Processing Uberon data

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.

Execution

To reconstruct the analysis, run the notebooks in the following order:

1. human-constraint.ipynb: Compares two methods for filtering the ontology for anatomies that exist in humans.
2. 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.

Datasets

The following datasets are created:

• terms.tsv: the identifiers and names of Uberon terms
• subset.tsv: the ontology subsets for terms
• xref.tsv: cross-references to external vocabularies
• human-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.

License

Uberon content and its derivatives are licensed under CC-BY. All original content in this repository is released as CC0.