Frequently Asked Questions (FAQs)
The MC2 Center has compiled the following FAQs to help with the data contribution and sharing process. If you have a question and can’t find an answer here, please Contact Us.
General
What is the MC2 Center?
Led by Sage Bionetworks, a non-profit organization based in Seattle, Washington, the Multi-Consortia Coordinating (MC2) Center serves as the coordinating center for several NIH/National Cancer Institute (NCI) Division of Cancer Biology (DCB) funded consortia programs which are made up of interdisciplinary communities of scientists. These scientists are working to integrate approaches, data, and tools to address important questions in basic and translational cancer research. The MC2 Center aims to catalyze collaboration, facilitate an ecosystem of data and resource sharing, and support outreach activities to create a stable and impactful cancer research community.
As the MC2 Center, Sage supports engagement and resource sharing within the cancer research community by maintaining the Cancer Complexity Knowledge Portal (CCKP).
The MC2 Center is supported by the NIH/NCI under award number U24CA274494.
What are the Synapse and the Cancer Complexity Knowledge Portal (CCKP)?
Synapse serves at the backend data warehouse of the Cancer Complexity Knowledge Portal (CCKP). More details:
Synapse: Sage Bionetworks developed the Synapse data sharing platform as part of efforts to advocate for open science. Synapse unlocks collaborative data curation, analysis, and computational modeling, and is an NIH-supported generalist repository.
The CCKP: With funding from the NIH/National Cancer Institute (NCI) Division of Cancer Biology (DCB), Sage Bionetworks developed the CCKP as a community research resource to disseminate resources generated by NIH/NCI DCB-funded research programs. The CCKP serves as an access point to find or discover research data, publications, grants, and other relevant cancer research resources, and is an NIH-designated domain-specific repository. Visit About the CCKP to learn more.
If you are interested in learning more about Synapse and the CCKP, please Contact Us to request guidance and demos to help you with your resource sharing needs.
Why should I store and share data in Synapse?
As an NIH-supported generalist repository, Synapse enables you to:
Store content and regulate access in private workspaces with configurable project-, folder-, and file-level sharing settings
Flexibly organize data by project (and sub-projects), output or study (e.g. publication, dissertation), or personnel (e.g. graduate student, technician)
Structure and navigate information with annotated folders, tables, and datasets that grow with your research outputs
Collaborate using shareable DOIs, queryable content, and rich documentation
Synapse has also been developed with effective governance controls to enable a spectrum of resource and data sharing, in response to community needs and the pace of research:
Secure, compliant access - so you can focus on the science
Privacy templates for data sharing agreements, to share data responsibly
Right-sized permissions & built-in guardrails that satisfy HIPAA, GDPR, NIH, & institutional policies
Clear use conditions displayed in standard ontologies so researchers know what’s allowed
Researcher-driven enablement that scales with data & projects
User stories that shape our governance roadmap and that apply friction only where necessary
Rapid release workflows for data discoverability and efficient adjudication of controlled-access data.
What level of support is available from the MC2 Center to store and share data in Synapse and the CCKP?
The MC2 Center serves as the coordinating center for several NIH/National Cancer Institute (NCI) Division of Cancer Biology (DCB) funded consortia programs: CCBIR, CSBC, MetNet, PS-ON, and Cancer TEC (see Consortia). The MC2 Center is actively supporting the curation and dissemination of resources emerging from grants within these consortia programs to support dissemination to the broader cancer research community. While the CCKP is accessible to everyone, the specific resource storage, curation, and dissemination support provided by the MC2 Center are only available to individuals funded by these consortia programs.
See FAQs associated with:
If I am a member of a consortium supported by the MC2 Center… OR
If I am NOT a member of a consortium supported by the MC2 Center…
If I am a member of a consortium supported by the MC2 Center…
How can I request help from the MC2 Center to share my data?
For members of consortia supported by the MC2 Center, we are happy to support storage, curation, and dissemination on the CCKP. If you are interested in sharing resources and/or data on the CCKP, please review the requirements and steps in Initiating the Data Contribution & Sharing Process to start the process and request assistance from the MC2 Center. For more information about the data contribution and sharing process, please take a look at High-Level Steps & Expectations
Where can I learn more about MC2 center offerings and available data sharing support?
Please Contact Us to set up a time to learn more, or for information to join our weekly MC2 Center Resource Management Office Hours, Thursdays at 10AM PT/1PM ET. The MC2 Center has adaptable approaches to support your resource and data sharing needs, enabling timely data sharing and empowering reuse. Some areas of data sharing support include, but are not limited to:
Large file sizes: The MC2 Center works with contributors to set up project structures within Synapse, collaborate on file upload and organization, and support metadata annotation for datasets exceeding 6TB. Check out an example shared on the CCKP here.
New assay types with unclear or no sharing standards: As an NIH-designated generalist repository, Synapse offers flexibility to host multiple data modalities. The MC2 Center recognizes that the data landscape is ever-evolving, with the need to share both common and emerging assay and data types. The MC2 Center works with contributors to understand and prepare for sharing new data types, including extension of the MC2 Center Data Model to accommodate new annotation terms. See also What does annotation, or annotating your data, mean?
Pre-publication sharing and data availability statements: The MC2 Center can help you organize and curate publication-related datasets, and can work with you to coordinate timely public data release on the CCKP upon publication. For publications under review, stable DOIs can be minted for data stored in Synapse to include in data availability statements, and access can be provided to editors and reviewers.
Data with access restrictions / conditions of use: The MC2 Center works with contributors to establish and apply any applicable data sharing and reuse conditions to data stored and shared in Synapse and the CCKP. These may be defined by different funding requirements, regulatory requirements, data sharing policies, and/or journal requirements, and may be applicable to specific data modalities (i.e. human genomics data). See also Is there a mandate to upload and store my data in Synapse?
The MC2 Center works with contributors to document details related to these areas of support within a data sharing plan. See also Why do I need to submit a data sharing plan (DSP)?
Is there a mandate to upload and store my data in Synapse?
Funding requirements, regulatory requirements, data sharing policies, and journal requirements can help you identify where, how, when, and what data need to be shared. Synapse is a generalist repository which can host multiple data modalities in one place. The MC2 Center can help you determine if storing your data in Synapse fulfills policy obligations. If not, alternative repositories will be recommended to you, based on your data sharing requirements. The CCKP and Synapse are also able to connect to other repositories like GEO, dbGAP, Figshare, Xenodo, NIH General Commons, etc. Some data modalities (i.e. human genomics data) may be required to be stored in repositories other than Synapse, in accordance with the policies and specific terms of your award (e.g. NIH Genomic Data Sharing Policy). We encourage you to contact us to help navigate sharing requirements. Regardless of whether you choose to upload data to Synapse or to another repository, please let us know of your intent and we can work with you to make sure your data are findable on the CCKP.
Once uploaded, how long will my data live in Synapse?
Any data uploaded to Synapse by consortia members supported by the MC2 Center will be stored for 10 years after completion of MC2 Center project in 2027. After this time, data may be migrated to a cold storage solution to minimize storage costs, however, data will be retrievable upon request. Data and annotations will remain findable through the CCKP for the lifetime of this portal.
Why do I need to submit a data sharing plan (DSP)?
A data sharing plan (DSP) helps the MC2 Center data curation team prepare for your data intake, so they can better assist you with your resource and data sharing needs. DSPs document and notify the MC2 Center of upcoming deadlines, intended release dates, as well as any access requirements or terms of sharing associated with your data. DSPs also help indicate to the MC2 Center the need to prepare for new data types by extending the MC2 Center Data Model to accommodate new annotation terms.
What does annotation, or annotating your data, mean?
Annotation is the process of labeling your data files with terms from the MC2 Center Data Model. By adding clinical or experimental annotations to your data files, you will help make the data easier for others to find and understand things like: what type of data it is, what sort of experiment was performed, what type of biological system it came from, and what format the data is. Metadata/annotation is not a substitute for sharing protocols or methodology; it won’t help someone reproduce an experiment from scratch, but it will help them get a basic understanding of the nature of the data, and can be very helpful to people who aim to reuse the data (or even future you)!
In Synapse and the CCKP, annotations live alongside data files. Rather than being in the file itself, these annotations are surfaced in Synapse and publicly in the CCKP to allow people looking for data to easily search and filter by the annotation values.
The MC2 Center will help you navigate the annotation process and will link you to relevant metadata templates for completion and validation based on the information provided in your DSP. You can also refer to information on the annotation process within our how-to guides: [PLACEHOLDER]: Files and Metadata: Annotation and Organization .
Where can I find more information and definitions for annotation terms in the MC2 Center Data Model?
Versioned releases of the MC2 Center Data Model are hosted on Github in CSV and JSON format. To learn more, please also see the about the MC2 Center Data Models Explorer.
I’ve already shared my data to another repository. How can I make my data findable on the CCKP?
If you have already submitted your data to another NIH supported repository, please Contact Us to get assistance on how your data can be annotated, listed, and made findable through CCKP.
How do I cite my data in the CCKP?
To reference datasets listed on the CCKP, you should use the information available via the “Cite As” feature of the dataset information card on with the Datasets Explore Module.
It is also recommend that you reference the Synapse ID (e.g. syn61795458) or DOI (e.g. 10.7303/syn61795458.1), when available, for the data or study that you are referencing. These are persistent accession numbers that will help others find the data you have shared or used.
If I am NOT a member of a consortium supported by the MC2 Center…
How can I make my data findable on the CCKP?
The CCKP is powered by the generalist data repository Synapse, hosted by Sage Bionetworks. Please review the Sage Offerings to find various ways how you could share your data and make it findable on CCKP.
If you have already submitted your data to another NIH supported repository, please Contact Us to get assistance for how your data can be made findable through CCKP.
How can I get involved with the MC2 Center-supported consortia?
The MC2 Center serves as the coordinating center for several NIH/National Cancer Institute (NCI) Division of Cancer Biology (DCB) funded consortia programs: CCBIR, CSBC, MetNet, PS-ON, and Cancer TEC. While the CCKP is accessible to everyone, the specific resource storage, curation, and dissemination support provided by the MC2 Center are only available to individuals funded by these consortia programs. If you are not currently a funded member of any of these consortia, and you'd like to get involved, you could consider applying for Associate Member status with one of the three programs that offer it. You can learn more here. You can also subscribe to the monthly MC2 Center Community Newsletter (subscribe).