Read OMIM Data

Reads and formats OMIM data copied or manually downloaded from https://omim.org/, or downloaded with download_omim() (permission required), and appends columns to speed up subsequent curation activities. read_omim() will attempt to process and correct headers including fixing multi-line or misarranged column headers, and will trim whitespace.

Usage

read_omim(file, keep_mim = c("#", "%"), ...)

Arguments

file

The path to a file (possibly compressed) with copy/pasted or manually downloaded data from https://omim.org/ (see "Manual Input Requirements" for details), or downloaded with download_omim().

keep_mim

[OMIM search data only] The MIM symbols representing the data types to keep, as a character vector, or NULL to retain all (default: "#" and "%").

The OMIM defined MIM symbols are:

MIM symbol	MIM type
*	gene
+	gene, includes phenotype
#	phenotype
%	phenotype, unknown molecular basis
^	deprecated
none	phenotype, suspected/overlap

...

Arguments passed on to read_delim_auto

Value

An omim_tbl (tibble) with an omim column containing OMIM CURIEs as formatted in DO xrefs, followed by complete OMIM data arranged as seen on omim.org for OMIM entries (where possible). If the omim.org "Download as" button was used to download the data, the omim_tbl will be additionally modified based on the download type:

• Search list download: Additional omim_search class and search column containing the search used.

• OMIM phenotypic series titles download: Additional omim_PS_titles class.

• OMIM phenotypic series download: Additional omim_PS class and a row representing the OMIM phenotypic series itself.

Output with columns typical OMIM phenotype entries, including omim_PS, will have an additional geno_inheritance column containing a best guess at inheritance from the GENO ontology. This simplifies adding inheritance as logical subClassOf axioms supporting curation.

NOTE: OMIM phenotypic series on https://omim.org/ include the same data as entries but column are ordered differently.

Manual Input Requirements

The file with OMIM data copied or manually downloaded must include column headers at the top and should be tab- or comma-separated. If the data is copied & pasted from omim.org either to a spreadsheet program or to a text file, the data will likely be tab-separated. To improve parsing success, it is recommended that the copy-pasted data include both the copmlete table and the table type (e.g. "Phenotype-Gene Relationships"), which is usually directly above the table on a given omim.org entry. In most casees, there should not be a need to fix data copy/pasted from OMIM manually prior to reading with read_omim().

Available downloads

Some data are available for download without an API key. This includes:

1. The full list of phenotypic series titles (https://www.omim.org/phenotypicSeriesTitles/)

2. Any complete phenotypic series, from its PS page (https://www.omim.org/phenotypicSeries/{PS number})

   • Example: Achondrogenesis, MIM:PS200600 (https://www.omim.org/phenotypicSeries/PS200600)

3. OMIM gene entry ID relationships to external gene IDs, mim2gene.txt.

   • From downloads page: https://www.omim.org/downloads/

   • Direct: https://www.omim.org/static/omim/data/mim2gene.txt

Additional data is available with an approved API key.