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Dear Colleague,
Antibodypedia, the open-access online resource for antibody data and commentary, was a year old on December 4, 2012. Since our last newsletter update, in October, we’ve undergone some exciting changes we’d like to share with you. Please read on for an overview of our progress or visit the site to see what’s new.
In with the new
Version 7 of Antibodypedia, which radically changes the architecture of our search, was released in mid-November 2012. We decided to empower users to specifically identify their gene-product of interest by creating a dedicated "Antigens" page. From here, you're taken to a page presenting an overview of all our antibodies targeting that antigen. We've cannibalized our "Advanced Search" menu and developed filters containing some of the content it previously held: these are now on this dedicated "Antibodies" page and can be applied to refine search results and identify a panel of antibodies tailored to your needs.
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Out with the old
In previous versions, the "Advanced Search" function comprised both antibody- and antigen-specific attributes, allowing you to pinpoint the precise antigen you were looking for by selecting, for instance, the chromosome number for its encoding gene, and then to stipulate that you were searching for antibodies for a particular application; with references appended; or from a certain provider. "Advanced Search" can still be found next to the search box on the homepage, but now is strictly antigen-specific. We feel that this streamlines searching by allowing you to pinpoint your antigen of interest more accurately, and hope it's especially applicable to those of you working on some of the many gene-products with redundant names.
The "Antibodies" page, linked to from the "Antigens" page, now permits filtering on application; presence of references; provider; host; reactivity; or antibody type/ clonality. What's new here is the OR filters--formerly only AND and NOT searches were possible. While "references" is a binary choice (either you want antibodies annotated with references or you don't), the other filters can tolerate multiple selections. They're less stringent than before, permitting you to choose from among a greater range of products.
Another feature now on the "Antibodies" page is the "Compare" function. Checkboxes next to each antibody and provider let you select a few products to scrutinize side-by-side for applicability to your assays. We hope this makes your reagent search a little easier. Let us know what you think! |
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Hot or not?
Our antibody scores are an essential feature of Antibodypedia – without them everything would be jumbled in together without regard to efficacy. So in Version 7 we made some tweaks to scoring that may affect both the scores themselves and providers' rankings.
When scoring our antibodies, we assign marks reflecting capabilities in each application (these depend on the quantity and type of the data available for antibody performance). The sum of these marks produces the antibody's cumulative score, and the provider with the highest-scoring antibody against a given antigen will be ranked first. So what if there's a tie? In that case we hold a "runoff" among providers, and the one with the second-highest-scoring antibody decides the outcome of the vote.
We used to use a complicated formula to calculate these values and decided it was introducing bias, hence our new, simplified system. But we only factor in the presence of data when determining scores, and hence ranks. Send us your feedback! Are there any other attributes we should be considering?
Pride of place
And now to the data! They decide rankings, but where are they?
From the "Antibodies" page you're taken to the "Antibody Details" page, which outlines all the information appended to our antibody listings. At the top of the page is an overview of the applications in which an antibody has been tested, along with its scores. Lower on the page is a series of tabs with antibody specifics; references; data (organized by application); and comments. Remember that you can submit these to us too! Links can be found just below the data tabs.
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Fast and furious
Speaking of data, we've been steadily accumulating them all autumn. A few months ago we had reached just over 100,000 images, but now we're in the neighborhood of 250,000!
We feel that presenting our users with these data during antibody searches is integral to our utility. We assemble a great deal of information in one place for quick discrimination among products. Most data do come from antibody providers, though, and we want to present as comprehensive and unbiased a picture of functionality as possible. So to motivate YOU to submit more, we'd like to announce that we'll soon be starting a contest to:
Anything you submit before the deadline will be entered into drawings for free subscriptions to Nature journals of your choice and other goodies. We'll keep you up-to-date on our plans.
Putdowns and plaudits
Development is underway day-by-day at Antibodypedia, but we are always eager to hear your opinions and next priorities. Please email us or visit our Facebook page to share your likes, dislikes, and general thoughts. We'll be waiting! |
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Thank you for reading this far. I hope that when you use Antibodypedia you find it helpful in guiding you toward
The right antibody for the right application |
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Yours,
Christopher Surridge
Associate Publisher, Antibodypedia |
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