A Beginner’s step-by-step Guide to Contributing to BugSigDB
I am an open source contributor, a DevOps Engineer, Solutions Architect and Technical Manager. I am an innovative technology professional with progressive IT, documentation, web engineering, technical writing, open-source, community building, and developer relations experience in for-profit startups and non-profit technology and education organizations. I am also an aspiring bioinformatician who has been contributing to open source. https://bugsigdb.org/Special:Contributions/Tosin
Illustration by [Tosin Adeshile] via Canva
In my previous blog post, I mentioned that I would be writing a step-by-step guide on how to contribute to BugSigDB. If you are new to open science or open source and are unsure where to start, I encourage you to take your time and go through this blog post.
In this post, I will explain what BugSigDB is all about and walk you through how to contribute, especially if you’re just starting out. You do not need to be an expert in microbiome science and biocuration to get involved. Having a basic understanding of what the microbiome is can be helpful, and if you enjoy reading and analyzing research papers across different health conditions or diseases, that’s a plus. But most importantly, what really matters is curiosity, attention to detail, and a willingness to learn.
If you would like to know more about the project as a whole, you can watch video tutorials here. Future Outreachy applicants can also check out the official documentation and guidelines here.
What is BugSigDB?
BugSigDB is a comprehensive, community-driven database of published microbial signatures. In simple terms, it collects and standardizes significant differential abundance results from published peer-reviewed microbiome studies.
The project focuses specifically on microbial signatures which are sets of microbes reported as significantly different in relative abundance between two or more study groups (for example, healthy vs. disease, treated vs. untreated, exposed vs. non-exposed).
By curating this information in a structured and standardized way, BugSigDB improves:
searchability of microbiome research,
reproducibility of findings,
enrichment analysis across studies, and
community collaboration and learning.
Although the process may seem simple at first glance, curating a study requires careful attention to detail and adherence to curation guidelines.
How to Contribute in 3 Simple Steps:
To begin contributing, there are three main steps:
Select a paper of interest from the GitHub issues tracker
Curate the paper in BugSigDB
Review or correct curations on GitHub.
Below is a more detailed explanation of each step.
Step 1: Select a Paper from GitHub
The first step in contributing to BugSigDB is choosing a paper to curate.
If you are new, you do not need to search for papers on your own. There is usually a list of studies already added to the GitHub issues tracker. These papers are shared by members of the community to make it easier for everyone to get started.
You can simply go through the unassigned open issues and pick one that interests you. If the paper is already assigned to the curator, you will see on the right a red highlighted label “assigned”.
Before selecting a paper, make sure to double-check that:
It reports significant differences in microbial abundance
Look for taxa (bacteria, fungi or viruses) that are reported as significantly different between groups.
The significance threshold by default is usually p ≤ 0.05 or q ≤ 0.05 which still varies depending on the paper, the statistical test, or the specific comparison.
For a paper with the above stated threshold for instance, only taxa meeting this threshold should be curated in BugSigDB.
It clearly defines the study groups
Most studies have at least two groups: Group 0: Control group and Group 1: Case group or both as case groups.
Some studies may compare three or more groups; make sure the groups for comparison are clearly stated.
There is a clear statistical test between the groups in comparison
Common tests include LEfSe, Mann-Whitney (Wilcoxon), Kruskal-Wallis etc.
You can usually find this information in the curatable figures or table captions, in the supplementary material or in the methods section.
There is mention of the study location and the host species
- This varies from humans or animals with their specific scientific name in Latin.
The paper is available to curate
- Ensure the GitHub issue does not already have the “assigned” tag unless you intend to collaborate.
The paper has not already been curated on BugSigDB platform
Search the PMID (obtained from the cite section of the paper in PubMed) of the paper in BugSigDB.
Search the paper title in the GitHub issues page.
If everything looks good:
Leave a comment on the issue to request an assignment by clicking the topic of the paper you are interested in and tagging a mentor.
Await assignment and once done, you can begin curating.
Step 2: Curating the Paper
This is the main part of the contribution process.
Curating in simple terms means carefully reading the study and recording its information into BugSigDB in a structured way.
Create a GitHub/BugSigDB account:
Note: Skip this step if you already have a GitHub and BugSigDB account
Add the study:
Go to the BugSigDB homepage
Click “Add a Study”
Paste the PMID digits only e.g the PMID of this paper is "34069916"
Click "create or edit"
Input the study design of the paper or article from the dropdowns
Click auto and all details would reflect automatically
Change the form's data to complete
Add a new experiment: Most studies contain at least one experiment.
Click “Add a new Experiment”
Fill in details about the location, body site, host species, condition, sample sizes, group names, antibiotics exclusion, lab and statistical analysis and alpha diversity
After completing the form, save and mark it as Complete.
Add the Signatures (Important Step): This is where you enter the actual microbial results.
From the experiment page click “Add a new Signature”.
You will usually add:
One signature for microbes that increased in abundance, the signature 1.
One signature for microbes that decreased in abundance, the signature 2.
Make sure that:
Microbial names are entered exactly as reported if not seen as the heterotypic, homotypic synonym or basionym obtained from NCBI or UniProt.
You carefully follow the taxonomy guidelines from the curation policy.
Note that some studies only report one direction (only increased or only decreased), so always follow what the paper reports.
It is also important to note that you can always refer back to the curation policy if you are unsure about the details to include in your curation.
Once everything is saved properly, your curation is ready for review.
Step 3: Reviewing and Correcting Curations
Every curation must go through a review process before it can be officially closed as complete to ensure that the information entered is accurate, consistent, and in line with the project’s guidelines. This step is important because BugSigDB aims to maintain high-quality, reliable data.
Request the peer review:
After completing your curation, you can request a peer review from other contributors in the #bsdb-peer-reviews channel on Zulip.
Share the link to your curated study together with the link to the original paper so that other contributors can check your work and provide feedback if necessary.
Request the official review:
This is the final review conducted by a mentor.
Make a comment in the corresponding GitHub issue to request the official review by mentors, for example: “https://bugsigdb.org/34069916 ready for review”.
When receiving Feedback:
Carefully read the comments provided by reviewers or mentors.
Go back to your curation and correct any issues that were pointed out, such as missing fields, incorrect entries or formatting issues.
In case of doubt, do not hesitate to ask for clarification.
Once the corrections are made, tag the specific mentor who gave feedback and reply to the reviewed comment in the GitHub issue to indicate that the changes have been addressed.
Advanced contributions
- Peer reviewing: This is another way contributors and community members can help improve the quality of curated studies by reviewing the work of others. This review is done before the official review to help catch small mistakes, identify missing information, ensure the study follows the curation guidelines and improve overall accuracy. Peer review requests are usually made in #bsdb-peer-reviews on Zulip.
Once you become familiar with the curation process, you can also contribute by reviewing studies directly through GitHub issues.
To perform a peer review on GitHub:
Head to the GitHub issues
Select the study you are interested in reviewing
Tag a mentor and request to be assigned to do this
Ensure that your reviews are concise, precise and clear
Give Feedback and tag a mentor with the study link indicating completion.
2. Identifying papers with significant differences and adding it to the GitHub issues open to all. You can use PubMed, Crossref, Google Scholar for paper search. To add such papers:
Click on "New issue" on GitHub
Select "BugSigDB curation by DOI"
Input the accurate DOI link.
Click "agree to the code of conduct agreement"
Select "Create"
Note: all the details about the paper will be automatically added in the GitHub comment.
3. Working on a BugSigSimpleR issue.
4. Fixing curation issues.
Further notes
Always pay attention to detail when adding, curating, reviewing studies, or resolving curation issues.
Join the weekly meetings to stay up to date and be present during discussions and analyses. These meetings also give you the opportunity to learn from the approaches other contributors have used to solve challenges they’ve encountered.
Engage actively within the community by offering help to others who may be stuck during their contributions.
Do not hesitate to ask questions when you are unsure about something.
Make use of the appropriate Zulip channels:
#bsdb-introductions to introduce yourself
#bsdb-peer-reviews to review and assist fellow contributors
#bsdb-questions to ask questions
#bugsigdb as the main project discussion channel
AND, enjoy!
