diff --git a/README.md b/README.md index f25b08e..319d850 100644 --- a/README.md +++ b/README.md @@ -33,13 +33,6 @@ og2dot simple-og.json > test.dot dot test.dot -Tpng -Grankdir=BT > test.png ``` -Command line; from [python obographs package](https://github.com/biolink/biolink-api/tree/master/obographs) - -```bash -ogr -p subClassOf BFO:0000050 -r obo:go -t png g nucleus -``` - - ### API ```javascript @@ -268,25 +261,19 @@ As well as configuring via style sheets, an individual node or edge can configur ``` -## Obographs python - -See: - -https://github.com/biolink/biolink-api/tree/master/obographs - -(note: this python API may move to its own repo in future) +## Ontology Access Kit -obographs-python command line: +This library is integrated into [Ontology Access Kit (OAK)](https://github.com/INCATools/ontology-access-kit) to support its [`viz` subcommand](https://incatools.github.io/ontology-access-kit/cli.html#runoak-viz). For example: ```bash -ogr -p subClassOf BFO:0000050 -r go -t png a nucleus +runoak -i ontobee: viz HP:0000787 ``` This proceeds by: - 1. Using the python obographs library to extract a networkx subgraph around the specified node + 1. Using the [python oaklib library](https://incatools.github.io/ontology-access-kit/intro/tutorial02.html) to extract a subgraph around the specified node 2. Write as obographs-json - 3. Calls og2dot.js + 3. Calls og2dot ## Use from biolink-api REST