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    "ontology_index",
    "propagate_relations",
    "prune_descendants"
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      "title": "GO index",
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      ],
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      "table": true,
      "tojson": false
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      "title": "HPO index",
      "object": "hpo",
      "file": "hpo.RData",
      "class": [
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      ],
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      "table": true,
      "tojson": false
    },
    {
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      "title": "MPO index",
      "object": "mpo",
      "file": "mpo.RData",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ontologyIndex-package",
      "title": "Functions for Reading Ontologies into R",
      "topics": [
        "ontologyIndex-package",
        "ontologyIndex"
      ]
    },
    {
      "page": "as.data.frame.ontology_index",
      "title": "Case 'ontology_index' object to 'data.frame'",
      "topics": [
        "as.data.frame.ontology_index"
      ]
    },
    {
      "page": "check",
      "title": "Check an ontology index object",
      "topics": [
        "check"
      ]
    },
    {
      "page": "exclude_descendants",
      "title": "Exclude terms descending from any in a given set of root terms",
      "topics": [
        "exclude_descendants"
      ]
    },
    {
      "page": "get_ancestors",
      "title": "Get set of terms containing all ancestors of terms in a given set",
      "topics": [
        "get_ancestors"
      ]
    },
    {
      "page": "get_descendants",
      "title": "Get set of terms containing all descendants of terms in a given set",
      "topics": [
        "get_descendants"
      ]
    },
    {
      "page": "get_ontology",
      "title": "Read ontology from OBO file into R",
      "topics": [
        "get_OBO",
        "get_ontology"
      ]
    },
    {
      "page": "get_relation_names",
      "title": "Get names of relations used in OBO file",
      "topics": [
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      ]
    },
    {
      "page": "get_term_descendancy_matrix",
      "title": "Get logical descendancy matrix for set of terms",
      "topics": [
        "get_term_descendancy_matrix"
      ]
    },
    {
      "page": "get_term_frequencies",
      "title": "Get frequency of each term in a set of phenotypes",
      "topics": [
        "get_term_frequencies"
      ]
    },
    {
      "page": "get_term_info_content",
      "title": "Get information content of each term in a set of phenotypes",
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    },
    {
      "page": "get_term_property",
      "title": "Get property of individual ontological term",
      "topics": [
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    {
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      "topics": [
        "go"
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    },
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      "title": "HPO index",
      "topics": [
        "hpo"
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    },
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      "topics": [
        "intersection_with_descendants"
      ]
    },
    {
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      "title": "Remove redundant/implied terms from a set of terms",
      "topics": [
        "minimal_set"
      ]
    },
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      "title": "MPO index",
      "topics": [
        "mpo"
      ]
    },
    {
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      "topics": [
        "ontology_index"
      ]
    },
    {
      "page": "print.ontology_index",
      "title": "Print 'ontology_index' object",
      "topics": [
        "print.ontology_index"
      ]
    },
    {
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    },
    {
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      "title": "Exclude terms descending from a given set of roots but include those roots which were originally implicitly present.",
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      ]
    }
  ],
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      "source": "reading-ontologies.Rmd",
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