Outreachy contribution phase — Week 1

Success is not only an instant achievement; progress is defined by daily advancements and our resilience, regardless of failure.

The key to success lies in our ability to keep moving with unwavering faith in our abilities.

So I got the mail, my initial Outreachy application had been accepted.

I celebrated and started by following all the links attached to the acceptance mail.

On day two, I went through all available projects — and selected the one I desired to contribute to and fit my skills, The BugSigDB Microbiome project — (I know its advised to shoot at two organizations, but I chose one, and I intend to give it my all; not only my best.)

Afterward, I joined the Bioconductor BugSigDB community platform, introduced myself, and noticed the enthusiasm of everyone in the community and projects (every other applicant as well –😅😅).

The BugSigDB project requires that you make the first general contribution before you can work on any other contributions. I researched how to deliver quality work for my first contribution.

The initial contribution focused on a mini-curation process, which involved identifying various aspects such as signatures, groups, alpha diversity, taxa, and more.

Signature: There are specific patterns, features, or characteristics identified within a dataset, often through analysis or observation (they serve as building blocks for understanding the relationship between the microbiomes and health).

Groups: Groups refer to categories sharing similar characteristics or attributes (could be data points, samples, organisms, or other entities being studied or analyzed).

Alpha-diversity: Describes the diversity of species within a specific habitat or sample. It measures the variety and abundance of diverse species present in a single location or sample.

Taxonomy “Taxa”: Taxonomy is the science of naming and classifying organisms based on their characteristics and evolutionary relationships. Taxa can range from broad categories like kingdoms and phyla to more specific groups like genera and species. These groups start with big categories like “animals” or “plants” and get more specific from there. For example, under “animals,” you might have “mammals,” and under “mammals,” you might have “dogs” and “cats.” Each of these is a different taxon.

I progressed to picking a full curation as my second contribution, “Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota”.

It was not business as usual, but with experience with the initial mini-curation contribution, it was somewhat easier to navigate.

During this same week, we had our first official office hour with Svetlana, Chioma Onyido, Peace Sandy, and Afuape Esther the mentors of the BugSigDB project.

I enjoyed connecting with other contributors and learning about the projects.

These are excerpts from the call;

• Always remember to check for supplementary materials during curation. These materials are at the beginning or end of the paper.
• Consider creating a talk page to guide other curators or reviewers.
• Prioritize quality over quantity when conducting curation. Take the necessary time to ensure a thorough and high-quality curation process.
• Condition — This is relative to the case group, which refers to the disease or condition present in the patient population but absent in the healthy population.
• Experiments in BugSigDB are comparisons.
• Conditions are contrasts, basically, what’s in group A and not in group B.
• If you can’t find the PMID or the DOI input the link you can find and also curate that section manually.
• If there is no alpha diversity in your paper, you can curate the paper but omit the signature page.
• BugSigDB is currently interested in alpha diversity and not beta diversity, so do not record for beta.

With this knowledge, I set out to work on my second full curation. I started by populating my study with the data from my chosen article. I struggled to identify the actual groups conducted and the alpha diversities used and solved it with help from quality community contributors, I got help from Aleru Divine and Ima-ubong Aimah, and I identified the confusing sections of the experiment study in turn, I helped review their curation studies as well.

And I have made progress in completing my second curation.

So far this week, I have learned:

• Nothing is unlearnable — you can learn and understand anything if you give your heart, time, and energy.
• Support is a vital ingredient for success (I am glad for the numerous supports from the community, friends, and dear ones thus far.)
• It is easy to desire great goals, but it takes strength, commitment, and discipline to keep going.
• Quality/accuracy is pivotal to being outstanding.
• Success is making progressive advancement towards achieving set goals.

Shout out to every BugSigDB contributor and the awesome mentors! ✨🎉

Thank you for reading.

Until next time!

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