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Experience from Kids First (KF)

Authors: Abhijna Parigi, Marisa Lim

Maintainers: Abhijna Parigi, Marisa Lim

Version: 1.0

License: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Objectives:

This is a cookbook recipe documenting the extract & transform (ETL) process of converting the Kids First data into the C2M2 model.

In other words, process Kids First data for input into C2M2 model to produce Level 1 tables

Step by Step Process:

Step 1: Download data from the Kids First (KF) portal

  • Visit the KF portal website: https://portal.kidsfirstdrc.org/dashboard
  • Log in using your ORCID credentials (preferred), gmail or facebook credentials.
  • Select the File Repository tab on the main navigation bar at the top of the website.
drawing


  • Data can and must be downloaded a couple of different ways:
  • Click the columns option and select all columns. Click Export TSV.
  • Click Download and choose the option File Manifest (4th option of the dropdown menu).
  • Click Download and choose the option Biospecimen Data (3rd option of the dropdown menu)
drawing


Step 2: Data pre-processing:

  • Initial preprocessing: remove all the columns that do NOT have any headers.
  • Look at the KF datasets and select KF column names that correspond to the right C2M2 table column names. For the first, only the "core" C2M2 tables (Tables 1-4) and one association table (Table 5) were filled in. Core tables are the blue and black tables shown in the C2M2 documentation page.

The mapping used for the first pass of KF data is shown in the following tables. The number of rows for each table corresponds to the number of unique id entries.

Note: id_namespace and project_id_namespace have repeating values of cfde_id_namespace:3.

Table 1: file.tsv

source: exported TSV file

C2M2 colnames KF colnames
id_namespace
id File ID
project_id_namespace
project Study ID
persistent_id
creation_time
size_in_bytes File Size
sha256
md5
filename File Name
file_format File Format
data_type Data Type

Table 2: biosample.tsv

source of Biospecimen ID: exported TSV file source of Experiment Strategy: File Manifest source of Composition: Biospecimen Data

C2M2 colnames KF colnames
id_namespace
id Biospecimen ID
project_if_namespace
project Study ID
persistent_id
creation_time
assay_type Experiment Strategy
anatomy Composition

Table 3: subject.tsv

source: exported TSV file

C2M2 colnames KF colnames
id_namespace
id Participants ID
project_if_namespace
project Study ID
persistent_id
creation_time
granularity .

Note: granularity has this repeating value: cfde_subject_granularity:0. persistent_id and creation_time were left empty.

Table 4: project.tsv

source: exported TSV file

C2M2 colnames KF colnames
id_namespace
id Study ID
persistent_id
creation_time
abbreviation
name Study Name

Note: persistent_id, creation_time, and abbreviation were left empty.

Table 5: subject_role_taxonomy.tsv

source: exported TSV file

C2M2 colnames KF colnames
id_namespace
id Participants ID
role_id
taxonomy_id .

:octocat: warning: role_id has this repeating value: cfde_id_namespace:3 taxonomy_id has this repeating value: NCBI:txid9606

  • Find and replace KF variables in raw data TSVs with C2M2's controlled vocabulary (CV):

    • file_format: replace with corresponding EDAM terms from this link
    • data_type: replace with corresponding data terms from this link. Look for the data: tag.
    • anatomy: replcae with corresponding UBERON ID from this link
    • assay_type : replace with corresponding terms from this link. This was done programatically (in R) for the first pass because there are only 3 possible values.
WGS: OBI:0002117, whole-genome sequencing assay
RNA-Seq: OBI:0001271, RNA-seq assay
WXS: OBI:0002118, exome sequencing assay

Step 3: Find the gold tables

  • The gold tables are supplied by CFDE to the DCC and contain information that goes into the blue and green tables. They can be downloaded here.
  • If you are using the default Git repo structure for KF trial dataset, ensure that the three gold tables are in the folder titled KF_sample_C2M2_Level_1_bdbag.contents

Step 4: Add empty association tables

  • All association tables (i.e. all lighter blue and grey tables in the diagrams) must be provided in the folder containing the gold tables mentioned in step 3.
  • These tables must have the right column names, in the right order, but may remain otherwise empty.

Step 5: Running R script to wrangle data

  • Once you have downloaded your data, pre-processed it and made sure the columns are chosen, open up the R script
  • Ensure that the path to the raw data tables is set correctly.
  • Search (cmd + F) the script for write.table(). There should be 5 results. At each spot, make sure you edit the path to the folder in which you wish to write your .tsv files.
  • Run the entire script.
  • Navigate to your output folder and check the files.
  • If following this Git repo structure, paste all newly created tsvs into the folder called KF_sample_C2M2_Level_1_bdbag.contents.

Step 6: Building 'green' tables from core entity tables

  • This term-scanner script (with modifications to input/output path code) is used to auto-generate the green tables for the C2M2 Model Level 1 model. Currently, this script generates four of the five green tables for Level 1.
  • Default paths direct to the HMP example tsv files.

Inputs

  • It currently takes in biosample.tsv and file.tsv (two of the core-entity ETL instance TSVs, aka two of the three black tables) from the --draftDir (default is ../draft-C2M2_example_submission_data/HMP__sample_C2M2_Level_1_bdbag.contents)

  • It will load OBO and ontology files from --cvRefDir (default is external_CV_reference_files):

EDAM.version_1.21.tsv

OBI.version_2019-08-15.obo

uberon.version_2019-06-27.obo

Run script

The term-scanner script is named build_term_tables.py and you can run it like so:

# with default directory locations: change directory to `model`
cd ./model
python build_term_tables.py

# full command, if not using any default paths
./build_term_tables.py --draftDir [path/to/tsv/file/dir] --cvRefDir [path/to/external/CV/ref/files/dir] --outDir [dir/path/where/you/want/outputs/saved]

Run it with -h for command line help.

Outputs

It will produce these four green tables for Level 1: file_format.tsv,data_type.tsv, assay_type.tsv, and anatomy.tsv. The outputs are saved in --outDir (default is ./007_HMP-specific_CV_term_usage_TSVs).

Step 7: After all tables are created

  • Double check that all newly created tsvs (NOT raw data) are in the KF_sample_C2M2_Level_1_bdbag.contents folder.
  • Add the C2M2_Level_1.datapackage.json file to this folder.
  • Send the repo to CFDE tech folks.

Conclusion:

  • This recipe provides an examplar of how to convert a dataset from a DCC, KidsFirst in this example, into the format used by CFDE format for persistence into the DERIVA system.
  • Other examples of transformation are available or will be made available as guidance.