BenchSci Blog

Antibody Search Engines: What Are Your Options?

Posted by Maurice Shen, PhD. on Aug 31, 2017 2:11:43 PM
Maurice Shen, PhD.
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If you’re a biomedical research scientist, chances are you have a unique personal story about using antibodies. Not only are research antibodies one of the most commonly used research reagents (88% of scientists, to be exact), they also play a crucial role in the reproducibility of any groundbreaking research findings.

However, finding the right antibody is like finding a needle in a haystack: There are over 300 antibody suppliers selling over 3 million antibodies, and the successful use of each antibody is highly dependent on the experimental contexts in which the antibody was applied. Moreover, a recent article from Nature reported that approximately 50% of research antibodies do not work as intended, which highlights the importance of conducting proper searches for this critical research reagent.

The current gold standard for antibody search is to sift through papers after papers on PubMed and Google Scholar to find published data that supports the use of antibodies. However, these databases were designed to help scientists keep up to date with the latest findings, not for antibody search.

Fortunately, several "antibody search engines" have been developed to help research scientists more easily identify antibodies best suited for their experiments. This article aims to provide an in-depth analysis of the options available so research scientists can take advantage of these resources. These will be introduced in alphabetical order and analyzed by:

  • Number of antibodies (Figure 1.)
  • Types of data available (Table 1.)
  • Pros and cons
  • Uniqueness

 

Number of Antibodies in Database

Figure 1: Comparison of number of antibodies in databases.
* Numbers for Bioz not available.

 

Data Available in Each Search Engine
  Antibody Specifications Paper References Independent Reviews Supplier Images Published Figures 3rd-Party Validations
BenchSci Y Y Y Y Y Y
Labome Y Y Y   Y  
Antibodypedia Y Y Y Y    
Biocompare Y Y Y Y    
Antibody Registry Y Y        
Bioz Y Y        
CiteAb Y Y        
Linscott's Directory Y          

Table 1: Types of data available in each search engine. 
* 3rd-party validations refers to data produced by non-profit groups such as Human Protein Atlas & ENCODE

 

Antibodypedia

www.antibodypedia.com
The Antibodypedia database was originally developed in 2008 within the 6th framework EU program, Proteome Binders. It contains information about publicly available antibodies generated by academic or commercial providers that are directed against human protein targets.

Size

  • 2,845,873 antibodies from 76 suppliers

Pros

  • Lists publications associated with each antibody
  • Antibodies are filterable by product specifications
  • Allows submission of independent validation data

Cons

  • Listed papers are not filterable by specific experimental contexts
  • Does not contain papers from closed-access journals

Uniqueness

  • Has a scoring system based on the data provided by the suppliers and/or independent labs

 

Antibody Registry

antibodyregistry.org
The Antibody Registry assigns unique and persistent identifiers to each antibody so that they can be referenced within publications. Founded in 2010, it includes commercial antibodies from hundreds of commercial vendors as well as thousands of individual labs.

Size

  • 2,472,303 antibodies from 1175 suppliers (both commercial & academic)

Pros

  • Contains antibodies produced by independent academic labs

Cons

  • The majority of the antibodies lack literature references

Uniqueness

 

BenchSci

www.benchsci.com
BenchSci is the newest antibody search engine on this list. Founded in 2015, BenchSci leverages machine learning to read millions of publications and extracts individual published figures showing which and how antibodies were used in the literature.

Size

  • 3,690,656 antibodies from 168 suppliers

Pros

  • Scientists can choose to view a list of published figures or a list of products
  • Both figures and products are filterable by specific experimental contexts (841,201 published figures) as well as product specifications
  • The published figures can be viewed directly on the platform; links to the original papers are also available
  • Also contains validation data from the original suppliers and independent labs
  • Provides an overview on how frequent each antibody was used for each technique

Cons

  • Still in the process of acquiring data from additional closed-access journals (in addition to JAMA, FASEB, and ASPET for which BenchSci has data)
  • Requires registration (free)

Uniqueness

  • BenchSci is the only one on this list that provides scientists with the capability of filtering through publication data to find antibodies that have been used under specific experimental conditions

 

 

Biocompare

www.biocompare.com/Antibodies/
Founded in 1999, Biocompare is a company that lists a wide range of life sciences research products, from assays kits to biomolecules, from various suppliers. A branch of Biocompare is dedicated to antibodies.

Size

  • 3,142,961 antibodies from 155 suppliers

Pros

  • Antibodies are filterable by product specifications

Cons

  • Does not provide information on how each antibody was used in the literature

Uniqueness

  • Also allows scientists to find reagents other than antibodies

 

Bioz

www.bioz.com
Founded in 2013, Bioz is another search tool on this list that uses machine learning to break down the usage of antibodies in publications.

Size

  • Accurate numbers not available

Pros

  • Antibodies are filterable by product specifications and by keywords in the citations
  • Extracts paragraphs from "Materials & Methods" that contain the cited antibodies
  • Also lists research reagents other than antibodies

Cons

  • The figures from citations cannot be filtered by specific experimental contexts
  • Does not contain papers from closed-access journals
  • The keywords analyzed are not well-defined

Uniqueness

  • Developed its own rating system to rank antibodies

 

CiteAb

www.citeab.com
CiteAb is a biotechnology company spun out of the University of Bath in 2013. Its search engine ranks antibodies by the number of times they have been cited to help scientist quickly find out the frequency of use in the literature for their antibody of interest.

Size

  • 3,668,397 antibodies from 150 suppliers

Pros

  • Ranks antibodies by number of citations (1,145,519 references)
  • Antibodies are filterable by product specifications
  • Clean and user-friendly interface

Cons

  • Citations not filterable by specific experimental contexts
  • Does not contain papers from closed-access journals

Uniqueness

  • Generates reports on the “Most Cited” antibodies and their suppliers to help scientists make better decisions and to encourage rigorous antibody validation practices amongst suppliers

 

Labome

www.labome.com
Founded in 2009, Labome manually curates antibody applications from selected publications to develop a "Validated Antibody Database."

Size

884,336 antibodies from 175 suppliers

Pros

  • Lists publications associated with each antibody (50,005 published figures)
  • Antibodies are filterable by product specifications
  • Also lists a subset of antibodies validated by knock-out studies
  • Allows submission of independent validation data

Cons

  • Citations not filterable by specific experimental contexts
  • Does not contain papers from closed-access journals

Uniqueness

  • Highlights antibodies that have been validated in knock-out studies

 

Linscott’s Directory

www.linscottsdirectory.com
Founded in 1980 by Dr. William Linscott, an Immunology professor at UCSF, Linscott’s Directory is the very first antibody database. 37 years later, the database is still up-to-date and also lists non-antibody products.

Size

2,602,169 antibodies from 88 suppliers

Pros

  • Clean and user-friendly interface.
  • Antibodies are filterable by product specifications.

Cons

  • Does not provide information on how each antibody was used in the literature

Uniqueness

  • Partners with pAbmAbs to facilitate sharing of independent antibody reviews 

 

Conclusion

We live in a time where groundbreaking technologies, such as CRISPR and optogenetics, were developed to accelerate biomedical discoveries. Given the central role of antibodies in biomedical research, it is natural for there to also be technologies that can make the antibody search process more efficient, which is the common goal amongst the antibody search engines listed in this article.

While each antibody search engine has its pros and cons, we're (obviously) biased towards BenchSci, as we've devoted the past two years building it specifically to address deficiencies with existing solutions. It's not perfect, but with feedback from the research community we're working to make BenchSci the best antibody search solution available. We always welcome any suggestions and comments, and we would love to hear from you!

 

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