Function reference • DO.utils

All functions

DO_colors: Human Disease Ontology Official Colors

DOrepo(): Instantiate a DO Repository

all_duplicated(): Identify all duplicates

append_empty_col(): Append Empty Columns

append_to_url(): Append to URL

as_tibble(<esummary_list>) as_tibble(<esummary_list_nested>): Convert esummary Object into Tibble

as_tibble(<scopus_search>) as_tibble(<scopus_search_list>): Convert scopus_search Object into Tibble

batch_id_converter(): Convert IDs in Batches

build_hyperlink(): Build Hyperlinks

is_blank() is_missing(): Character value predicates

partition(): Partition vectors

citedby_pmid(): Get Cited By PMIDs from PubMed

citedby_pubmed(): Get Cited By List from PubMed

citedby_scopus(): Get Cited By List from Scopus

collapse_col(): Collapse Column(s)

collapse_col_flex(): Collapse Column(s) Flexibly

collapse_to_string(): Create a String from Inputs

confine_list() release_list(): Convert (Nested) List to/from Character Vector

count_alliance_records(): Count Alliance Records

count_delim(): Count Delimited Columns

cur_yr(): Get Current Year

download_alliance_tsv(): Download Alliance .tsv.gz File

download_file(): Download File(s) from the Internet

download_obo_ontology(): Download OBO Foundry Ontology File

download_omim(): Download OMIM Files

drop_blank(): Drop Blanks

elucidate(): Elucidate the Data in an Object

extract_as_tidygraph(): Extract OWL/RDF as a tidygraph

extract_class_axiom(): Extract Class Axioms

extract_eq_axiom(): Extract Equivalent Class Axioms

extract_ordo_mappings(): Extract mappings from ORDO

extract_pm_date(): Extract Publication Date from PubMed Citations

extract_pmid(): Extract PubMed ID

extract_pmid(<elink>): Extract PubMed ID from elink object

extract_pmid(<elink_list>): Extract PubMed ID from elink_list object

extract_subclass_axiom(): Extract 'Subclass Of' Axioms

extract_subtree(): Extract Subtree

format_axiom(): Format Logical Axioms

format_doid(): Format DOIDs

format_hyperlink(): Format URLs as Hyperlinks

format_obo(): Format OBO Foundry IDs

format_subtree(): Format a Subtree

get_bioc_pkg_stats(): Get Bioconductor Package Statistics

iff_all_vals(): Test for All Values

install_robot(): Install OBO Foundry ROBOT Tool (Mac/Linux ONLY)

inventory_omim(): Assess whether OMIM Data is in DO

invert_sublists(): Invert Sublists

is_curie(): CURIE (RDF ID) Predicate

is_invariant(): Test if an Object is Invariant

length_sort() length_order(): Sort by Character Length

lengthen_col(): Lengthen Column(s)

lexiclean(): Prepare Text for Matching

is_boolean(): Logical predicate

make_contributor_html(): Make "Contributors" HTML

make_use_case_html(): Make HTML for DO Use Case Tables

make_user_list_html(): Make HTML for DO User List (DEPRECATED)

match_carefully(): Matches Carefully

match_citations(): Citation Matching

match_fz(): Fuzzy (Approximate) String Matching

ns_prefix obo_prefix obo_prop_prefix not_obo_prefix: Namespace Prefixes

is_positive() is_negative() is_whole_number() is_scalar_whole_number(): Number value predicates

is_valid_obo() is_valid_doid(): OBO ID predicates

obofoundry_metadata: OBO Foundry Metadata

onto_missing(): Identify Data Missing from an Ontology (DEPRECATED)

owl_xml(): Instantiate an owl_xml object

parse_mapping(): Parse Mapping

plot_branch_counts(): Plot Branch Counts

plot_citedby(): Plot Publications Citing DO by Year

plot_def_src(): Plot Definition Sources

plot_term_def_counts(): Plot DO Term & Definition Counts

plot_xref_counts(): Plot Xref Counts

pmc_summary(): Get PubMed Central Summary

print(<oieb>): Print OMIM inventory report statistics

priority_sort(): Sort Vectors by Priority

progress_bar-class progress_bar: Progress Bar (RefClass)

pub_id_match: Prioritized List of Publication IDs & Regex's for Matching

pubmed_summary(): Get PubMed Summary

DO_pubs ST_pubs: Publication Info

pyDOID: pyDOID

pyobo_map(): Map Terms to Terms of Specified Namespace

queue_xref_split(): Curation Queue: DOIDs to split?

read_alliance(): Read Alliance .tsv.gz File

read_ga(): Read Google Analytics Exports

read_omim(): Read OMIM Data

read_pubmed_txt(): Read in PubMed Citations (from txt file)

replace_blank(): Replace Blanks with Specified Value

replace_na(<list>): [DEPRECATED] Replace NAs with specified value

replace_null(): Replace NULLs with specified value

restore_names(): Restore Element Names

robot(): Execute Robot Commands

robot_query(): Execute a SPARQL Query with ROBOT

round_down(): Round Number Down

round_up(): Round Number Up

round_zero(): Round Number to Zero

sandwich_text(): Sandwich Text Between Placeholders

save_alliance_counts(): Writes Alliance Counts to File

search_pmc(): Search PubMed Central

search_pubmed(): Search PubMed

set_scopus_keys(): Set Keys for Scopus API Access

theme_DO(): DO Theme for Stats Plots

tidy_pub_records(): Tidy Publication Records

tidy_pubmed_summary(): Convert PubMed summary to tibble (DEPRECATED)

tidy_sparql(): Tidy SPARQL Query

to_curie(): Convert URI to CURIE

to_range(): Convert Vectors to Range String

to_uri(): Convert CURIE to URI

today_datestamp(): Today's Date Stamp

unique_if_invariant(): Return Unique Value for Invariant Vectors

unnest_cross(): Unnest data frame list columns

unnest_mapping(): Unnest Mapping

update_website_count_tables(): Update Counts in DO Website HTML

vctr_to_string() unique_to_string(): Convert Vectors to Strings

wrap_onscreen(): Wrap an On-screen Message

write_graphml(): Write a Graph to .graphml File

write_gs(): Write Data to a Google Sheet