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Attempting to read a JSON ontology with Jackson like so:
```java
ObjectMapper objectMapper = new ObjectMapper();
GraphDocument graphDocument = objectMapper.readValue(Files.newInputStream(Paths.ge…
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[obographs](https://github.com/geneontology/obographs) is a handy new JSON format for OBO-ish OWL ontologies such as FBbt. It would be if we could get FBbt (and other FB ontologies) released in this …
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Phenol is going to be difficult to use in Java 11 applications since OWLAPI seems to have what is known as split packages that do not play nicely with the Java 11 module system. This in turn makes it …
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getting this error when running `multi_owl_to_json_kg.py` on kg2dev:
```
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.base/java.lang.AbstractStringBuilder.(Abst…
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Hi there, pronto looks great!
Looking for feedback on a json format for bio-ontologies; it's intended to make it such that you don't have to write Yet Another obo parser, or complex OWL transform
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@pnrobinson I think it might be a good idea to pull out `org.monarchinitiative.phenol.annotations.hpo` and `org.monarchinitiative.phenol.io.annotations.hpo` into an HPO-specific module which imports t…
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The JSON files are not in order so creating large diffs after every re-release. Distracting :P
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I'd like to generate a JSON version of http://purl.obolibrary.org/obo/geno.owl (there doesn't appear to be a release with this conversion). JSON conversion works fine for the various OBO ontologies I…
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So that GitHub diff is not confused every time we make a new release involving json serialisation of our ontologies. Low priority, but would be greatly appreciated!
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Fastrun on [obographs_DO.py](https://github.com/SuLab/scheduled-bots/blob/master/scheduled_bots/ontology/obographs_DO.py) is not very fast anymore. I ran it through Pycharm's profiler, and I think it …