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Migrate to Java 11

5

Given that Java 8 support is running it in a few months (https://endoflife.date/java), we should migrate to Java 11. Also blocking some issues such as #934

matentzn

ROBOT reduce does not reduce subclasses between names by default

3

Currently: ``` robot reduce -i o.ofn -o reduced.ofn ``` Does not reduce A = B, A Sub B , B Sub A to A = B (where A and B...

matentzn

Include git commit hash in --version output

1

I think this would be good for any version, but especially useful for SNAPSHOT versions. I'm not sure how to make it happen. I don't want to increase churn by...

jamesaoverton

Is there any reason why `relax` does not work with arbitrary definitions?

2

I am wondering on the exact scope of relax. Is there a _formal_ definition of relax? The documentation is pretty hazy: https://robot.obolibrary.org/relax In particular, what should relax do in the...

matentzn

Bump OWLAPI version to match Protege

9

I like to stay in sync the the version of OWLAPI used by the latest release of Protege. It looks like we're behind: - Protege 5.5.0 uses OWLAPI 4.5.9 -...

jamesaoverton

Error in Robot command running (windows)

11

Well, I try to run this command line (and others similar): robot template --template robot_pesticide.tsv --input "peston-merged.owl" --prefix "PESTON:http://purl.obolibrary.org/obo/PESTON_" --ontology-iri "http://purl.obolibrary.org/obo/peston/imports/pesticide_import.owl" --output pesticide_import.owl and I get 'object cannot be null'...

marco-medici

SPARQL query CSV/TSV output - make literals simple and implement CURIEs

2

Currently the Jena CSV/TSV writer is used. We may have to implement our own writer here (should be sraightforward iteration over ResultSet) to implement the two requirements here for TSVs:...

cmungall

Should unparsed triples be a WARN instead of ERROR?

12

Every time we load OBI now, we get the following error message: ``` 2021-02-22 18:43:34,590 ERROR org.obolibrary.robot.IOHelper - Input ontology contains 42 triple(s) that could not be parsed: - _:genid2147494670....

beckyjackson

Enabling OBO IRIs as inputs

7

Right now, we cannot use OBO purls as `--input` to ROBOT commands. For example: ``` robot convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.obo -o ncbitaxon.owl ``` Will lead to ``` Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@4602c2a9 Stack trace:...

matentzn

Question about use of robot extract

12

The docs state: > The reuse of ontology terms creates links between data, making the ontology and the data more valuable. But often you want to reuse just a subset...

rpgoldman