Changelog

Source: NEWS.md

KGExplorer 0.99.09

Bug fixes

• test-map_ontology_terms.R: Fixed expected number of NA CL names.

New features

• Remove downloadR dependency as it was causing unnecessary complications.

KGExplorer 0.99.08

Bug fixes

• map_upheno_data:
  • Updated Monarch FTP endpoint subdir="latest/tsv/all_associations/" –> subdir="monarch-kg/latest/tsv/all_associations/"
  • Remove “monarch” option for now (broken due to files being deleted on Monarch FTP server)
• get_monarch: Fix example
• map_upheno: Fix plotting error

KGExplorer 0.99.07

New features

• get_ontology: Saves files with release version control.

KGExplorer 0.99.06

Bug fixes

• get_opentargets: Limit threads and files to import in example.
• Merge fixes by @HDash https://github.com/neurogenomics/KGExplorer/pull/2
• dt_to_kg: fix reference to graph g.
• get_hpo
  • Remove ported function to avoid conflicting namespaces. Instead, simply use get_ontology("hpo")

KGExplorer 0.99.05

New features

• get_hpo
  • Port function from HPOExplorer package to prevent circular dependency.

Bug fixes

• DESCRIPTION
  • Update remote for monarchr.
• Tests
  • Add skip_if_offline to tests that (may) require internet access.
• ontology_to
  • igraph::as_adj (deprecated) -> igraph::as_adjacency_matrix.

KGExplorer 0.99.04

Bug fixes

• test-get_ontology_levels
  • Check for range rather than fixed values.
• filter_ontology
  • Move terms processing block to after check for character, as appropriate.
• get_ontology_dict
  • Add error handling for missing alternative_terms when include_alternative_terms=TRUE.
• plot_ontology_heatmap
  • Fix default value for argument annot– cast one@elementMetadata to data.frame first.
• prune_ancestors
  • Add value for argument id_col in example.
• set_cores
  • Reduce workers during R CMD CHECK if required.

KGExplorer 0.99.03

New features

• map_ontology_terms:
  • Can now recognize alternative_terms slot in simona object (https://github.com/jokergoo/simona/issues/6)
  • Automatically uses “short_id” when “id” is set, as the “id” column can sometimes contain long ID formats (http://purl.obolibrary.org/obo/MONDO_0100229 vs. MONDO:0100229)

KGExplorer 0.99.01

Bug fixes

• Fix get_ontology_dict data.table construction.

KGExplorer 0.99.0

New features

• Added a NEWS.md file to track changes to the package.

Bug fixes

• Removed Dockerfile and switched to using rworkflows.