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Dear Colleague,
We've been continually updating Antibodypedia, the free, open-access online resource for antibody data and commentary, since its launch in December 2011. Recently we've made some improvements which we'd like to share with you. Please read on or visit the site for more information!
Mergers and acquisitions
In March we passed the 600,000 mark, and now list upwards of 640,000 antibodies against human or mouse antigens. Cumulatively these reagents detect at least one protein isoform encoded by 90% of human genes or their mouse cognates. Additionally, more than 300,000 validation data images are now available as proof of efficacy in 14 experimental categories.
Although the majority of the products we list are from commercial providers, we're hoping to begin reporting antibodies generated by a few academic consortia in the near future. Along with their validation data, these will be searchable in Antibodypedia over the next few months. Are you making antibodies in-house as well? If so, we'd love to hear about them, especially if they detect hard targets.
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Zooming in
In our last newsletter, in January 2013, we announced substantial alterations to our search. Whereas previously it was necessary to select terms from the "Advanced Search" menu in order to refine search criteria, the changes implemented in Antibodypedia version 7 made it possible to apply filters directly on search results pages to find antibodies more specifically suited to a precise experimental schema. We also simplified our algorithm so that providers were ranked only according to the scores of their best antibodies--those for which we listed the most data--rather than by weights applied to every antibody, which, we worried, might bias our results toward vendors with many antibodies against the same antigen.
However, it's made sense to us to reassess our scoring system once more over the past few months. We're convinced that data are essential to determining an antibody's effectiveness, but we don't have access to raw images indicative of every antibody's use in every application (although we'd like to, and our users should feel free to contribute!). Antibodies' citations in the literature are just as informative as data, and often even more helpful if they contain details for usage conditions. So we've begun to factor the number of references appended to each of our antibodies into our scores, and now rank antibodies based on both citations and data.
(One caveat: because product numbers may not be reported in the literature, or may only be found in non-searchable supplementary information, we believe we are under-reporting references. We do communicate with antibody providers about supplying curated lists of references, and we encourage you to submit them as well.)
Another subtle change, but one that may make your life easier: in response to your comments, we've separated antibodies tailored to protein immunoprecipitation studies from those for chromatin immunoprecipitation. You should now be able to browse or search for ChIP-validated antibodies without impediment. Please contact us if you have any other suggestions of applications (or other content) to add! |
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Got data?
In our last newsletter we mentioned a contest we're holding to populate the site with independently sourced user data. Our eventual goal is to have a minimum of one image for each antibody we list, in at least the more-commonly performed applications reported in Antibodypedia. But considering the infinite variety of cells and tissues in which these reagents could be tested, and the fact that we'd like to build a compendium reflecting the entire spectrum of applications and organisms in which a given antibody might work, it will take us a long time to reach saturation. Help us to reach our goal! As an enticement, you'll be eligible to win subscriptions to Nature journals if you enter the
contest. Full details, including a list of our 50-most-searched antigens, for which we're most keen to show independent data, can be found at http://www.antibodypedia.com/validate.php?t=annotate_this_protein. Send us your data and read a year's worth of great science!
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Flack and felicitations
We work constantly to improve the site, but without your comments we'll never know how successful we are. Make sure you keep in touch! Send us your feedback--email us at contact@antibodypedia.com or find us on Facebook. What's frustrating? What development should we prioritize? And what are we getting right? |
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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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