SOP Splitting Terms¶
Overview of workflow¶
- Identify a term that should be split.
- If the term should be split into two new terms, assign the new ID for that term in advance.
- Check to see if the term is being used by EFO, ClinGen or other users, where possible.
- Notify users of the the users that the term will be split.
- If there are no objections, make the changes after two release cycles have passed.
- The workflow involves two steps:
- Create new terms and IDs for the term that will be split.
- Obsolete and merge the existing term into the new term.
Example:¶
OMIM may rename a disease from FOO to FOO 1, and create a new phenotypic series (PS) with the name FOO. (For an example, see OMIM:606176 Diabetes mellitus, permanent neonatal 1, which is part of the phenoypic series PS606176 Diabetes mellitus, permanent neonatal and the respective Mondo ticket #1803. In this case, we should follow the Splitting a more specific term into a more generic term workflow.
Workflow:¶
- Add the label FOO and FOO1 to the ROBOT_CreateNewTerm Template
- Add obsoletion tag to FOO via the ROBOT_NewTermSplit-ObsTag and via instructions in Merge a ROBOT template into Mondo.
- At the time of the release, generate the sparql report for obsoletion candidates and share with the Mondo users list.
- After two release cycles have passed, obsolete and merge the terms.
Detailed Workflow¶
Add obsoletion tags to terms to be split¶
- Identify a term that should be split.
- If the term should be split into two new terms, assign the new ID for the new terms in advance by adding the label to this ROBOT template.
- Add the obsoletion tags to the terms to be obsoleted:
- In ROBOT_NewTermSplit-ObsTag:
- add the IDs for the terms to be obsoleted in columnn A
- add the labels in column B (for human readability)
- the labels in column E should be automatically populated from the ROBOT_CreateNewTerm template
- add a link to the GitHub ticket in column G
- Follow the instructions to Merge a ROBOT template into Mondo.
- At the time of the release, generate the sparql report for obsoletion candidates and share with the Mondo users list:
- In terminal, run
sh run.sh make report-obsoletioncandidates-withcomment
- The report will be in the src/sparql/reports folder
Tips¶
- Tip 1: If you want to look a the report quickly, type in Terminal
atom reports/report-disease-labeled-terms.tsv
. This will open it in Atom. - Tip 2: In Terminal,
open reports
- this will open the file in Finder.
Split Terms¶
- When we're ready to split the terms, we need to add the new terms to Mondo, that the old terms will be merged into.
- Follow the instructions to Merge a ROBOT template into Mondo with the ROBOT_CreateNewTerm template.
- Follow the instructions for splitting classes.
- If terms are to be obsoleted and merged into new classes, follow the instructions here.