{
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  "Package": "simona",
  "Type": "Package",
  "Title": "Semantic Similarity on Bio-Ontologies",
  "Version": "1.10.0",
  "Date": "2026-01-30",
  "Authors@R": "person(\"Zuguang\", \"Gu\", email = \"guzuguang@suat-sz.edu.cn\", role = c(\"aut\", \"cre\"),\ncomment = c('ORCID'=\"0000-0002-7395-8709\"))",
  "VignetteBuilder": "knitr",
  "Description": "This package implements infrastructures for ontology\nanalysis by offering efficient data structures, fast ontology\ntraversal methods, and elegant visualizations. It provides a\nrobust toolbox supporting over 70 methods for semantic\nsimilarity analysis.",
  "biocViews": "Software, Annotation, GO, BiomedicalInformatics",
  "URL": "https://github.com/jokergoo/simona",
  "BugReports": "https://github.com/jokergoo/simona/issues",
  "SystemRequirements": "Perl, Java",
  "License": "MIT + file LICENSE",
  "RoxygenNote": "7.3.2",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:36 UTC",
  "RemoteUrl": "https://github.com/bioc/simona",
  "RemoteRef": "RELEASE_3_23",
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  "NeedsCompilation": "yes",
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  "Author": "Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>)",
  "Maintainer": "Zuguang Gu <guzuguang@suat-sz.edu.cn>",
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  "_assets": [
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    "manual.pdf"
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  "_homeurl": "https://github.com/jokergoo/simona",
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  "_exports": [
    "add_annotation",
    "all_group_sim_methods",
    "all_term_IC_methods",
    "all_term_sim_methods",
    "alternative_GO_terms",
    "annotated_terms",
    "avg_children",
    "avg_parents",
    "CA_terms",
    "create_ontology_DAG",
    "create_ontology_DAG_from_GO_db",
    "create_ontology_DAG_from_igraph",
    "dag_add_random_children",
    "dag_all_terms",
    "dag_ancestors",
    "dag_as_dendrogram",
    "dag_as_DOT",
    "dag_as_igraph",
    "dag_children",
    "dag_circular_viz",
    "dag_depth",
    "dag_distinct_ancestors",
    "dag_enrich_on_genes",
    "dag_enrich_on_items",
    "dag_enrich_on_offsprings",
    "dag_filter",
    "dag_graphviz",
    "dag_has_terms",
    "dag_height",
    "dag_is_leaf",
    "dag_leaves",
    "dag_longest_dist_from_ancestors",
    "dag_longest_dist_to_offspring",
    "dag_n_leaves",
    "dag_n_relations",
    "dag_n_terms",
    "dag_offspring",
    "dag_parents",
    "dag_permutate_children",
    "dag_random",
    "dag_random_tree",
    "dag_reorder",
    "dag_root",
    "dag_shiny",
    "dag_shortest_dist_from_ancestors",
    "dag_shortest_dist_from_root",
    "dag_shortest_dist_to_leaves",
    "dag_shortest_dist_to_offspring",
    "dag_siblings",
    "dag_treelize",
    "group_sim",
    "import_obo",
    "import_ontology",
    "import_owl",
    "import_ttl",
    "LCA_depth",
    "LCA_term",
    "longest_distances_directed",
    "longest_distances_via_LCA",
    "max_ancestor_id",
    "max_ancestor_path_sum",
    "max_ancestor_v",
    "mcols",
    "mcols<-",
    "method_param",
    "MICA_IC",
    "MICA_term",
    "n_ancestors",
    "n_annotations",
    "n_children",
    "n_connected_leaves",
    "n_offspring",
    "n_parents",
    "NCA_term",
    "ontology_chebi",
    "ontology_DAG",
    "ontology_go",
    "ontology_hp",
    "ontology_kw",
    "ontology_pw",
    "ontology_rdo",
    "ontology_reactome",
    "ontology_vt",
    "partition_by_level",
    "partition_by_size",
    "random_items",
    "random_terms",
    "shortest_distances_directed",
    "shortest_distances_via_NCA",
    "show",
    "simona_opt",
    "term_annotations",
    "term_IC",
    "term_sim"
  ],
  "_help": [
    {
      "page": "subset",
      "title": "Create sub-DAGs",
      "topics": [
        "[,ontology_DAG,ANY,ANY,ANY-method",
        "[,ontology_DAG,ANY,ANY,missing-method",
        "[,ontology_DAG,ANY,missing,ANY-method",
        "[,ontology_DAG,ANY,missing,missing-method",
        "[,ontology_DAG,missing,ANY,ANY-method",
        "[,ontology_DAG,missing,ANY,missing-method",
        "[,ontology_DAG,missing,missing,ANY-method",
        "[,ontology_DAG,missing,missing,missing-method",
        "[[,ontology_DAG,character,missing-method"
      ]
    },
    {
      "page": "add_annotation",
      "title": "Add annotations to the DAG object",
      "topics": [
        "add_annotation"
      ]
    },
    {
      "page": "all_methods",
      "title": "Supported methods",
      "topics": [
        "all_group_sim_methods",
        "all_term_IC_methods",
        "all_term_sim_methods"
      ]
    },
    {
      "page": "create_ontology_DAG",
      "title": "Create the ontology_DAG object",
      "topics": [
        "create_ontology_DAG"
      ]
    },
    {
      "page": "create_ontology_DAG_from_GO_db",
      "title": "Create the ontology_DAG object from the GO.db package",
      "topics": [
        "alternative_GO_terms",
        "create_ontology_DAG_from_GO_db"
      ]
    },
    {
      "page": "create_ontology_DAG_from_igraph",
      "title": "Create the ontology_DAG object from the igraph object",
      "topics": [
        "create_ontology_DAG_from_igraph"
      ]
    },
    {
      "page": "dag_all_terms",
      "title": "Names of all terms",
      "topics": [
        "dag_all_terms",
        "dag_n_leaves",
        "dag_n_relations",
        "dag_n_terms"
      ]
    },
    {
      "page": "dag_as_igraph",
      "title": "Convert to an igraph object",
      "topics": [
        "dag_as_igraph"
      ]
    },
    {
      "page": "dag_viz",
      "title": "Visualize the DAG",
      "topics": [
        "dag_as_DOT",
        "dag_circular_viz",
        "dag_graphviz"
      ]
    },
    {
      "page": "dag_depth",
      "title": "Depth and height in the DAG",
      "topics": [
        "dag_depth",
        "dag_height",
        "dag_shortest_dist_from_root",
        "dag_shortest_dist_to_leaves"
      ]
    },
    {
      "page": "dag_distinct_ancestors",
      "title": "Distinct ancestors of a list of terms",
      "topics": [
        "dag_distinct_ancestors"
      ]
    },
    {
      "page": "dag_enrich_on_items",
      "title": "Enrichment analysis on the number of annotated items",
      "topics": [
        "dag_enrich_on_genes",
        "dag_enrich_on_items"
      ]
    },
    {
      "page": "dag_enrich_on_offsprings",
      "title": "Enrichment analysis on offspring terms",
      "topics": [
        "dag_enrich_on_offsprings"
      ]
    },
    {
      "page": "dag_enrich_on_offsprings_by_permutation",
      "title": "Enrichment analysis on offspring terms by permutation test",
      "topics": [
        "dag_enrich_on_offsprings_by_permutation"
      ]
    },
    {
      "page": "dag_filter",
      "title": "Filter the DAG",
      "topics": [
        "dag_filter"
      ]
    },
    {
      "page": "dag_has_terms",
      "title": "Whether the terms exist in the DAG",
      "topics": [
        "dag_has_terms"
      ]
    },
    {
      "page": "dag_longest_dist_to_offspring",
      "title": "Distance from all ancestors/to all offspring in the DAG",
      "topics": [
        "dag_longest_dist_from_ancestors",
        "dag_longest_dist_to_offspring",
        "dag_shortest_dist_from_ancestors",
        "dag_shortest_dist_to_offspring"
      ]
    },
    {
      "page": "dag_terms",
      "title": "Parent/child/ancestor/offspring terms",
      "topics": [
        "dag_ancestors",
        "dag_children",
        "dag_offspring",
        "dag_parents",
        "dag_siblings"
      ]
    },
    {
      "page": "dag_random",
      "title": "Generate a random DAG",
      "topics": [
        "dag_add_random_children",
        "dag_random",
        "dag_random_tree"
      ]
    },
    {
      "page": "dag_reorder",
      "title": "Reorder the DAG",
      "topics": [
        "dag_permutate_children",
        "dag_reorder"
      ]
    },
    {
      "page": "dag_root",
      "title": "Root or leaves of the DAG",
      "topics": [
        "dag_is_leaf",
        "dag_leaves",
        "dag_root"
      ]
    },
    {
      "page": "dag_shiny",
      "title": "A shiny app for the DAG",
      "topics": [
        "dag_shiny"
      ]
    },
    {
      "page": "dag_treelize",
      "title": "Reduce the DAG to a tree",
      "topics": [
        "dag_as_dendrogram",
        "dag_treelize",
        "print.ontology_tree"
      ]
    },
    {
      "page": "group_sim",
      "title": "Semantic similarity between two groups of terms",
      "topics": [
        "group_sim"
      ]
    },
    {
      "page": "import_obo",
      "title": "Import ontology file to an ontology_DAG object",
      "topics": [
        "import_obo",
        "import_ontology",
        "import_owl",
        "import_ttl"
      ]
    },
    {
      "page": "mcols_ontology_DAG",
      "title": "Get or set meta columns on DAG",
      "topics": [
        "mcols,ontology_DAG-method",
        "mcols<-,ontology_DAG-method"
      ]
    },
    {
      "page": "method_param",
      "title": "All Papameters of a given method",
      "topics": [
        "method_param"
      ]
    },
    {
      "page": "common_ancestor",
      "title": "Various types of common ancestors",
      "topics": [
        "CA_terms",
        "LCA_depth",
        "LCA_term",
        "max_ancestor_id",
        "max_ancestor_path_sum",
        "max_ancestor_v",
        "MICA_IC",
        "MICA_term",
        "NCA_term"
      ]
    },
    {
      "page": "n_annotations",
      "title": "Number of annotated items",
      "topics": [
        "has_annotation",
        "n_annotations"
      ]
    },
    {
      "page": "n_terms",
      "title": "Number of parent/child/ancestor/offspring/leaf terms",
      "topics": [
        "avg_children",
        "avg_parents",
        "n_ancestors",
        "n_children",
        "n_connected_leaves",
        "n_offspring",
        "n_parents"
      ]
    },
    {
      "page": "ontology_DAG-class",
      "title": "The ontology_DAG class",
      "topics": [
        "ontology_DAG",
        "ontology_DAG-class"
      ]
    },
    {
      "page": "ontology",
      "title": "Import ontologies already having gene annotations",
      "topics": [
        "ontology_chebi",
        "ontology_go",
        "ontology_hp",
        "ontology_kw",
        "ontology_pw",
        "ontology_rdo",
        "ontology_reactome",
        "ontology_vt"
      ]
    },
    {
      "page": "partition_by_level",
      "title": "Partition the DAG",
      "topics": [
        "partition_by_level",
        "partition_by_size"
      ]
    },
    {
      "page": "print.print_source",
      "title": "Print the source",
      "topics": [
        "print.print_source"
      ]
    },
    {
      "page": "random_terms",
      "title": "Randomly sample terms/items",
      "topics": [
        "random_items",
        "random_terms"
      ]
    },
    {
      "page": "distance",
      "title": "Distance on the DAG",
      "topics": [
        "longest_distances_directed",
        "longest_distances_via_LCA",
        "shortest_distances_directed",
        "shortest_distances_via_NCA"
      ]
    },
    {
      "page": "show-ontology_DAG-method",
      "title": "Print the ontology_DAG object",
      "topics": [
        "show,ontology_DAG-method"
      ]
    },
    {
      "page": "simona_opt",
      "title": "Global options",
      "topics": [
        "simona_opt"
      ]
    },
    {
      "page": "annotation",
      "title": "Term-item associations",
      "topics": [
        "annotated_terms",
        "term_annotations"
      ]
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