The PsychENCODE Knowledge Portal is an application developed by Sage Bionetworks, the National Institute of Mental Health (NIMH), and the PsychENCODE Consortium to promote a community for sharing data from neuropsychiatric disease research. Anyone can explore the portal to find data and learn more about the ongoing research in this field.

The PsychENCODE Consortium brings together multidisciplinary teams including biologists, neurologists, clinicians, bioinformaticians, data scientists, and data engineers from multiple research institutions. These researchers are funded by different NIMH grants to generate resources including data files and publications. These resources are contributed to the data storage platform, Synapse, so that they can be shared with the community.

Below, read more about the relationship between Sage Bionetworks, Synapse, and the PEC portal.

The resources uploaded to Synapse are released to PsychENCODE Knowledge Portal users on a continuous basis to maximize their impact. Additionally, all resources have been annotated with administrative, descriptive, and research metadata to help make them F.A.I.R (Findable, Accessible, Interoperable and Reusable).

Our Data Lifecycle

The PsychENCODE Knowledge Portal research lifecycle operates with several phases:

  1. During the data generation phase, data are uploaded to the data storage platform, Synapse. During this phase, the data are typically not available for download on the portal, but some information is exposed, such as study title, study description, and metadata.

  2. Data curation mostly occurs behind the scenes of the portal on our data storage platform, Synapse. This stage enables data discovery, powering search on the portal.

  3. Computational tools that enable data analysis are linked. As data is analyzed, transformations are tracked through provenance.

  4. Data interpretation is enabled through various Synapse features, including wikis and discussion forums, but can also be explored on the portal via published data and associated publications.

  5. Data dissemination includes the PsychENCODE Knowledge Portal, publications and our results visualization tool PsychSCREEN.

How is the PsychENCODE Knowledge Portal structured?

Within the PsychENCODE Knowledge Portal, you can use the Explore tab on the homepage to browse the available resources. We organize the research outputs (Data and Publications) around the Grants and Studies that produced them. We also provide information about the People (Principal Investigators, their teams, and collaborators) who generated these resources to foster a collaborative community and to encourage data sharing.

For more information about how to explore these different sections, see Navigating the Portal and Accessing Data.

PEC Knowledge Portal ↔︎ Synapse

How does Sage Bionetworks, Synapse, and the PEC Portal fit together? Let’s break this down:

Sage Bionetworks

First, there’s Sage Bionetworks - a name you may or may not have come across. While Sage is not a tool you’ll be using, you should know who we are: a non-profit organization based out of Seattle, Washington. Sage is dedicated to promoting and advancing open science, as well as engaging patients in the research process. Sage acts as the Data Coordinating Center (DCC) for several different portals, including the PEC Knowledge Portal. The scientists, developers, and designers that built the tools you’re using are all employed by Sage. You can learn more about Sage Bionetworks and its initiatives here.

Synapse

In line with advocating for open science, Sage developed a software platform called Synapse. This platform is what allows for collaborative data curation and analysis, computational modelling, and more. It allows users to upload, store, analyze, and track data in a private space, before releasing it to the public-facing PEC Knowledge Portal. Think of Synapse as the back-end for all the data to live in.

PEC Knowledge Portal

If Synapse is the back-end for data, the PEC Knowledge Portal is the front. It’s essentially the user interface (UI) or entry point for you to view data and other shared content. Data gets uploaded into Synapse, where it is then processed into readable form for you to access in the portal.

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