manuscript structure

Most research articles consist of a Title page, Abstract, Introduction, Methods, Results, Discussion and References. Many medical journals want abstracts with subheadings. Read more

Penelope relies on being able to find these headings in order to carry out subsequent checks. If your manuscript does have those headings but Penelope can't find them, try removing formatting and line numbers. 

For some article types, like meta-analyses, case reports or letters, Penelope expects a different structure. You can tell Penelope what kind of manuscript you are submitting by answering questions during upload.

title page

Title and abbreviated title

Titles are used by search engines, so it's important to pick relevant words so that others find your work. In general, your title should include your study design, sample population, and what you were measuring. Most journals also ask for an abbreviated title (sometimes called running head) which typically has fewer than 50 characters. It's useful to put this running head as a header on all pages of your manuscript. 

Authors

You should give the full names of all authors. Most journals also ask for their highest degrees and current place of work. A good idea is to include everyone's ORCID, which means they won't get confused with other researchers that have the same name. You should specify one of the authors as a corresponding author, and provide their email address. 

Keywords

You should provide a few keywords that sum up your work. These are useful when identifying potential reviewers, and can later be used by search engines. Medical research should get their keywords from the MeSH thesaurus. 

Counts

You should give a word count. Generally you don't need to include the references when counting words. It's also useful to specify how many tables and figures should be present so that reviewers can make sure they see everything. 

FUNDING

You should have a section titled "Funding Statement" where you explain who funded the research. You should include all of your grant numbers. 

CONFLICTS OF INTERESTS

Your manuscript should include a "Conflicts of Interests" section where you declare any financial or personal relationship that might bias or be seen to bias your work. State whether sponsors had any specific role in the production of the paper. If there are no conflicts of interest, write: "The authors report no conflicts of interest and have no proprietary interest in any of the materials mentioned in this article.".

ACKNOWLEDGEMENTS 

Your "Acknowledgements" section should credit contributors who did not meet the criteria for authorship. 

ORCIDs are unique, personal identifiers that distinguish you from other researchers with similar names. They help link all of your professional outputs together so that you can be recognised for all your work. 

Data Access

Many journals require authors of original research articles to publish their underlying raw data. This could well be a requirement of your funding, so you should check your funder’s policy.

You should:

1. Publish your data in a suitable repository

2. Cite the dataset in a “Data Availability” section. 

3. Include the citation in your references list, so that your manuscript and dataset can be linked together.

Publishing your data doubles your research outputs, and there are lots of metrics you can use to track the impact of your data. If you’re worried about sharing data, not sure what data to share, or want to learn about embargo periods, you can learn more at the digital curation centre.

reporting guidelines

Guidelines exist for many types of medical research. These guidelines have been written by experts and set out lists of important things other people need to know about your work. Reviewers and editors use these guidelines when assessing submissions, so if you forget to mention anything your work may be returned to you.

In your methods section, state that your manuscript adheres to the relevant guideline, and then cite them in your reference section.

The EQUATOR Network has a comprehensive library of guidelines. The most common are listed below, and we have a tool that can help you work out which is right for you. 

• CONSORT for randomised trials:
  
  Schulz KF, Altman DG, Moher D, for the CONSORT Group. CONSORT 2010 Statement: updated guidelines for reporting parallel group randomised trials. Trials. 2010;11:32. PMID: 20334632
   
• ARRIVE for research involving laboratory animals:
  
  Kilkenny C, Browne WJ, Cuthill IC, Emerson M, Altman DG. Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PLoS Biol. 2010;8(6):e1000412. PMID: 20613859
   
• PRISMA for systematic reviews:
  
  Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group. Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. PLoS Med. 2009; 6(7):e1000097. PMID: 19621072
   
• MOOSE for reviews and meta-analyses of observational studies:
  
  Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group. Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. PLoS Med. 2009; 6(7):e1000097. PMID: 19621072
   
• ENTREQ for synthesis of qualitative research:
  
  Tong A, Flemming K, McInnes E, Oliver S, Craig J. Enhancing transparency in reporting the synthesis of qualitative research: ENTREQ. BMC Med Res Methodol. 2012;12(1):181. PMID: 23185978
   
• CARE for clinical case reports and case series:
  
  Gagnier JJ, Kienle G, Altman DA, Moher D, Sox H, Riley D; the CARE Group. The CARE Guidelines: Consensus-based Clinical Case Reporting Guideline Development. BMJ Case Rep. 2013; doi: 10.1136/bcr-2013-201554 PMID: 24155002 
   
• SRQR for qualitative research:
  
  O'Brien BC, Harris IB, Beckman TJ, Reed DA, Cook DA. Standards for reporting qualitative research: a synthesis of recommendations. Acad Med. 2014; 89(9):1245-1251 PMID: 24979285
   
• STROBE for observational studies:
  
  von Elm E, Altman DG, Egger M, Pocock SJ, Gotzsche PC, Vandenbroucke JP. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: guidelines for reporting observational studies. Ann Intern Med. 2007; 147(8):573-577. PMID: 17938396 
   
• STARD for diagnostic accuracy studies:
  
  Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig L, LijmerJG Moher D, Rennie D, de Vet HCW, Kressel HY, Rifai N, Golub RM, Altman DG, Hooft L, Korevaar DA, Cohen JF, For the STARD Group. STARD 2015: An Updated List of Essential Items for Reporting Diagnostic Accuracy Studies. BMJ. 2015;351:h5527. PMID: 26511519 
   
• REMARK for prognostic modelling studies using biomarkers:
  
  McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM. REporting recommendations for tumour MARKer prognostic studies (REMARK). Br J Cancer. 2005;93(4):387-391. PMID: 16106245 
   
• TRIPOD for prediction modelling studies for prognosis or diagnosis:
  
  Collins GS, Reitsma JB, Altman DG, Moons KG. Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD): The TRIPOD statement. BMJ 2015; 350:g7594. PMID: 25569120

Research resource identifiers

ANIMAL IDENTIFIERS

To help other people replicate your experiment, it's good practice to identify the exact organism you used by citing its unique resource identifier. You can search for identifiers here and learn more about identifiers for research animals here.

ANTIBODY IDENTIFIERS

Identify the exact antibodies you used by citing their unique resource identifiers. This allows other researchers to know exactly what you used. You can search for identifiers here and learn more about identifiers for research animals here.

reporting percentages

When reporting percentages it's useful to give the absolute figures too e.g.

"65% of people reported improved symptoms after treatment (13/20), only 6% of people reported negative side effects (1/17)".

The absolute numbers are important because they show us that even though 65% sounds high, it's based on a modest sample size. The denominator is useful as we see that the two results are based on different number of responses; 20 in one group and only 17 in the other.  

p-values

You should report p-values as exact figures (e.g. p = 0.043), not inequalities (e.g. p < .05) unless the value is less than .001. You should explain which significance threshold you used in the methods section (e.g. "The significance threshold was .05"). Every p-value should be accompanied by its test statistic and a measure of precision, typically the 95% confidence interval. 

Reporting ANOVAs

When reporting an ANOVA you should include the following information. 

1. State what kind of ANOVA you used: Was it one-way, two-way, repeated measures or mixed? 
2. Check and state that your data is normally distributed: Your data should follow a normal distribution. Check this by plotting the data on a histogram or scatter graph. For independent data you should plot the residuals. For a repeated measures ANOVA you should plot the residuals at each time point. If the chart peaks in the middle and is roughly symmetrical then your data is normal. Otherwise, you should use a Kruskal-Wallis test (for independent data) or Friedman test (for repeated measures data).
3. State the degrees of freedom and the test statistic: Write this as F(df1, df2) = F-statistic.
4. Include a measure of precision: generally a 95% confidence interval. 

The SAMPL guidelines explain how to report statistics. 

t-tests

When reporting a t-test you should include the following information. 

1. State whether you used an independent or paired t-test: You should use a paired t-test if you took repeated measurements of the same variable from the same sample. Otherwise use an independent t-test.
2. Check and state that your data is normally distributed: Your data should follow a normal distribution. Check this by plotting the data on a histogram or scatter graph. For an independent t-test you should plot the data for each group. For a paired t-test you should plot the paired differences. If the chart peaks in the middle and is roughly symmetrical then your data is normal. Otherwise, you should use a Wilcoxon or Mann-Whitney test. 
3. Check and state that variances are equal (for independent t-tests): you can use Levene's test for this. If variances aren't equal, you can correct for this by adjusting the degrees of freedom using the Welch-Satterthwaite method and by not using the pooled estimate for the error term for the t-statistic. Some statistical softwares will do this for you automatically - look for a row in the output called something like "Equal variances not assumed". Alternatively, you could use a MannWhitney test. 
4. State the degrees of freedom and the test statistic: Write this as t(df) = t-statistic.
5. Include a measure of precision: generally a 95% confidence interval. 

If you want to plot your results you should use a box plot (for exploratory research) or a confidence interval plot (if you are testing a hypothesis). 

See the SAMPL guidelines for more general information about how to report statistics, and this guide to learn more about common statistical tests. 

Reporting correlations

The SAMPL guidelines explain how to report statistics. When reporting a Pearson's correlation you should include the sample size (n) that was used to calculate the r statistic. Write this as r(n = ___) = r statistic. Alternatively, you can report the degrees of freedom (df) instead of the sample size. You calculate this as n - 2, and write it as r(df = ___) = r statistic.

Figures

Check with your chosen journal to see what file format and resolution you should use, and whether you should put figures in the manuscript or keep them separate. Take extra care with digital images. 

Every figure should have a legend below it, starting with “Figure“ and the figure number, followed by a caption. Figure legends are one of the more commonly read parts of a manuscript, so it’s worth spending time on writing the perfect legend. 

If your figure presents data, make sure the legend includes units, and define any error bars as the standard deviation, 95% confidence intervals or other measure if used.

Tables

See general advice for preparing tables here. If using Microsoft Word, you should make tables using Word's table function. Don't embed excel tables or PDF tables, as these can't be read by all journal submission softwares. Avoid using merged cells, putting returns inside cells or using special formatting as these can get corrupted. Check with your journal to see if they want your tables to be embedded into the manuscript or kept separate. 

Every table should have a title. Generally it's best to keep this title short and put any detailed explanations into footnotes, but check to see what your journal wants, 

References

Your manuscript should have a section titled 'References’ where you list your cited sources. All references should be cited, and vice versa. Try to avoid citing sources that haven’t been published yet or aren’t peer reviewed, and avoid excessively citing your own work.

You should order your references either:

1. Numerically in the order they are mentioned in the text

2. Alphabetically according to the first author

Most medical journals use a numbered system, but you should check what your journal wants.