Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits. Why not let us know how they compare to the tools that you use in the comment threads?
Chris Surridge is Chief Editor of Nature Protocols and Associate Publisher the Protocol Exchange. He is also involved in a collaboration between NPG and Antibodypedia a database of information about publically available antibodies created by scientists at the Royal Institute of Technology, Stockholm, Sweden.
Antibodies are the workhorses of cell biological research. Take a wander through the research published in any cell biology journal and you will quickly become convinced that almost no research could be done without these adaptable little molecules. Immunoprecipitation, immunolocalisation, immunofluorescence, Elisa, Western blot – it is very difficult to find any research papers in the field that don’t employ at least one of the multitude of antibody based techniques.
With so much research depending on them, it is no surprise that the amount of antibodies available is pretty daunting. There are over a million antibodies available to researchers supplied by companies numbering in the low hundreds. Some suppliers are small, producing a handful of specialist reagents; a few are large enough to supply tens of thousands of antibodies. With such choice, how does the researcher at the bench know which to rely on for their experiments?
We did a quick online survey last year and among the things that we asked was what factors were important when selecting an antibody. The answer isn’t that surprising really: 82% of researchers said that they consulted the published literature, while 75% said they asked colleagues, often borrowing antibodies to test out before they bought. That is great, apart from the fact that the research literature rarely details the exact antibodies that have been used in the research it reports and not everyone has a friend down the corridor who happens to have used the antibody they now need.
A lot of the time you are on your own, faced with the prospect of searching through the websites of various suppliers, looking to see whether they have antibodies against the targets you are interested in and then hoping they have information about their performance in the experiments that you are about to attempt. In the face of that, is it any wonder that more than half the people in our survey admitted to ‘shopping around’ occasionally at most, more normally sticking with the supplier that they have always used?
The problem of how to select from an array of products from a multitude of suppliers isn’t uncommon. If I’m looking for a new electric kettle, or home insurance, a mobile phone or a hotel in Timbuktu, I sit down with my computer and within a couple of minutes will be consulting a website that aggregates information from the businesses offering what I’m looking for. I can easily compare the specifications; I can read the opinions of people who have bought these products; I can make an informed decision and then I can go to a company’s website and buy what I want.
That is exactly the service that Antibodypedia is attempting to provide: a comparison site for the antibodies available to a researcher, providing or linking to all the information about how a particular antibody performs so that they can make an informed choice. Just like with insurance, Antibodypedia isn’t the only place on the web you can go to find this information, but it has been designed to fit with how a researcher is most likely to be looking for an antibody.
Antibodypedia is structured slightly differently from other antibody search engines you might find: its organization is gene-centric detailing the antibodies directed against a single protein target. At the moment Antibodypedia holds information about 186,789 antibodies against 17,248 antigens which cover 84% of the human genome. ‘Advanced search’ lets you find antibodies that are recommended for one or more types of experiment, sold by a particular provider, and linked to reference citations, among other things. The search functions are always under development, so please let us know if it is missing something you’d find useful.
But what is most important is the information we have on the antibodies themselves. There is basic information such as the antibody type (monoclonal, polyclonal, etc.), the reactivity and such like information from the supplier of the antibody, as well as a direct link that suppliers page for the antibody. There is a list of research papers in which the antibody has been used. What we also provide, though, is data on the behaviour of antibodies in specific assays. Some of this data comes from the suppliers of the antibodies but we also publish data from independent researchers.
Actually you can think of Antibodypedia as a microjournal, publishing bite-sized bits of data rather than full-length manuscripts. The data from working scientists – the control experiments in lab notebooks that may make it into supplementary data or more likely never be made public at all – are the best evidence for how antibodies perform in a real lab. But we do not put up just any data that we receive. Just like a ‘macropublication’ we show these data to experts in the field who peer-review it. Those data that are well described and appear accurate get presented on the site and are assigned a DOI so that they can be cited.
There are plenty more features of Antibodypedia that are well worth mentioning but I’ll mention just one: the side by side comparisons. Once you have found the antibodies to your antigen of interest that appear to be what you need, rather than look at the information about each separately you can select multiple antibodies and compare them side by side. This kind of feature is great when you are buying a new washing machine (and given that my kitchen was ankle deep in water last week I’m speaking from recent experience) and it is just as useful when you are stocking up on antibodies for the lab.
There are plenty of hackneyed phrases about the need for good raw materials to build with, and even a porcine parable or two. Hopefully Antibodypedia will really help scientists find the silk they need to construct their research purses rather than struggling to do their best with sows’ ears.
You can follow the online conversation on Twitter with the #ToolTales hashtag and you can read Mary Mangan’s Tool Tale here, Dr Peter Etchells’s Tool Tale here, Alan Cann’s here, Jerry Sheehan’s here, Boris Adryan’s here, Anthony Salvagno’s here, Daniel Burgarth and Matt Leifer’s here, Zen Faulkes’s here, Jenn Cable’s here , Mike Biocchi’s here, Susanna Speier’s here, Derek Hennen’s here, Musa Akbari’s here, Benedict Noel’s here and Gerd Moe-Behrens’s here.