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The Annotator semantic expansion with is-a hierarchy does not work with SKOS vocabularies. #26

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jonquet opened this issue Feb 6, 2023 · 0 comments

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syphax-bouazzouni pushed a commit that referenced this issue Feb 28, 2024
syphax-bouazzouni added a commit that referenced this issue Feb 28, 2024
* Gemfile.lock update

* Gemfile.lock update; fixed ncbo/sparql-client#3

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* implemented #40 - Add incremental logging when the dictionary is being created

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Remove ffi gem version pin

* Gemfile.lock

* Gemfile.lock

* Gemfile.lock update

* pinned oj to v2.X for all projects due to an error in latest oj 3.13.1

* Gemfile.lock update

* Restore Gemfile.lock

Appears to have been accidentally deleted in the commit prior

* Pin faraday gem to 1.9

* Fix "same gem twice" parsing error

* Fix bundle install duplicate entry warnings

* Update Gemfile.lock

* Gemfile.lock update

* Update Gemfile.lock

* Update Gemfile.lock

* add docker support for unit testing

* remove wait-for-it

* add config file for testing

* Update branch specifier to develop

* remove deprecated ncbo_resource_index

* update ruby v2.6 -> 2.7

ncbo/bioportal-project#241

* ruby v2.7, bundler optimization - v2.3

* Reset branch specifier to develop

* Update Gemfile.lock

* Update Gemfile.lock

* Add Linux platform

* Update Gemfile.lock

* Fix - deprecation warning for pipelining commands on a Redis instance

Addresses #19
Pipelining commands on a Redis instance is deprecated and will be removed in Redis 5.0.0.

redis.pipelined do
  redis.get("key")
end

should be replaced by

redis.pipelined do |pipeline|
  pipeline.get("key")
end

* Remove duplicated line

* Restore branch specifier to master

* Update Gemfile.lock

* Bump tzinfo from 0.3.60 to 0.3.61

Bumps [tzinfo](https://github.com/tzinfo/tzinfo) from 0.3.60 to 0.3.61.
- [Release notes](https://github.com/tzinfo/tzinfo/releases)
- [Changelog](https://github.com/tzinfo/tzinfo/blob/master/CHANGES.md)
- [Commits](tzinfo/tzinfo@v0.3.60...v0.3.61)

---
updated-dependencies:
- dependency-name: tzinfo
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Reset branch specifier to develop

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile had references to develop branch

* Gemfile.lock update

* Allow setting ruby version in the docker-compose file

* Add codecov reporting

* fixed a failing unit test, test_annotate_minsize_term

* Gemfile.lock update

* Set mgrep default port to 55556

* gem version update

* fixed #26 - annotator cache generation failure - Unsupported command argument type: RDF::URI

* Gemfile.lock update

* bundle update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* resolved an issue with the Recommender query in AllegroGraph

* an improved fix to ncbo/ncbo_ontology_recommender#21

* Add AllegroGraph backend to unit test matrix

* minitest style change for troubleshooting purposes

* Gemfile.lock update

* Gemfile.lock update

* update test CI

* add lemmatizer_jar config default value

* fix annotator after updating RDF version to 3.0

* update agraph version to 8.1.0

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: mdorf <mdorf@stanford.edu>
Co-authored-by: Alex Skrenchuk <alexskr@stanford.edu>
Co-authored-by: Jennifer Vendetti <vendetti@stanford.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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