Uberon is "an integrated cross-species ontology … representing a variety of anatomical entities. [source]" We use Uberon as the vocabulary to represent anatomical structures for our drug repurposing research.
To reconstruct the analysis, run the notebooks in the following order:
human-constraint.ipynb
: Compares two methods for filtering the ontology for anatomies that exist in humans.process.ipynb
: Downloads and processes the Uberon ontology in OBO format. Creates TSVs of terms, xrefs, and subsets. Additionally, creates Uberon hetio-slim
, a subset of Uberon terms for inclusion in our hetnet.The following datasets are created:
terms.tsv
: the identifiers and names of Uberon termssubset.tsv
: the ontology subsets for termsxref.tsv
: cross-references to external vocabularieshuman-constraint.tsv
: assessments of whether a term exists or not in humans based on two methods.hetio-slim.tsv
: the slim term set used for our drug repurposing project.Uberon content and its derivatives are licensed under CC-BY. All original content in this repository is released as CC0.