search

cthoyt / obo-foundry-graph

Demonstrate combining all OBO Foundry ontologies via Bioregistry, Bioontologies, and ROBOT
MIT License
1 stars 0 forks source link

readme

obo-foundry-graph

A demonstration of building a unified knowledge graph of OBO Foundry ontologies building on ROBOT for parsing ontologies, bioontologies for wrapping ROBOT in Python and providing an object model of OBO Graph JSON, and the Bioregistry for standardization.

Warning Despite the commitment of the OBO community to adopting share semantics, it's clear from the high-level summary of relations that many relationships remain unstandardized and from the example triples that many entities remain unstandardized, so this graph should not be used directly without the generation and application of additional rules to fix its content.

Data

graph.tsv.gz

The graph is a gzipped tab-separated values file that contains the following columns:

  1. subject - the subject entity as a CURIE when possible to normalize
  2. prediate - the predicate entity as a CURIE when possible to normalize
  3. object - the object entity as a CURIE when possible to normalize
  4. sources - a pipe-delimited list of ontologies in which the triple was found

Build

The graph can be re-built with the following code:

$ git clone https://github.com/cthoyt/obo-foundry-graph.git
$ cd obo-foundry-graph
$ pip install tox
$ tox