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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
suggest_regex()
Suggest a Regular Expression That Will Match All Input
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