Bulk Editing Using Regular Expressions

Bulk Editing Using Regular Expressions¶

by Nicole Vasilevsky and Nico Matentzoglu
updated 2021-05-12

Objective:

Regular expressions can be used for mass editing in the mondo-edit.obo text file. A very helpful reference for writing regex patterns is available here: regex101.

Workflow¶

Create a new branch.
Make the changes in the mondo-edit.obo text file (src/ontology/mondo-edit.obo). Sublime (for Mac) or Atom (for Mac) are recommended text editors.
Note: The 'Regular Expresission' button must be checked (.*) and the 'Case sensitive' button (Aa) in your text editor.
Make a pull request (PR)
Once all other bulk change PRs are merged after the build has passed, run these commands on the command line:
sh run.sh make NORM
mv NORM mondo-edit.obo

Notes¶

( ) these means you declare a group in Regex
$1 first group
$2 second group
[ ] means single character

Abbreviations¶

Description: Add an 'abbrevation' tag to synonyms.

Find
^(synonym: "[A-Z]+["] EXACT)( [0-9: a-zA-Z\[\],/\.-_\-]*)$ or ^(synonym: "[A-Z0-9]+["][ ][A-Z]+[ ])\[

Replace $1ABBREVIATION [

Replace all the mentions of a label¶

Description: This specifically replaces all the mentions of 'mental retardation' with 'intellectual disability', but this could be applied to other strings by replacing the terms 'mental retardation' with the a new label (replace 'intellectual disability'.

Step 1: Update all the exact synonyms.¶

Find ^(synonym: ".)mental retardation(.EXACT)( [.*)$

Replace $1mental retardation$2 DEPRECATED$3 $1intellectual disability$2$3

Find ^(synonym: ".)mental retardation(.RELATED)( [.*)$

Replace $1mental retardation$2 DEPRECATED$3 $1intellectual disability$2$3

Remove kboom scores¶

Description: This removes the source annotation that contained kboom scores.

Find
, source="MONDO:kboom-pr-[0-9].[0-9]+/[0-9].[0-9]+/[0-9]+.[0-9]+ source="MONDO:kboom-pr[0-9]+-[0-9]+”, source="MONDO:kboom-pr-[0-9].[0-9]+/[0-9].[0-9]+/[0-9].[0-9]+",

Description: This changes related synonyms to exact synonyms, for synonyms that come from OMIM.

Find ^(synonym:.)(RELATED)(.OMIM)

Replace $1EXACT$3

Add subClassOf axiom to a group of terms¶

Description: This specifically adds the subClassOf axiom 'has modifier' some inherited to every term that is equivalent to an OMIM phenotypic series (OMIMPS). This is a 'relationship' in the text file. In addition, this adds the source to the axiom, that is the OMIMPS ID.

Find:
^(xref:.)(OMIMPS[:][0-9]+)(.equivalentTo.*)

Replace:
$1$2$3 relationship: has_modifier MONDO:0021152 {source="$2"} ! inherited

Split OMIM synonyms and abbreviations¶

Description: By default, OMIM terms and synonyms are written as the long name and abbreviation combined, for example Barber-Say syndrome, BBRSAY. This will split the synonym and abbreviation, for example Barber-Say syndrome and BBRSAY (see MONDO:0008853). This should be followed by adding the abbreviation tag to the abbreviation synonyms (see above).

Find:
^(synonym:.); (.["])(.)(.OMIM.*)

Replace:
$1"$3$4 synonym: "$2$3$4

Find a single letter¶

Description: Find a label that contains a single letter.

Find:
^(name: .* )[a-z]$

Example:
id: MONDO:0014986
name: Fanconi anemia complementation group R

Remove MONDO:superClassOf and MONDO:subClassOf source axiom annotations¶

Related to: https://github.com/monarch-initiative/mondo/issues/4688

Find:
(xref: .)source="MONDO:subClassOf", (.) or (xref: .)source="MONDO:superClassOf", (.) or (xref: .), source="MONDO:subClassOf"(.) or (xref: .), source="MONDO:superClassOf"(.) or (xref: .)source="MONDO:subClassOf"(.) or (xref: .)source="MONDO:superClassOf"(.) or

Relace: $1$2

Bulk Editing Using Regular Expressions