Describe datasets

README.md

@@ -1,17 +1,28 @@
 # User-friendly extensions to the Disease Ontology
 
-Code and data for the [Disease Ontology](http://disease-ontology.org/) (DO) [[1](https://doi.org/10.1093/nar/gkr972)].
+This repository creates user-friendly extensions to the [Disease Ontology](http://disease-ontology.org "Disease Ontology Homepage") (DO) [[1](https://doi.org/10.1093/nar/gkr972 "Disease Ontology: a backbone for disease semantic integration")]. 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](https://doi.org/10.15363/thinklab.4, "Thinklab · Repurposing drugs on a hetnet").
+
+## Notebooks
 
 [`DO-xrefs.ipynb`](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`](slim.ipynb) reads [DO Slim](https://doi.org/10.15363/thinklab.d44#144 "Creating a slim DO") terms and generates slim-specific datasets.
+
+## Directories
+
 `IGS_scripts` contains the [scripts](https://github.com/IGS/disease-ontology/tree/master/scripts) from the `IGS/disease-ontology` [repo](https://github.com/IGS/disease-ontology). These scripts were converted into python 3 and a few conversion errors were manually fixed.
 
 [`download`](download) contains a subversion checkout of the master DO.
 
-[`data`](data) contains files created by us.
+[`data`](data) contains created datasets which include:
 
-See our project on ThinkLab for more information:
-http://thinklab.com/p/rephetio
++ [`term-names.tsv`](data/term-names.tsv) — names including synonyms for DO terms
++ [`xrefs.tsv`](data/xrefs.tsv) — cross-references to external disease vocabularies
++ [`xrefs-prop.tsv`](data/xrefs-prop.tsv) — cross-references where diseases inherit all cross-references of the diseases they subsume
++ [`slim-terms.tsv`](data/slim-terms.tsv) — a ([semi-manually created](http://doi.org/10.15363/thinklab.d44#144 "Creating a slim DO")) slim term set referred to as DO Slim
++ [`slim-terms-prop.tsv`](data/slim-terms-prop.tsv) — all subsume relationships for DO Slim
++ [`xrefs-slim.tsv`](data/xrefs-slim.tsv) — cross-references to external disease vocabularies for slim terms
++ [`xrefs-prop-slim.tsv`](data/xrefs-prop-slim.tsv) — cross-references for slim terms where diseases inherit all cross-references of the diseases they subsume.
 
 ## License