Jim Balhoff
Jim Balhoff
If the OWLAPI dependency is updated, a test related to oboformat saving fails.
TableRenderer seems to output only classes and instances. Is there a reason to exclude properties? https://github.com/owlcollab/owltools/blob/178e1f994aa4a5e9e4d43c7a5243145436c553a8/OWLTools-Core/src/main/java/owltools/io/TableRenderer.java#L44-L45
Building obographs requires Java 8 at the moment. Running on Java 11 gives this error: ``` [ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs) on project obographs: MavenReportException: Error while creating...
 - [biolink:negatively_regulates](https://w3id.org/biolink/vocab/negatively_regulates) EquivalentTo [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) (most probable) 0.8 - [biolink:negatively_regulates](https://w3id.org/biolink/vocab/negatively_regulates) ProperSuperClassOf [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630) (most probable) 0.8 - [biolink:process_negatively_regulates_process](https://w3id.org/biolink/vocab/process_negatively_regulates_process) ProperSubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) 0.06 - [biolink:acts_upstream_of_negative_effect](https://w3id.org/biolink/vocab/acts_upstream_of_negative_effect) EquivalentTo [acts upstream of,...
Hi, I opened issues related to this before (e.g. #301 more than a year ago) but I think I made a mistake in closing that when opening #397. The simplified...
 - [biolink:acts_upstream_of_positive_effect](https://w3id.org/biolink/vocab/acts_upstream_of_positive_effect) EquivalentTo [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) (most probable) 0.8 - [biolink:entity_positively_regulates_entity](https://w3id.org/biolink/vocab/entity_positively_regulates_entity) EquivalentTo [directly positively regulates activity of](http://purl.obolibrary.org/obo/RO_0002450) (most probable) 0.8 - [biolink:acts_upstream_of_or_within](https://w3id.org/biolink/vocab/acts_upstream_of_or_within) EquivalentTo [acts upstream of or...
Are there any mappings to CHEBI that could be added for small molecule? If there is no single parent term, are there a few more specific terms that could be...
We are using the [RDF rendering of biolink-model](https://github.com/biolink/biolink-model/blob/master/biolink-model.ttl) to enable bridging from Biolink into our RDF database for the Translator CAM KP. In previous builds of our database, we used...
Typically the IRI identifying an OWL ontology should be resolvable and return the latest version of the ontology. The Biolink model OWL file uses the IRI `https://w3id.org/biolink/biolink-model`: ```turtle a owl:Ontology...
Fixes #530. I deleted 'synapse part' and its subclasses 'presynaptic membrane' and 'postsynaptic membrane'. None of them had any usages in axioms. I didn't see any automated way to regenerate...