How do you use the CiteAb reagent search engine? Interview with Dr Harvinder Virk
In this blog:
- Learn more about the Only Good Antibodies community and forum
- How does Dr Virk use the CiteAb search engine for his research?
- Get in touch if you’d like to be featured in a CiteAb blog!
This year, our life science reagent search engine turned 10!
To mark this ten year milestone, we have been speaking to our users to learn more about their work and how they use CiteAb. We have previously spoken to Dr. Andrea Radtke from the NIAID/NIH, and Dosh Whye from Boston Children’s Hospital, about their research and experience of CiteAb.
Do you use CiteAb, and want to be featured in a CiteAb blog? Just get in touch with the team!
Today, we speak with Dr. Harvinder Virk, an NIHR Academic Clinical Lecturer from the University of Leicester, UK.
Dr Virk is a clinical researcher working in the NHS (UK) in respiratory medicine. While his clinical interest lies in lung fibrosis, his research interest revolves around working in interdisciplinary teams to make the pathway from basic research to clinical translation more efficient, with a focus on tools such as antibodies. Together with Dr Eva Krockow, University of Leicester, Dr Virk co-leads the Only Good Antibodies community and forum, who are working to do just this.
CiteAb recently organised the 4th International Antibody Validation meeting at the University of Bath, where Dr Virk showcased a poster on the OGA community. In this meeting, 100 delegates from around the world came together to discuss the state of the field and how to drive progress.
Read on to hear more about the OGA community and how Dr Virk has used CiteAb to easily identify where antibodies have been used in the literature, feeding into his work on antibody validation. Plus, he signposts resources on the issue of reproducibility and current work in the validation field.
Here’s our conversation:
Could you tell us a little more about the work you are involved in?
‘Unfortunately, a large proportion of antibodies used for research purposes do not recognise the target they are meant to, or they also recognise lots of other proteins. Two large studies suggest that this is a problem for more than half of available antibodies. This leads to expensive waste of resources and failures of expensive research projects and drug development.
The reasons for this problem are complex, but include that it has been historically slow, expensive and difficult to perform all the best quality control experiments. There is also a need to change the research culture to address this problem. The OGA community and forum are working to address this problem.
The OGA community will work with all stakeholders to accelerate scientific and drug discovery research by:
1. Increasing the availability and use of good antibodies
2. Eliminating the use of poorly performing antibodies
Good antibodies (or affinity reagents) are potent and selective in the application of interest and display no lot-lot variability.
The OGA community and forum was established in April 2023 using the support of the Leicester Institute of Advanced Studies Pioneering Partnership Award, with further support from two BBSRC impact accelerator awards.
We are part of the wider movement to improve research integrity and reproducibility, we are becoming an affiliate stakeholder in the UK reproducibility network (UKRN) and are also working with the UK Research Integrity Office (UKRIO). We are learning from this wider community, and our work also represents an opportunity for learning in the wider context of research reproducibility and integrity.
We are a diverse collaboration of basic, clinical, data and behavioural scientists and technicians from academia, industry, and non-profit organisations.
If you support our mission goals, you are already part of our community! But we believe that to achieve our mission we should work together, and the OGA community and forum represents a way to help us collaborate better. We support open science and transparency, and we believe a no blame culture helps facilitate better collaboration and progress.’
So, how do you use the CiteAb platform in this work?
‘We find that CiteAb is a very powerful way to try and establish where in the published literature some antibodies have been used.
It helped us to identify where in the published literature antibodies with potential performance problems had been used, and to quantify the potential impact of this on the literature, please see the eLife publication from YCharOS and RRID that we contributed to for more information: https://doi.org/10.7554/eLife.91645.1
In the eLife publication we used CiteAb to try to find the majority of papers in the literature that had used ~80 antibodies, in order to try to understand whether they had supportive validation data in the literature for their specific use in immunofluorescence. Unfortunately, for this set of antibodies that failed to show selectivity in the YCharOS Inc pipeline, in the majority of publications (87.5%), validation data was not presented.’
Given the scale of the validation issue, demonstrated in this recent e-Life publication, it is evident that sharing validation data and growing awareness is necessary to prevent circumstances where cited antibodies that are not specific to the target continue to be used.
To this end, we encourage antibody vendors to get in touch if you have validation data that is not currently on CiteAb!
We include validation data on CiteAb when available, and link to full publications for researchers to evaluate and assess if any validation had been carried out in the individual publication. We will be adding a link to YCharOS validation data on product pages very soon – so do keep an eye out for this!
What do you like about using CiteAb?
‘CiteAb is intuitive to use, and has a clear and transparent system for ranking antibodies according to the number of citations in the literature. In this respect it does what it says on the tin!’
You can try out the antibody search engine here;
Is there anything else you’d like to flag or signpost for our readers?
Our UK reproducibility network webinar can be found here: Antibodies and Research Reproducibility: A technical, open data, behavioural, and policy challenge
The YCharOS pipeline data can be accessed here: https://f1000research.com/ycharos
The eLife paper can be found here: https://doi.org/10.7554/eLife.91645.1
The following publications highlight some of our other contributions to this issue:
Kahn, Richard A., Harvinder S. Virk, and Peter S. McPherson. “Heed a decade of calls for antibody validation.” Nature 620.7974 (2023): 492. https://doi.org/10.1038/d41586-023-02566-w
Aponte Santiago, Nicole, et al. “Tales of the unexpected.” Elife 12 (2023): e87444. https://doi.org/10.7554/eLife.87444
Virk, H. Singh, et al. “Validation of antibodies for the specific detection of human TRPA1.” Scientific reports 9.1 (2019): 18500. https://doi.org/10.1038/s41598-019-55133-7
We want to thank Dr Virk for speaking with us about his work for this blog!
Initiatives such as the OGA community are essential to help address the issue of antibody validation and drive change.
We are excited to see the work of the OGA community in the future, and to reflect on the overall progress in the field at the next International Antibody Validation meeting.
- Skye and the CiteAb team