To cite ontologyIndex in publications use:

Greene D, Richardson S and Turro E (2017). ontologyX: a suite of R packages for working with ontological data. Bioinformatics, pp. btw763.

Corresponding BibTeX entry:

  @Article{,
    title = {{ontologyX}: a suite of R packages for working with
      ontological data},
    author = {Daniel Greene and Sylvia Richardson and Ernest Turro},
    journal = {Bioinformatics},
    year = {2017},
    pages = {btw763},
    publisher = {{Oxford Univ Press}},
  }