Antibodypedia

The Antibodypedia [1] is a web service intended to provide better data on the usability of anti-protein antibodies. It's currently limited to human proteins but expansion to other species is planned (see comments). The website provides standardised results for about 963.000 antibodies against 18.900 genes covering 91% of the human genome [2]. The antibodies are scored using an algorithm that takes into account the amount of supportive data present for the antibody [3]. Submissions by researchers are encouraged and have to pass review. Pages are not editable but scientists can comment on individual antibodies.

Creation & Funding

Initiated by Mathias Uhlén, Erik Björling, and colleagues [4] from the Royal Institute of Technology in Stockholm in 2008 [5]. The database was kick-started with about 4000 polyclonal antibodies generated by the Human Protein Atlas but now contains submissions from numerous commercial antibody vendors. The database software was improved in subsequent versions according to researcher and provider comments: versions 2 & 3 in 2009, versions 4 & 5 in 2010 [6], version 6 (as part of a collaboration with Nature Publishing Group) in 2011, version 7 in 2012, and version 8 in 2013. The project is funded by the 6th and 7th European Framework Programme and the Knut and Alice Wallenberg Foundation, Sweden.

Example search

Part of the results returned by Antibodypedia when queried for HER2.

The results are displayed with the highest ranking antibody on top. The ranking is based on scores received for amount of supportive data in terms of images and citations [7].

Antibodies of interest can be selected and compared before proceeding to an antibody provider product page.

Comment

I asked whether the AntibodypediA will be extended to common model organisms like mouse, etc. This is the reply I received via email: "We are also planning to include mouse antibodies in Antibodypedia. We will begin working towards that during 2012. Already today we have antibodies reactive to both human and mouse. To find all antibodies stated to be reactive in mouse you can use the search [8]." --- JS 10:36, 20 October 2011 (EDT)

I'm still wondering whether an open submission system may result in more user contributions.

Links

• homepage of the project
• search Antibodypedia for antibodies reactive to mouse proteins

News pieces describing the service

• "Antibodypedia, a portal for sharing antibody and antigen validation data" by Erik Björling and Mathias Uhlen [9]
• "Antibodypedia - A web portal to share antibody validation data" by Veronique Kiermer [10]
• "Antibodypedia seeks to answer the question: “How good is that antibody?”" by Katie Cottingham [11]
• "Antibodypedia is up and running!" by Christopher Surridge [12]
• "Antibodypedia on Facebook" by nature.com Communities Team [13]
• "Nature Publishing Group collaborates with unique antibody database" PRESS RELEASE FROM NATURE PUBLISHING GROUP [14]
• "The first few months of Antibodypedia" by Christopher Surridge [15]
• "Antibodypedia" by 3D Virtual Cell [16]
• "Antibodypedia: Searchable database of antibodies" by chromocyte [17]
• "Antibodypedia tops half a million antibodies" PRESS RELEASE FROM NATURE PUBLISHING GROUP [18]
• "A World of Antibodies at your Fingertips" by Frederick Gruber [19]
• "Tool Tales: Antibodypedia – Searching for the Perfect Partner" by Soapbox Science Editor [20]

Antibodypedia in the news

• "Generation and validation of affinity reagents on a proteome-wide level" by Mathias Uhlén, Sophia Hober [21]
• "HAI brings antibody researchers together" by Katie Cottingham [22]
• "The 6th HUPO Antibody Initiative (HAI) Workshop: Sharing Data About Affinity Reagents and Other Recent Developments September 2009, Toronto, Canada" by Kalle Jonasson, Lisa Berglund, Mathias Uhlen [23]
• "Generation of monospecific antibodies based on affinity capture of polyclonal antibodies" by Barbara Hjelm, Björn Forsström, et al [24]
• "Energy matters: Mitochondrial proteomics for biomedicine" by Elisabetta Gianazza, Ivano Eberini, Cristina Sensi, et al [25]
• "Method of the Year 2012 - New method and tool developments are helping to bring targeted proteome analysis technologies to a broader array of biologists" editorial Nature Methods [26]
• "Affinity-based microarrays for proteomic analysis of cancer tissues" by Jörg D. Hoheisel, Mohamed S. S. Alhamdani, Christoph Schröder [27]
• "Finding the right antibody for the job - As new research applications for antibody-based assays emerge, the quest for quality intensifies in a crowded marketplace" by Vivien Marx [28]
• "Integrated View of the Human Chromosome X-centric Proteome Project" by Tadashi Yamamoto, et al [29]