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The Annotator semantic expansion with is-a hierarchy does not work with SKOS vocabularies. #26
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syphax-bouazzouni
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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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e.g.,
http://services.agroportal.lirmm.fr/annotator/?text=protozoa&ontologies=ANAEETHES&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=false&negation=false&temporality=false&lemmatize=false&expand_class_hierarchy=true&class_hierarchy_max_level=3&display_links=false&display_context=false
We need to be sure this semantic expansion of annotation following the hierarchy is also available for SKOS.
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