Uploading Sample and Data Relationship Format for Proteomics (SDRF-Proteomics) to CKG as Experimental Design and Clinical Data.

Here, we show how to easily upload SDRF-proteomcis standard format to CKG by converting it into the Experimental design and clinical data required by CKG.

from ckg.graphdb_builder import builder_utils

Read SDRF file and convert it to CKG format

df = builder_utils.convert_sdrf_file_to_ckg('../assets/example.sdrf')

df.head()

	subject external_id	biological_sample external_id	analytical_sample external_id	grouping1	tissue	Alkaline phosphatase measurement (88810008)	Aspartate aminotransferase measurement (45896001)	Bilirubin level (302787001)	Body mass index (60621009)	Fasting blood glucose level (271062006)	Low density lipoprotein cholesterol measurement (113079009)	Alanine aminotransferase measurement (34608000)	Waist circumference (276361009)
0	31	31	31_C6	Healthy	blood plasma	54.0	30.0	15.0	27.774423	5.07	2.1	24.0	108.0
1	32	32	32_C7	Healthy	blood plasma	27.0	28.0	17.0	28.727377	6.09	4.3	27.0	108.0
2	33	33	33_C8	Healthy	blood plasma	69.0	21.0	9.0	28.841532	4.93	4.1	18.0	90.0
3	34	34	34_C9	Healthy	blood plasma	101.0	26.0	12.0	42.056933	5.33	4.8	22.0	134.0
4	35	35	35_C10	Healthy	blood plasma	61.0	25.0	8.0	29.434851	4.80	3.9	18.0	102.0

Extract Experimental Design

experimental_design_cols = ['subject external_id', 'biological_sample external_id', 'analytical_sample external_id', 'grouping1']
experimental_design_data = df[experimental_design_cols]

experimental_design_data.head()

	subject external_id	biological_sample external_id	analytical_sample external_id	grouping1
0	31	31	31_C6	Healthy
1	32	32	32_C7	Healthy
2	33	33	33_C8	Healthy
3	34	34	34_C9	Healthy
4	35	35	35_C10	Healthy