This is a guest post from Victoria Newman
Hello, I’m Victoria.
I’m the curator of Antibodypedia, an open-access database of antibody validation data and user commentary initially founded as part of the Human Antibody Initiative/Human Protein Atlas. In addition to running Nature Protocols, Chris is in charge of the collaboration that has started between Nature Publishing Group and Antibodypedia which is my excuse for posting on this blog. I was hired as curator last June and am psyched to say that we finally launched the new Antibodypedia site on December 4 at the ASCB’s annual meeting.
The problem facing anyone who uses antibodies in their research is that for any given target there are a lot of antibodies available so how can you tell which one will work for you. What is needed is somewhere researchers can go which has a comprehensive list of antibodies available with information about how they perform in the various applications for which antibodies are employed. That is exactly what Antibodypedia is attempting to create.
There are quite a few antibody comparison forums out there if you search the web, so what makes Antibodypedia special?
First, we’re gene-centric: search for any antigen (human now, but expanding into other model systems in 2012) and you’ll pull up a whole list of antibodies directed against that target. You can sort and refine the results in a number of ways: by the antibody’s host, the types of experiments in which it’ll work, or whether or not it’s been used in research publications, among other things.
Secondly, you can submit your own data to us (with experimental protocols, please). We are of course making available the data that the providers of antibodies have but I’m sure you will agree that the most valuable information is that from researchers doing the same kind of experiments as yourselves. We hope this will do a number of things: showing whether and how to use a particular antibody for a specific experiment; helping decide the working concentration or dilution that are appropriate for an assay; identifying whether the antibody works as described by the vendor or in more (or fewer) assays.
This is all valuable information and yet all too often the data about the performance of antibodies languishes in researchers notebooks. The control experiments that had to be done before the ‘real’ experiments, those that will see publication in a research paper, could be started. Rather than forcing scientists in different labs to pointlessly duplicate these experiments we would like to see them made available to everyone, and see the researchers getting some credit for their experimentation. We are looking at these data as a ‘micro-publication’ and will be giving them DOIs to make them easily citable.
We want to encourage best practice for different experimental categories, so we’ve put together submission guidelines with suggested controls that will make your blank western blot immediately interpretable by everyone.
One more thing—you can also find additional resources, including links to useful sites and online tools, at Antibodypedia, and we’ve assembled a list of hundreds of Nature Protocols and Protocol Exchange protocols using antibody based techniques.