How to write an abstract
Sep 24, 2019
In this blog post, I try to break down how to write an effective abstract for a scientific research paper using examples from our recent PNAS paper, Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.
Components of an effective abstract
The abstract is usually the first, perhaps only, part of your paper read by the reader. Perhaps this abstract is for a talk you are giving. Perhaps it is for a poster presentation at a conference. Perhaps it is for a paper. There are many different ways to go about writing an abstract and sometimes what goes into an abstract will depend on factors like character limitations. But in all cases, I believe an effective abstract should address at minimum four general questions:
Why did you do the research? Is there a gap in our understanding of important disease process? Is there a question that necessitates the development of a new computational method? Example:
The spatial organization of RNAs within cells and spatial patterning of cells within tissues play crucial roles in many biological processes.
How did you address this problem? Did you develop a new method? Did you use a particular technique like single-cell sequencing? Example:
Here, we demonstrate that multiplexed error-robust FISH (MERFISH) can achieve near-genome-wide, spatially resolved RNA profiling of individual cells with high accuracy and high detection efficiency.
What did you end up finding? What did you discover? What are your results? Example:
Using this approach, we identified RNA species enriched in different subcellular compartments, observed transcriptionally distinct cell states corresponding to different cell-cycle phases, and revealed spatial patterning of transcriptionally distinct cells. Spatially resolved transcriptome quantification within cells further enabled RNA velocity and pseudotime analysis, which revealed numerous genes with cell cycle-dependent expression.
So, what are the implications of your research? What do your results mean? Where can we go from here? Example:
We anticipate that spatially resolved transcriptome analysis will advance our understanding of the interplay between gene regulation and spatial context in biological systems.
Based on the answers to these four questions, the reader can make an informed decision as to whether to attend your talk, go seek out your poster at the conference, or read the rest of your paper.
Things to avoid in an abstract
1. Unsubstantiated grandiose claims
In my opinion, the worst abstracts are those that get your hopes up and then underdelivers. How do you feel when you watch a great trailer but then the movie turns out to be awful?
2. Unnecessary details
Abstracts are usually very short. This means you do not have a lot of space to tell me about your paper. Do not waste this space on irrelevant background details or methodological minutiae.
3. Jargon and abbreviations
Abstracts should generally be understandable for a wide audience. Jargon and abbreviations that would otherwise be elaborated on or defined in a longer introduction should be avoided in an abstract in order to minimize confusion while maintaining brevity.
Do I write the abstract first or last?
Both. Writing is an iterative process.
In theory your abstract should be an abbreviated version of your paper (talk or poster) so it should reflect what is in your paper. Therefore, it is helpful to write the abstract last after you’ve already decided on what is in the rest of your paper. However, writing an abstract first can help guide the rest of your paper by organizing your thoughts and condensing your results down to the main findings for example.
It’s ok to write many drafts of an abstract, especially as the main paper develops and matures. You can even use “filler sentences” that generally capture the idea that you’re going for but perhaps lack the concision and accuracy necessary for a publication-ready sentence. Personally, I find using such “filler sentences” helpful since it allows me to move on to writing the rest of the paper instead of fixating on perfecting a single sentence.
Draft 1: Spatial context is important.
Draft 2: The spatial context of cells is important for biological processes.
Draft N: The spatial patterning of cells within tissues play crucial roles in many biological processes.
Try it out for yourself!
Find a paper, even one that’s not in your field. Does the abstract address these four questions:
- Aligning 10X Visium spatial transcriptomics datasets using STalign with Reticulate in R on 05 November 2023
- Aligning single-cell spatial transcriptomics datasets simulated with non-linear disortions on 20 August 2023
- 10x Visium spatial transcriptomics data analysis with STdeconvolve in R on 29 May 2023
- Impact of normalizing spatial transcriptomics data in dimensionality reduction and clustering versus deconvolution analysis with STdeconvolve on 04 May 2023
- Aligning Spatial Transcriptomics Data With Stalign on 16 April 2023
- 3D animation of the brain in R on 08 November 2022
- Ethical Challenges in Biomedical Engineering - Data Collection, Analysis, and Interpretation on 15 October 2022
- I use R to (try to) figure out the cost of medical procedures by analyzing insurance data from the Transparency in Coverage Final Rule on 12 September 2022
- Annotating STdeconvolve Cell-Types with ASCT+B Tables on 30 August 2022
- Deconvolution vs Clustering Analysis: An exploration via simulation on 11 July 2022