run ingest: https://ci.monarchinitiative.org/job/build-omim/ note: right now only a few people can actually run this and it is likely to be replaced by the new ingest being developed by Dazhi soon. For the moment, ping Nico to run this ingest. Before continuing to step 2, make sure that the run has completed by checking that the last run in the build history is green.
In terminal: cd src/ontology
In terminal: sh run.sh make omim_slurp -B
If successful this command will create two files: mondo/src/ontology/tmp/ps_slurp_omim.obo and mondo/src/ontology/tmp/rest_slurp_omim.obo
Add all the classes from the slurped files to mondo-edit.obo. (Use a text editor, rathe than Protege).
If ps_slurp_omim.obo is not empty, go back to step 3 and run the slurp again until the ps_slurp_omim.obo is empty
Check Mondo to ensure the term does not already exist (ie the term was already added from another source).
If the term already exists in Mondo, add the OMIM ID as a dbxref, and add MONDO:equivalentTo.
Add any synonyms from OMIM (if they don't already exist), or add OMIM as a dbxref to any existing synonyms, as applicable.
Terms in the OMIM slurp include RELATED synonyms in the format TERM IN ALL CAPS; ABBREVIATION, for example: synonym: "MEGACYSTIS-MICROCOLON-INTESTINAL HYPOPERISTALSIS SYNDROME 2; MMIHS2" RELATED [OMIM:619351].
For these cases, we do not want to duplicate the label in the synonym, so delete the duplicate label.
In almost all cases, the synonym should be EXACT.
Mark the abbreviation with ABBREVIATION
For example: synonym: "MMIHS2" RELATED ABBREVIATION [OMIM:619351]