1_pS397

70 rows × 9 columns

df2a = gad.fetch_generic_assay_data(generic_assay_stable_ids=["TULP4_pS563", "TEP1_pS397", "ALAD_214_215_1_1_S215"],
                                    molecular_profile_ids=["brca_tcga_phosphoprotein_quantification","brain_cptac_2020_phosphoprotein"])
df2a

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	value	genericAssayStableId	stableId
0	NzMxNi0xNzgxOmJyYWluX2NwdGFjXzIwMjA	UFRfTTFSWU43QjA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-1781	PT_M1RYN7B0	brain_cptac_2020	-0.696372026845622	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
1	NzMxNi0xNzkwOmJyYWluX2NwdGFjXzIwMjA	UFRfRVNIQUNXRjY6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-1790	PT_ESHACWF6	brain_cptac_2020	-0.890851197690543	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
2	NzMxNi04Nzg6YnJhaW5fY3B0YWNfMjAyMA	UFRfRVNIQUNXRjY6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-878	PT_ESHACWF6	brain_cptac_2020	-1.11503373579888	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
3	NzMxNi0yMTgxOmJyYWluX2NwdGFjXzIwMjA	UFRfR0g2OTNUVDg6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-2181	PT_GH693TT8	brain_cptac_2020	-0.819816432243918	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
4	NzMxNi0yMTQxOmJyYWluX2NwdGFjXzIwMjA	UFRfV0cyWjk1QjU6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-2141	PT_WG2Z95B5	brain_cptac_2020	-1.10382655624193	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
...	...	...	...	...	...	...	...	...	...
282	VENHQS1BUi1BMUFTLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFTOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-AR-A1AS-01	TCGA-AR-A1AS	brca_tcga	1.2692087467241393	TEP1_pS397	TEP1_pS397
283	VENHQS1BUi1BMUFWLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFWOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-AR-A1AV-01	TCGA-AR-A1AV	brca_tcga	-1.0879171469891096	TEP1_pS397	TEP1_pS397
284	VENHQS1BUi1BMUFXLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFXOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-AR-A1AW-01	TCGA-AR-A1AW	brca_tcga	-0.06646907668277764	TEP1_pS397	TEP1_pS397
285	VENHQS1CSC1BMERELTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMEREOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-BH-A0DD-01	TCGA-BH-A0DD	brca_tcga	-1.5077329846223932	TEP1_pS397	TEP1_pS397
286	VENHQS1CSC1BMERHLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMERHOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-BH-A0DG-01	TCGA-BH-A0DG	brca_tcga	0.18414782925259893	TEP1_pS397	TEP1_pS397

287 rows × 9 columns

df2b = gad.fetch_generic_assay_data(generic_assay_stable_ids=["TULP4_pS563", "TEP1_pS397", "ALAD_214_215_1_1_S215"],
                                    sample_molecular_identifiers=[
                                                      {"molecular_profile_id": "brca_tcga_phosphoprotein_quantification",
                                                       "sample_ids": ["TCGA-C8-A130-01", "TCGA-C8-A134-01"]},
                                                      {"molecular_profile_id": "brain_cptac_2020_phosphoprotein",
                                                       "sample_ids": ["7316-101", "7316-109"]}
                                                      ])
df2b

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	value	genericAssayStableId	stableId
0	NzMxNi0xMDE6YnJhaW5fY3B0YWNfMjAyMA	UFRfQ1dENzE3UTA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-101	PT_CWD717Q0	brain_cptac_2020	0.293524074916423	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
1	NzMxNi0xMDk6YnJhaW5fY3B0YWNfMjAyMA	UFRfNUZSMllBNkU6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-109	PT_5FR2YA6E	brain_cptac_2020	-0.709355260194312	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
2	VENHQS1DOC1BMTMwLTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTMwOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A130-01	TCGA-C8-A130	brca_tcga	0.31374650000644216	TEP1_pS397	TEP1_pS397
3	VENHQS1DOC1BMTMwLTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTMwOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A130-01	TCGA-C8-A130	brca_tcga	1.8338606392734915	TULP4_pS563	TULP4_pS563
4	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.13629911078391418	TEP1_pS397	TEP1_pS397
5	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	-0.2314224260050513	TULP4_pS563	TULP4_pS563

df2c = gad.fetch_generic_assay_data(sample_molecular_identifiers=[
                                                        {"molecular_profile_id": "brca_tcga_phosphoprotein_quantification",
                                                         "sample_ids": ["TCGA-C8-A130-01", "TCGA-C8-A134-01"]},
                                                        {"molecular_profile_id": "brain_cptac_2020_phosphoprotein",
                                                         "sample_ids": ["7316-101", "7316-109"]}
                                                        ])
df2c

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	value	genericAssayStableId	stableId
0	NzMxNi0xMDE6YnJhaW5fY3B0YWNfMjAyMA	UFRfQ1dENzE3UTA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-101	PT_CWD717Q0	brain_cptac_2020	0.293524074916423	ALAD_214_215_1_1_S215	ALAD_214_215_1_1_S215
1	NzMxNi0xMDE6YnJhaW5fY3B0YWNfMjAyMA	UFRfQ1dENzE3UTA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-101	PT_CWD717Q0	brain_cptac_2020	1.18589905169363	ALDOA_36_39_1_1_S36	ALDOA_36_39_1_1_S36
2	NzMxNi0xMDE6YnJhaW5fY3B0YWNfMjAyMA	UFRfQ1dENzE3UTA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-101	PT_CWD717Q0	brain_cptac_2020	1.05737336393577	ALDOA_36_39_1_1_S39	ALDOA_36_39_1_1_S39
3	NzMxNi0xMDE6YnJhaW5fY3B0YWNfMjAyMA	UFRfQ1dENzE3UTA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-101	PT_CWD717Q0	brain_cptac_2020	0.0624267000967347	ALDOA_46_52_1_1_S46	ALDOA_46_52_1_1_S46
4	NzMxNi0xMDE6YnJhaW5fY3B0YWNfMjAyMA	UFRfQ1dENzE3UTA6YnJhaW5fY3B0YWNfMjAyMA	brain_cptac_2020_phosphoprotein	7316-101	PT_CWD717Q0	brain_cptac_2020	-1.46987364905827	ANK1_1684_1693_1_1_S1686	ANK1_1684_1693_1_1_S1686
...	...	...	...	...	...	...	...	...	...
56312	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.6904941038059361	OTUD4_pS320	OTUD4_pS320
56313	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.5406159008386409	TBKBP1_pS415	TBKBP1_pS415
56314	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.34418985891868537	PTPN3_pS241	PTPN3_pS241
56315	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.6839793452245334	SIK2_pT484	SIK2_pT484
56316	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	0.36039894811889295	PKN2_pT958	PKN2_pT958

56317 rows × 9 columns

df3 = gad.get_generic_assay_data_in_molecular_profile(molecular_profile_id = "brca_tcga_phosphoprotein_quantification",
                                                      generic_assay_stable_id = "TULP4_pS563")
df3

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	value	genericAssayStableId	stableId
0	VENHQS1BOC1BMDlHLTAxOmJyY2FfdGNnYQ	VENHQS1BOC1BMDlHOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-A8-A09G-01	TCGA-A8-A09G	brca_tcga	-2.1236739808061182	TULP4_pS563	TULP4_pS563
1	VENHQS1DOC1BMTMwLTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTMwOmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A130-01	TCGA-C8-A130	brca_tcga	1.8338606392734915	TULP4_pS563	TULP4_pS563
2	VENHQS1DOC1BMTM0LTAxOmJyY2FfdGNnYQ	VENHQS1DOC1BMTM0OmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-C8-A134-01	TCGA-C8-A134	brca_tcga	-0.2314224260050513	TULP4_pS563	TULP4_pS563
3	VENHQS1CSC1BMThRLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMThROmJyY2FfdGNnYQ	brca_tcga_phosphoprotein_quantification	TCGA-BH-A18Q-01	TCGA-BH-A18Q	brca_tcga	-2.3187358473784534	TULP4_pS563	TULP4_pS563