Proteomics Data Commons Home

Proteomics Data Management has three subprojects; Proteomics Data Commons (PDC), Clinical Proteomics Tumor Analysis Consortium (CPTAC) Data Assay Portal and CPTAC DCC (Data Coordinating Center). PDC starts on April 1, 2020 while the other two projects will start August 31^st 2021. All three projects are already underway with ESAC, Inc. The PDC is part of NCI’s CRDC. Reports are provided to Division of Cancer Biology (DCB) and through the BIDS monthly reporting system. Anticipated period of performance is 4 years, with severable funding. EPLC is needed and an ATO is already in place (held with ESAC).

Project Details:

YT20-068 (FCAS ID is NCI-CSSI-20-YT0057)

Task Order Title and Number: NCI Operational Task Order: 75N91019F00129

Contract type: Severable

Base period of performance: Date of Award - August 30, 2020

PIDS:

600.129.27.01.014.002.0001 – Proteomic Data Mgmt
600.129.27.01.014.002.0001.001 – Proteomic Data Mgmt;Gen
600.129.27.01.014.002.0001.007 – Proteomic Data Mgmt;TPM
600.129.27.01.014.002.0001.003 – Proteomic Data Mgmt;DEV

Subcontracts:

ESAC, Inc. Authorization to Proceed - April 1, 2020. To be replaced by Task Order under IDIQ for 20X042F (ESAC, Inc.).

Scope:

The vision for a Cancer Research Data Commons (CRDC) is a virtual, expandable infrastructure that will eventually support collaboration among researchers, computational scientists, and tool developers. It will house multiple cloud-based Commons Nodes for multiple data types, initially including genomic, imaging, and proteomics data. In the future, additional nodes will support other data types. Genomics data in the CRDC is supported by the Genomic Data Commons (GDC), which provides a means of data submission, user interfaces, and search & visualization tools. The proteomics data node, as described below, will incorporate data from the Clinical Proteomics Tumor Analysis Consortium (CPTAC) and other sources. The Office of Cancer Clinical Proteomics Research works closely with CBIIT to integrate the PDC with CRDC.

The Proteomic Data Commons (PDC) is a node of the CRDC that collects, harmonizes, and hosts proteomic data across a variety of sample types. It incorporates data from various programs including CPTAC and ICPC where the majority of data are generated from quantitative mass spectrometry-based proteomic targeted assays. The PDC is open access and provides a space to query, visualize, and download available datasets. PDC has migrated to production and can be viewed here: https://pdc.esacinc.com/pdc/ .

Anticipated PDC benefits:

Enhance access to NCI and research community-generated cancer proteomic data and tools
Take advantage of increases in compute efficiency and scalability
Accelerate bioinformatics tool development
Serve the individual researcher who has limited or no access to high-performance computing
Make proteomic data and analysis tools readily accessible to the broad cancer research community
Support collaboration across research institutes and scientific disciplines
Reduce data storage redundancies

Approach:

Leidos Biomed proposes to deliver on the baseline scope by organizing the project into six main activities; continue development and operations of the PDC, develop a PDC outreach plan, evaluate the current PDC system architecture, recommend any architecture changes, prepare for the option year scope, and project management. The PDC program is expected to continue after the current baseline POP (April 1st, 2020 – August 30th, 2020). The two other programs, CPTAC DCC and CPTAC Assay Portal will also begin but after the baseline POP.

Leidos Biomed’s approach to monitoring progress made by ESAC will include review of the monthly technical and financial status reports from ESAC and these reports will be supplemented with demonstrations by ESAC of new data and portal features. Leidos Biomed will work closely with NCI and ESAC to ensure that any discussions regarding this project’s scope clarifications, requirement completion status or prioritizations are held with all relevant stakeholders from Leidos Biomed, ESAC, and NCI. Moreover, the Leidos Biomed TPM will ensure that decisions are documented and shared with all the relevant stakeholders.

A. Continue development and operations of the PDC

The PDC was built by ESAC under direct contract with the NCI. The NCI wish to continue development and operations of the PDC without interruption even though NCI are transferring the project to the FNL. FNL will subcontract the PDC to ESAC to ensure continuity of the PDC. This activity will include:

A.1. Receive data for PDC from CPTAC, ICPC, and other NCI approved data sources
A.2. Conduct public releases of datasets through PDC
A.3. Develop workspaces in PDC
A.4. Continue integration of PDC with other nodes and resources of the CRDC
A.5. Continue development of PDC to enable submission of proteomic/proteogenomic analysis pipelines to CRDC
A.6. Continue user support for PDC
A.7. Develop and/or modify approved functionality for the PDC
A.8. Adhere to appropriate security regulations (FISMA low).

B. Develop a PDC Outreach Plan

The proteomics community must be made aware of the PDC and the value it brings to the researcher’s analysis needs. The FNL will develop an outreach plan to increase awareness and utility of the PDC for proteomic research. The plan will be developed with ESAC, the PDC Advisory Committee and the NCI. Additionally, the plans development and continued maintenance will be coordinated with the CRDC communication plan developed by CBIIT. This activity will include:

B.1. Discussions with the NCI, the PDC Advisory Committee and other relevant stakeholders identified in consultation with the NCI
B.2. Coordination and integration with CBIIT on their overarching CRDC communications plan
B.3. Create a written plan and distribute to NCI

C. Evaluate the current PDC system architecture

ESAC has custom built the PDC, work that started approximately two years ago. Leidos Biomed will establish a clear and complete understanding of the current and ESAC planned future state of the PDC system architecture. This activity will include:

C.1. Review PDC architecture documents
C.2. Review PDC architectural roadmap documents
C.3. Discuss documents and roadmap with ESAC’s PDC architect

D. System Recommendation

The PDC is and will continue to be a node in the CRDC. The PDC was started before the CRDC had established some standards for interoperability for component nodes. However, this raised the possibility that a gap in architectural alignment may have evolved. This activity will include:

D.1. Comparison of the current and future PDC architecture states to the CRDC interoperability roadmap
D.2. Documentation of any gaps in alignment and the possible impact
D.3. Identify and comment on other suggested architectural improvements for PDC
D.4. Suggest options to the NCI on how to address any gaps deemed significant

E. Option year 1 preparation

The YT contains option years, with the first option year continuing support for PDC but also planning for option transition of Assay Portal capabilities into PDC. We will need to prepare for this work in the baseline period and ensure continuity of operations. This activity will include:

E.1. Identify and prioritize CPTAC Assay Portal features/infrastructure that need to migrate to PDC within option year 1
E.2. Completing technical and financial response for option year 1
E.3. Contracting materials for PDC, for a POP that starts August 31st, 2020

F. Project Management

Project management will continue through the life of the project, across all the project’s activities/tasks and will be led by the Leidos Biomed TPM. The TPM will track technical progress, financial status and be a liaison for any subcontracting topics. This activity will include

F.1. Arrange a kick-off meeting with Leidos Biomed, ESAC and NCI. The kick-off meeting will review scope and timeline of the project, define roles and responsibilities, establish communication expectations and review subcontract level responsibilities.
F.2. Subcontracting. The Leidos Biomed TPM will work with Leidos Biomed subcontracting group to ensure all necessary subcontracts are completed.
F.3. Monitoring. The Leidos Biomed TPM will receive technical and financial status reports from the Subcontractor. If, after analyzing the reports, the TPM has any concerns about technical or financial aspects of the project, those concerns will be discussed and addressed with the Subcontractors. Monthly, the NCI will be kept informed on financial and technical status (see Deliverables).
F.4. Integrated Project Team. The Leidos Biomed TPM will ensure there is a clear, timely, documented and effective process in place to ensure that NCI, Leidos Biomed and ESAC are aligned with regards to all project activities. This will include tracking and monitoring items such as clarification & prioritization requests by ESAC, selection of data to be imported and any other item related to the project’s activities.

To do: