User-friendly extensions to the Disease Ontology

This repository creates user-friendly extensions to the Disease Ontology (DO) [1]. Simple TSV files are extracted from the OBO-formatted ontology including datasets for term names, cross-references, and subsumption relationships. Additionally, a slim term set is extracted, which we use for our drug repurposing research.

Notebooks

DO-xrefs.ipynb extracts cross-references from download/HumanDO.obo and produces easy-to-read mappings files. data/xref-prop.tsv contains propagated cross-references, so that for example xrefs to relapsing remitting multiple sclerosis would be transmitted to multiple sclerosis.

slim.ipynb reads DO Slim terms and generates slim-specific datasets.

Directories

IGS_scripts contains the scripts from the IGS/disease-ontology repo. These scripts were converted into python 3 and a few conversion errors were manually fixed.

download contains a subversion checkout of the master DO.

data contains created datasets which include:

• term-names.tsv — names including synonyms for DO terms
• xrefs.tsv — cross-references to external disease vocabularies
• xrefs-prop.tsv — cross-references where diseases inherit all cross-references of the diseases they subsume
• slim-terms.tsv — a (semi-manually created) slim term set referred to as DO Slim
• slim-terms-prop.tsv — all subsume relationships for DO Slim
• xrefs-slim.tsv — cross-references to external disease vocabularies for slim terms
• xrefs-prop-slim.tsv — cross-references for slim terms where diseases inherit all cross-references of the diseases they subsume.

License

Disease Ontology content and derivatives are licensed under CC-BY 3.0. All original content is licensed under CC0 1.0.