Welcome Outreachy Applicants!

Note: This task can be completed by multiple Outreachy applicants.

BugSigDB Project

BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes.

Prep Work

To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
BugSigDB project information, estimated time: 15 minutes (link)
Reading materials on the human microbiome, estimated time: 2 hours (link)
Step-by-step guidance on how to document a signature in BugSigDB (link)
View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
Video trainings on BugSigDB curation (link)

First Contribution Task

1. Go to the first curation form
2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design)
3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM.

Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0OMKrhXPm1GsFCu

Please submit a fully completed mini-curation via the form above before continuing to the second contribution task.

Second Contribution Task (Optional)

As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged "paper to curate" and work on a full curation.

To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded.

To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation.

Assessment & Grading

Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric:

1. All elements marked "Needs review" (none "Incomplete") (1 point):
2. Correct study design (1 point):
3. Entered all relevant experiments and no irrelevant experiments (1 point):
4. Body site correctly identified (i.e. does not include multiple sites) (1 point):
5. Condition entered according to contrast (correct EFO ontology) (1 point):
6. Contrast groups correctly identified (1 point):
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point):
8. Antibiotic exclusion correctly identified (1 point):
9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points):
10. Identified correct statistical test (1 point):
11. Identified MHT correction (1 point):
12. Correctly recorded matched on variables (1 point):
13. Entered correct number of statistical tests per experiment (1 point):
14. All diversity measures identified (1 point):
15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point):
16. All signature sources correctly identified (-1 for each error) (2 points):
17. Abundance direction correctly selected (1 point):
18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points):
19. Correct use of NCBI taxonomy (don't deduct if can't easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points):

Total (maximum 23 points):

Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Zulip channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading.

Questions

Communication regarding specific tasks should be done on a task's GitHub issue or on the Zulip channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://chat.bioconductor.org/. After you log in, join the channel #bugsigdb. If you are having issues to join in, feel free to contact @jwokaty at andres.wokaty@sph.cuny.edu.
There are three focused channels:
#bsdb-introductions → for intros and check-ins
#bsdb-questions → for task/process/tooling questions
#bsdb-peer-reviews → for feedback and review requests
Here’s the onboarding guide with examples and best practices: [Google doc]

NOTE: Please do not use the channels #general, #random and #introductions to introduce yourselves.

To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Office Hours

Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95

Contributions

Remember to record your contributions in Outreachy.