Introduction
Welcome to another post of my blog! This is my fifth week working on the Bioconductor project with BugSigDB. In this post, I will share my experience and insight to help you understand what BugSigDB is and what you can expect if you decide to contribute to this exciting project. Whether you are a seasoned developer or new to the world of open-source contributions, I hope this post provides a clear and engaging overview.
What is BugSigDB?
BugSigDB is an open-source resource within the Bioconductor project that provides manually-curated, expert-reviewed, syntax-standardized reporting of the published literature on microbial signatures associated with specific diseases, conditions, or environments. Bioconductor is a community dedicated to developing software tools for analyzing and understanding high-throughput genomic data.
The BugSigDB community is diverse, comprising bioinformaticians, microbiologists, data scientists, and software developers. Contributors range from academic researchers and industry professionals to students and interns like myself. This diversity fosters a collaborative environment where individuals with varying expertise work together towards a common goal.
The Problem BugSigDB Aims to Solve
Microbial communities are complex, and their roles in health and disease are not fully understood. Collecting and investigating bacterial signatures from the vast amount of scientific literature available can be very stressful and confusing. BugSigDB aims to solve this by providing a centralized, curated database where researchers can access and share bacterial signatures linked to various conditions.
This centralized database simplifies the process of finding relevant bacterial signatures. Instead of combing through countless papers and datasets, users can search BugSigDB for curated signatures related to their specific area of interest. This efficiency not only saves time but also improves the reliability and reproducibility of research findings.
New Terms and Concepts
I will proceed to explain some new terms I have become quite accustomed to and repeatedly used over the past month during the Outreachy contribution period and now my internship:
- Bacterial Signatures: These are like fingerprints for groups of tiny living things (microbes) such as bacteria. Just like a fingerprint can identify a person, a bacterial signature can help identify what bacteria are present in a specific place, like in a healthy person’s gut compared to someone with a disease. For example, the bacteria in a healthy gut might be less/more diverse and abundant from those in a gut with a digestive illness.
- Microbiome Curation: This is like organizing a big collection of books in a library, but instead of books, we are organizing information about different bacteria from many research studies. In BugSigDB, we collect and check data about which bacteria are found in different conditions, making it easy for researchers to find accurate information. I explained this term extensively in my previous blog post.
- Differential Abundance: This means comparing how much of certain microbes are present in different groups. Imagine you have two gardens of roses: one red and one white. Differential abundance is like counting how many roses are in each garden and seeing if there are more or fewer roses in the red garden compared to the white one. This helps scientists understand which microbes might be linked to health or disease.
- Relative Abundance: This is like looking at a pie chart of all the microbes in a community and seeing how big each slice is. For example, if there are 100 microbes in total and 10 of them are a specific type, then that type makes up 10% of the community. This helps researchers see which microbes are more common and which are rare.
- Confounders: These are extra factors that can mess up study results if not considered. For instance, if you are studying how a diet affects gut microbes, things like age, exercise, or medication can also influence the microbes. These are confounders, and scientists need to consider them to make sure they are studying the right thing.
- Matched-on: This is a way to make sure two groups in a study are similar in important ways, so the results are fair. For example, if you want to compare the gut microbes of people with and without a disease, you might match them on age and gender, meaning you compare people of the same age and gender to avoid these differences affecting the results.
The list goes on, but these are some of the everyday concepts I encounter. Understanding these concepts has been fundamental to my contributions to BugSigDB, and I have enjoyed the learning process.
Getting Started with BugSigDB
Before embarking on the exciting journey of microbial curation on BugSigDB, you need to:
1. Read the onboarding materials. This will provide you with an in-depth and extensive understanding of the BugSigDB world.
2. Watch the collection of video tutorials, which summarize and provide a step-by-step walkthrough of microbiome curation on BugSigDB.
3. Another very important step is to study the curation policy which provides the basic workflow for curation of a new study. This is a very helpful resource that I still reference.
4. A crucial step you should not miss is joining the community-bioc Slack team. Here, you can always seek help and provide help to others.
5. After going through these guides, you can immediately start contributing as much or as little as you want by proceeding to request an account.
6. Once your account is approved, voila! The BugSigDB help page provides different ways you can contribute to BugSigDB.
Hurdles and Doubts
When I first started, the sheer volume of scientific literature and the technical language used in microbiome research was overwhelming. Learning how to efficiently curate bacterial signatures and understanding the criteria for inclusion in BugSigDB took some time. However, with the guidance of my mentors and the supportive community, I was able to overcome these obstacles. Your first curation may not be perfect, and that is alright! With consistency and practice, you will get the hang of curation in no time.
Conclusion
Contributing to BugSigDB has been a fulfilling and educational journey. If you are considering applying to the Bioconductor community through Outreachy, or if you are simply interested in open-source contributions, I encourage you to dive in. You will not only gain valuable skills but also be part of a project that has the potential to make a significant impact in the field of microbiome research.
Thank you for reading! Feel free to reach out with any questions or comments.
