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Bulk Editing Using Regular Expressions

Bulk Editing Using Regular Expressions

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


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.


  1. Create a new branch.
  2. 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.
  3. Note: The 'Regular Expresission' button must be checked (.*) and the 'Case sensitive' button (Aa) in your text editor.
  4. Make a pull request (PR)
  5. Once all other bulk change PRs are merged after the build has passed, run these commands on the command line:
  6. sh make NORM
  7. mv NORM mondo-edit.obo


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


Description: Add an 'abbrevation' tag to synonyms.

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


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.

, 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.


$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).

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

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

Find a single letter

Description: Find a label that contains a single letter.

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

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

Remove MONDO:superClassOf and MONDO:subClassOf source axiom annotations

Related to:

(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