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Robot header

7

Resolves #1152 - [x] `docs/` have been added/updated - [x] tests have been added/updated - [x] `mvn verify` says all tests pass - [x] `mvn site` says all JavaDocs correct...

pk-mitre

`remove --axioms external` is removing transitivity axioms from in-base properties

3

When using `robot remove --base-iri --axioms external` to remove axioms relative to “external” entities (entities that are not in the `` namespace), all object properties within the base IRI namespace...

gouttegd

Add option to read in template information from a separate external file

17

Currently ROBOT template files as described [here](http://robot.obolibrary.org/template) have to include the template strings for each column as the second line in the input template file. An option to add the...

pk-mitre

Performing extract using ROBOT excludes GCIs

7

Reference (mostly for me): https://github.com/geneontology/go-ontology/issues/13725 We're stuck using owltools for module extraction in GO for bio-chebi for now. It's weird as both owltools and robot use SLME under the hood...

cmungall

Exclude some synonym types from duplicate_exact_synonym report query

4

Resolves #1175 - [x] `docs/` have been added/updated - [ ] tests have been added/updated - [x] `mvn verify` says all tests pass - [ ] `mvn site` says all...

allenbaron

Should `validate-profile` recognize `owl:onProperties`?

6

I have been doing some testing of general OWL syntax, and came across a curiosity as I was enumerating usages of OWL "Sequences" from the document [OWL 2 Web Ontology...

ajnelson-nist

invalid xref check is too strict

2

The invalid xref [check](http://robot.obolibrary.org/report_queries/invalid_xref) uses this regex: `"^[a-z|A-Z|_|\\-|0-9]*:(?!$)\\S*$"` It should allow `.` in the prefix part: https://www.w3.org/TR/1999/REC-xml-names-19990114/#NT-NCName

balhoff

Ignoring duplicate exact synonyms that are acronyms in robot report

8

Given https://github.com/information-artifact-ontology/ontology-metadata/issues/135, is the plan now for `robot report` to exclude from warnings duplicate exact synonyms that are annotated as acronyms? Overlapping acronyms are fairly common. _This is a follow-up...

allenbaron

ROBOT query --update strips prefixes when output is not .owl (RDF/XML)

3

The robot query command performing an update operation drops prefixes when the output is .ofn or .omn but not .owl (all I tested). This seems to be the same issue...

allenbaron

REMOVE misses annotations to remove

3

I tried to work around #1163 with `robot remove`. In case of the small example in #1163 it worked out with the following command: ```shell robot \ merge \ --input...

jmkeil