ArticleCell systems2019
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The molecular pathogenesis of placenta accreta spectrum disorder and its clinical applications.Archives of gynecology and obstetrics · 2025Review
- Cytoscape Web: bringing network biology to the browser.Nucleic acids research · 2025Article
- Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders.Cell systems · 2025Article
- Simplicity within biological complexity.Bioinformatics advances · 2025Article
- Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.bioRxiv : the preprint server for biology · 2024Article
- The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell.Bioinformatics advances · 2024Article
- Deep distributed computing to reconstruct extremely large lineage trees.Nature biotechnology · 2022Article
- Article
- PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains.BMC bioinformatics · 2021Article
- Interpretation of cancer mutations using a multiscale map of protein systems.Science (New York, N.Y.) · 2021Article
- Genetic dissection of complex traits using hierarchical biological knowledge.PLoS computational biology · 2021Article
- Mapping the multiscale structure of biological systems.Cell systems · 2021Review
- HiDeF: identifying persistent structures in multiscale 'omics data.Genome biology · 2021Article
- Identifying persistent structures in multiscale 'omics data.bioRxiv : the preprint server for biology · 2020Article
- Multiscale community detection in Cytoscape.PLoS computational biology · 2020Article
- IdentifyingFrontiers in genetics · 2020Article
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Authors and funding
10 authors.
Funding
Abstract
Systems biology requires not only genome-scale data but also methods to integrate these data into interpretable models. Previously, we developed approaches that organize omics data into a structured hierarchy of cellular components and pathways, called a "data-driven ontology." Such hierarchies recapitulate known cellular subsystems and discover new ones. To broadly facilitate this type of modeling, we report the development of a software library called the Data-Driven Ontology Toolkit (DDOT), consisting of a Python package (https://github.com/idekerlab/ddot) to assemble and analyze ontologies and a web application (http://hiview.ucsd.edu) to visualize them. Using DDOT, we programmatically assemble a compendium of ontologies for 652 diseases by integrating gene-disease mappings with a gene similarity network derived from omics data. For example, the ontology for Fanconi anemia describes known and novel disease mechanisms in its hierarchy of 194 genes and 74 subsystems. DDOT provides an easy interface to share ontologies online at the Network Data Exchange.
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