obographs

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obographs should distinguish between annotationProperty, objectProperty & dataProperty

1

[Current specification for node types](https://github.com/geneontology/obographs/blob/master/schema/obographs-schema.json#L147) has only: ```js "type" : { "type" : "string", "enum" : [ "CLASS", "INDIVIDUAL", "PROPERTY" ] }, ``` I guess that changing this enum now...

dosumis

This test is failing using Java "1.8.0_241". See inline comments below. $ mvn package ``` Failed tests: PrefixHelperTest.testPrefixHandling:78 Check JSON-LD expected:

blueharmony

EquivalentNodesSet.representativeNodeId() is not used in production code

1

EquivalentNodesSet.representativeNodeId() is used in the unit test, but never set in the production code. The EquivalentNodesSet is only used in FromOwl: https://github.com/geneontology/obographs/blob/f56ec1458f11e5af5b3b59581f3f4f0d24d9853a/src/main/java/org/geneontology/obographs/owlapi/FromOwl.java#L236-L239 Is this method really required as a setter?...

julesjacobsen

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...

balhoff

Help needed: oboInOwl spec vs obographs

2

I need a recommendation of what to do when people [physically include](https://github.com/monarch-initiative/GENO-ontology/blob/develop/src/ontology/geno.owl) the oboinowl ontology in their ontology; can I safely recommend to remove it in all cases? The reason...

matentzn

See for example: https://github.com/DiseaseOntology/HumanDiseaseOntology/pull/748

cmungall

Casting error needs to be more informative

3

This is unfortunately impossible to debug other than with binary search (deleting portions of the ontology until it works..) ``` uk.ac.manchester.cs.owl.owlapi.OWLAnonymousIndividualImpl cannot be cast to org.semanticweb.owlapi.model.OWLLiteral java.lang.ClassCastException: uk.ac.manchester.cs.owl.owlapi.OWLAnonymousIndividualImpl cannot be...

matentzn

There appear to be some `pred` definitions in go basic that don't have corresponding property nodes. I believe there were also some `val` values that were missing property nodes as...

MrCreosote

Gather feedback from developers of bioinformatics tools that consume ontology files

2

Many developers have written redundant obo parsers in various languages. Due to the details of the spec it is difficult to write a robust parser. OWL is very difficult to...

cmungall

Improve semantics of synonym types and subset defs

1

Hi! This is related to my current work on [`fastobo-graphs`](https://github.com/althonos/fastobo-graphs) to provide OBO JSON support in native Rust and Python. Currently, the synonym type case is handled the following way...

althonos