Step-by-Step Guide to Contributing to BugSigDB

Welcome to week 5 of my Outreachy internship. In my last blog post, I mentioned that I was preparing for my first presentation. To give a quick rundown, my presentation turned out great, and I talked about microbiome composition alterations and the pathological association between gut microbiome and polycystic ovary syndrome using metagenomic analysis. You can find my curation on the database here.

This week is a little different. I will be explaining the BugSigDB project and taking you through the contribution process as a beginner. It is important to know and start from the basics, so the first step to understanding the project will be having basic knowledge of the microbiome, having a passion for it, or simply being willing to learn and being teachable (welcome materials are available here).

What is BugSigDB?

BugSigDB, in simple terms, is a database of microbial signatures. Its primary function is to standardize key elements of published microbiome studies to improve searchability, enrichment analysis and to encourage community interactions.

There are 4 main steps to curating a study in BugSigDB, and I will be starting from the very first.

1. Identifying Curatable Papers

This step involves searching scientific journals for published papers on the microbiome of humans and animals. To identify curatable papers, you must make sure it has all of the following;

• Significant differential abundance results: These are results that show the differences in abundance of microbes (signatures) between the study groups of the experiment.

• A location: This is the location of the subjects of the study.

• A host species: This can either be animals or humans, and

• Study groups: These are the experimental groups in contrast.

For example, I am particularly interested in polycystic ovary syndrome, and here is a study I found in the Journal of Ovarian Research with curatable results (see Figure 4).

2. Adding the Papers to GitHub

After identifying that a research paper is curatable, you can go ahead and add it to the GitHub issues tracker page, but before you do this, you must take the following steps to ensure you are adding a fresh study and not a duplicate.

• Copy the PubMed Identifier (PMID) of the study and paste it in the search bar on BugSigDB. This is to check that the study has not already been curated.

• Copy the title of the study and paste it into the search for the GitHub issues. This is to check the study status.

If it passes the two checks above, then you can go ahead and create an issue on GitHub through the issues tracker page.

For example, after checkups by PMID and title, here are the studies I have added to the GitHub issue tracker page so far.

3. Curating Studies

This is the most interesting step, which involves meticulously entering data from the studies into BugSigDB. You can do this in the following simple steps.

• Go to the GitHub issue tracker and select a study to curate.

• Leave a comment under the study asking for it to be assigned to you, and wait to get assigned.

• After you have been assigned a paper, go to the BugSigBD main page and click on “Add a Study”. This will open up the ‘Add or Edit Studies’ Page.

• Copy the PMID of the study and paste it into the space provided. This will take you to the form for adding a page.

• Select the study design. You can identify study designs easily by reading the curation policy.

• Go to ‘This form’s data is’ at the bottom left of the page, and change it to ‘Complete’ and then save. This step is important because otherwise your study cannot be analysed.

• On the newly generated page, click on ‘Add a new Experiment’, which will open up a new page, and you can now start adding all your relevant data. Data on the subject of the study, the laboratory analysis and the statistical analysis. Do not forget to save and mark as ‘Complete’

• After that is done, the final step is adding the signatures. You can do this by clicking ‘Add a new Signature’ from the experiment page you just created and saved. The first signature you create will record the microbes with increased relative abundance reported in the study, and the second will record the decrease.

Please note that for most experiments, you have to add two signatures (Increased and Decreased), but in some cases, you only need to add one. This is fully dependent on the study and what is recorded as significant.

For example, my fellow curator Precious Chijioke got attracted to this paper and asked for an assignment.

4. Reviewing and making corrections

This is the final step, and you do this after curating your study. Two important reviews need to be done before your study can be closed as complete.

1. Peer review: This is a review that is done by fellow curators and community members before an official review. You can request a peer review on the BugSigDB channel in Zulip by leaving a request message that includes the study link and the article link.

2. Official review: This is a review that is done by a mentor. You can request this review by leaving a message that includes the study link under the GitHub issue you have curated.

After an official review, mentors and/or experienced curators write their feedback under the GitHub issue, and the curator gets a chance to make corrections (and learn!) and finalize their curated study.

Reviews take time because it is a very important step that is done to ensure the curated data is accurate before the study is marked as reviewed in BugSigDB and closed as complete on GitHub.

For example, the curator Precious asked for a final review on this study, and I suggested a few corrections, which went through another round of review before approval by the mentor Kate Rasheed. Together, we closed the study, and it got published in BugSigDB as “reviewed”.

You can check out the published study here.

Other ways to contribute to BugSigBD

Aside from adding papers to GitHub and curating studies, there are several other ways to contribute to BugSigBD.

• Reviewing curated papers: Every curation undergoes at least one or more review, which is done to ensure data accuracy. Everyone within the community is welcome to give a peer review on a study before the official review.

• Fixing curation issues: Issues like a missing NCBI or a study that is complete but not marked as ‘Complete’.

• Answering and asking questions on the communication channel is also a great contribution to the community.

Curating, Contributing and Learning

Curating studies requires some technical and soft skills, and most of them you can learn while doing. Skills like attention to detail, communication and collaboration, ability to read and interpret different data types, etc.

Contributing to the project means that you are making research more readily available and also building valuable skills.