obographs

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Dependent on agreement on #7 These have yet to be implemented: ``` Class: C SubClassOf: P value J ==> edges: - subj: C pred: P obj: J ``` ``` Individual:...

cmungall

Add a guide for command line tool hackers

2

One feature of obo is the ease of doing quick command line hacks, e.g. - http://read.biostarhandbook.com/ontology/02-sequence-ontology.html - https://github.com/cmungall/obo-scripts While not to be encouraged in production pipelines, these are certainly useful...

cmungall

Consider adding labels for properties directly in edges

1

see for example OLS JSON http://www.ebi.ac.uk/ols/api/ontologies/go/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0098743/graph cc @simonjupp @kltm

cmungall

Compare meta tag with what is used in other parts of bbop stack

1

@kltm - does documentation for this exist? Current UML for OG meta objects (geared towards OWL completeness with simply entry points for OBO-esque consumers)  cc @nathandunn

cmungall

The current examples have IDs (e.g. GO:nnnn) in them. These all correspond to PURLs. The expansion is controlled by a jsonld context. This should be documented with examples

cmungall

There is existing python code as described in #85 But we also want the reverse translation in java as part of this library, so it's usable by robot, phenol, etc....

cmungall

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.12.1 to 2.13.4.1. Commits See full diff in compare view [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter...

dependabot[bot]

Missing rdf:type owl:Ontology causes non-intelligible fail

2

ROBOT convert and generally the OWL API is robust to the absence of an ontology declaration like ` rdf:type owl:Ontology .` Can we make this statement optional for obographs parser...

matentzn

Coordinate with: - https://github.com/owlcollab/oboformat/issues/146

cmungall

Make "mappings" as a first class property to obographs?

16

Like this? ```json { "id": "http://purl.obolibrary.org/obo/MONDO_0014957", "meta": { "mappings": [ { "pred": "exact", "val": "UMLS:C4310678", "xrefs": [ "Orphanet:123" ], "meta": { "basicPropertyValues": [ { "pred": "sssom:mapping_justification", "val": "semapv:ManualMappingCuration" }, {...

matentzn