bifo-paper-1

BIFO: A Biological Information Flow Ontology for Knowledge Graph-Directed Pathway Analysis of Rare Variant Cohort Data

Deanne M. Taylor1,2 ^^, Benjamin Stear 1, Taha Mohseni Ahooyi 1, Yuanchao Zhang 1, Aditya Lahiri 1, Alan Simmons 3, Tiffany Callahan4, Jonathan Silverstein 3

1. Department of Biomedical Informatics, Children's Hospital of Philadelphia
2. Department of Pediatrics, University of Pennsylvania Perelman School of Medicine
3. University of Pittsburgh Medical Center
4. Manas AI, NY NY

^^corresponding author

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Manuscript

This repository uses Manubot for collaborative manuscript management. All content is in the content/ directory as Markdown files. The manuscript is built automatically on every push via GitHub Actions.

File	Content
content/01.abstract.md	Abstract
content/02.introduction.md	Introduction
content/03.methods.md	Methods (Sections 1–10)
content/04.results.md	Results (Sections 1–8)
content/05.discussion.md	Discussion
content/06.references.md	References
content/metadata.yaml	Authors, title, keywords

Code

All pipeline code is in the companion repository: TaylorResearchLab/bifo-graph

Status

Section	Status
Methods 1–9 (curated CHD benchmark)	Complete
Methods 10 (KF cohort)	Complete
Results 1–7 (curated CHD benchmark)	Complete
Results 8.1–8.2 (KF-CHD)	Complete — pending Supp tables S3–S5
Results 8.3 (cross-cohort)	Pending NBL pipeline results
Introduction	Outline only
Abstract	Pending
Discussion	Outline only

Building locally

# Install manubot
pip install manubot

# Build the manuscript
manubot process --content-directory=content --output-directory=output --cache-directory=ci/cache

# Or just view the auto-built version at the GitHub Pages URL after CI runs

Citation