Thursday, April 28, 2016

Variant Finder results may be saved, shared, and bookmarked

You may have noticed that our Variant Finder tool has a cleaner look and clearer instructions. But did you know that you can also save your search parameters, to re-create your search later or share it with a colleague?

First, construct your search. Here’s an example:

Click the image to view a larger version

After you click “Submit search request” you’ll be taken to the results page:

Click the image to view a larger version

And here’s the URL of the results page for this example search:

It isn’t pretty, but it encodes the search. You can bookmark it, save it, or email it and you’ll get back the same result next time you enter it in a browser.

There’s one small caveat here. On the results page, you can modify the results table by clicking on the + signs in the table header to see options for adding more data to the table. But if you do this, those changes will not be encoded in the URL (we plan to enable this in the future); only the original search is encoded.

Let us know how you like this feature and what other features might be useful to you. And check out our mini-tutorial on the Variant Finder to see full instructions on how to use this tool. 

Thursday, April 21, 2016

Type 2 Diabetes Knowledge Portal represented at Biocuration 2016 conference

Last week, the International Society for Biocuration held its 9th annual conference in Geneva, Switzerland. You might ask, “What is biocuration, anyway?” In a nutshell, it’s all about organizing biological data and making it accessible and understandable. It can be as small-scale as capturing the fine details about the function and role of a particular protein, or as large-scale as designing interfaces to analyze and explore genomes or huge genomic data sets. (See this article if you’re interested in the nitty-gritty details about what it’s like to be a biocurator.) The conference covered major topics in biocuration such as the visualization and integration of data, controlled vocabularies and ontologies, functional annotation, community curation, text mining, and more.

Our Manager of Content and Community attended the conference, since many of these issues are relevant to the T2D Knowledge Portal. As we tackle a relatively new challenge in biocuration—the integration of human genetic association data sets—it’s important for our project to be part of the biocuration community, to get feedback and become aware of others’ work in this area. And as we consider adding more biological information about human genes to the Portal, it’s important that whatever we do is consistent with ongoing efforts in the biocuration of human genes; we don’t want to reinvent the wheel or duplicate work.

Besides getting to attend a fascinating and energizing conference in a beautiful setting, the icing on the cake was that our poster on the Portal received one of five “Best poster” awards! We’re honored and pleased that our project had such a warm welcome into the biocuration community.

View or download original

Friday, April 1, 2016

It’s no April Fool’s joke: we’ve rolled out big improvements to the T2D Knowledge Portal today

The first thing you’ll see when you visit our home page is that it has a fresh new look. We’ve refined our mission statement and clarified the other text, and added a “What’s new” section featuring our latest news items. There are also new links to sign up for our email list (more on that below) and to see our Twitter feed.

Another major change is that we’ve redesigned the interface to our Variant Finder tool to make it much more user-friendly.  We even gave it a shorter name that's easier to remember! This tool lets you build simple or complex queries to retrieve sets of variants that meet your custom criteria. You can specify association with any of 25 phenotypes, significance, genomic location, effect on the encoded protein, and much more. For some extra help with this tool, we’ve created a tutorial (download PDF) that leads you step by step through the interface.

Finally, we’re reaching out to you, the Portal user, in a variety of ways. If you sign up for email updates, we’ll notify you when new features and new data are added. You can also follow us on Twitter, and join our LinkedIn group where you can ask questions about the Portal or suggest new features. And as always, you can contact us anytime at - no fooling!