blog

Each month we scan our poster and slides submissions and feature one as our ‘poster/slide of the month’. April’s choice is: “The Type 2 Diabetes Knowledge Portal: accelerating type 2 diabetes research through community access to human genetic information and tools”. It was presented by Maria Costanzo, from the Broad Institute, at the 9th International Biocuration Conference 2016 and is part of the channel that we host on behalf of the International Society for Biocuration.

This poster sparked particular interest with us, given our open access data policies for articles, as this resource provides open access to the results of the queries across multiple genetic data sets. The Type 2 Diabetes Knowledge Portal is an online resource for human genetic information on Type 2 Diabetes (T2D), acting as a central repository for data from large genomic studies. The T2D Knowledge Portal lets you browse for information on particular genes or variants, or build queries for the sets of variants associated with particular traits, using a sophisticated search engine. In addition to having access to a variety of datasets, the portal also provides results of pre-computed analyses and tools for custom analyses. Importantly, the website has a section showing you how to formally cite the data, ensuring proper credit is given to the original researchers.

When studying human genetic information, obtaining the informed consent of patients and protecting their confidentiality are of the utmost importance. Because of this, providing access to human health data is extremely complicated. Patients consent to sharing their information, but that consent may be limited: for example, investigators may be given permission to share the sequences of variant alleles in a patient’s genome, but not to share information about that patient’s health. Also, the data generated by individual projects are often in disparate locations, or siloed due to institutional and/or national regulations. All of these risks and regulations around sharing patient-level data can often limit data sharing on a large scale.

The T2D Knowledge Portal addresses these challenges by aggregating multiple genetic data sets, harmonizing and unifying them, and providing tools that enable researchers world-wide to query and analyze them, while protecting personal health information. All of the data are de-identified, preserving the confidentiality of individuals and making it safer to use patient-level data. At present, results represented in the Knowledge Portal query the underlying data that are stored securely at the Data Coordination Center at the Broad Institute. As the project continues to grow in size and aggregate larger numbers of datasets, federated nodes at other sites will also connect with the T2D Knowledge Portal to allow analyses across all data at all sites. This allows protected individual patient data to remain at its site of origin, in accordance with local regulations, while facilitating global access to analyses across all the data.

Take a look at the Biocuration Channel to see other examples of how software developers and researchers are working together to create databases for easy access to data that provide a strong basis for computational analysis and an accurate and comprehensive representation of biological knowledge.