PDC Template Data Submission

Source:
Version:
How to Submit Data:

Proteomic Data Commons

PDC Data Dictionary:
Contact:

https://pdc.cancer.gov/data-dictionary/dictionary.html
[email protected]

v1.11
https://pdc.cancer.gov/pdc/submit-data

PDC Worksheets

Purpose for Worksheet

Description

Program-Project

Workspace data entry

Highest level of organization. The Program name will be used when registering your Program to PDC Workspace. The
name of the Project will be used in your creation of Project on the PDC Workspace.

Case_Matrix

Metadata Upload

The mapping of all the case identifiers to their respected sample(s) and aliquot(s) used in a study.

Case

Metadata Upload

The collection of all data related to a specific subject.

Demographic

Metadata Upload

The collection of data that characterizes the individual by means of segmenting the population.

Diagnosis

Metadata Upload

The collection of data from the results of the investigation, analysis, and recognition of the presence and nature of
disease, condition, or injury from expressed signs and symptoms.

Exposure

Metadata Upload

The collection of clinically relevant patient information not immediately resulting from genetic predispositions.

Family History

Metadata Upload

Follow-Up

Metadata Upload

Treatment

Metadata Upload

The collection of records of a patient's background regarding cancer events of blood relatives.
The collection of records from a visit by a patient or study participant to a medical professional. A clinical encounter
that encompasses planned and unplanned trial interventions, procedures and assessments that may be performed
on a subject. A visit has a start and an end, each described with a rule. The process by which information about the
health status of an individual is obtained before and after a study has officially closed; an activity that continues
something that has already begun or that repeats something that has already been done.
The collection of records of the administration and intention of therapeutic agents provided to a patient to alter the
course of a pathologic process.
The collection of data relating to any material sample taken from a biological entity for testing, diagnostic,
propagation, treatment or research purposes.

Sample

Metadata Upload

Aliquots

Metadata Upload

Protocol

Workspace data entry

Study

Workspace data entry

Expt_Runmetadata

Workspace data entry

File_Metadata

Workspace data entry

NonRaw_File_Metadata

Workspace data entry

Publication

Workspace data entry

Reporter Ion Reagents

CDAP processing

You can also click the entity names throughout the worksheets for more information from
the PDC data dictionary.

Requirements for Worksheets

This worksheet is one of the 10 files needed for the Metadata upload of Clinical and
Biospecimen data.
If no data is present for numeric values, place as "null".
This worksheet is one of the 10 files needed for the Metadata upload of Clinical and
Biospecimen data.

This worksheet is one of the 10 files needed for the Metadata upload of Clinical and
Biospecimen data.

The collection of data pertaining to a portion of the whole of any one or more samples of something.
The formal plan of an experiment that provides the objective, design, and materials and methods used to conduct
the study. This information will be needed when creating your Protocol on PDC Workspace.
A detailed analysis of the study design. This information will aid in your Study creation on the PDC Workspace.
The general experimental metadata describing the study design(DIA,DDA). This information will aid in your Study
Attributes highlighted in blue are required as per experiment(label-free, iTRAQ or TMT
creation on the Workspace and provide guidance for copy/pasting aliquots in Create Study: Aliquot to Plex
channel).
The collection of files(".raw", ".d", ".wiff", ".wiff.scan", ".wiff.mtd", ".dat", ".mis") submitted by a user or generated
by a data analysis pipeline and the metadata associated to them. These files are to be uploaded to Workspace via
your local computer or S3. This information will aid in your Study creation on the Workspace and provide guidance
for copy/pasting plex or folder names and fraction number in Create Study: File to Plex
The collection of non-raw files from data submitters. May include those generated by a data analysis pipeline and the
metadata associated to them.
The published scientific research article describing a study.
Specifies the product number and lot number of all reagents used for each analytical sample within a study that is
part of the submission.

*Attributes highlighted in yellow are required fields to be filled out.
*All submitter IDs are assigned by you for purpose of tracking individual entities(e.g.:case, sample, study,etc..)