Annotation Bulk Removal/Update

Removing annotations in bulk

Use cases:

• removal of annotations in bulk. For example: removing an obsoletion-candidate tag from a lot of terms.
• update of annotations in bulk. For example: updating exclusion code from a lot of terms because these codes were updated.

Overview of the process:

1. A ROBOT template is created, including the annotations to remove.
2. An .owl version of the ROBOT template is created. This .owl file contains the annotations to be removed.
3. The .owl file created (containing the annotations to remove) is removed from the ontology using the "unmerge" command
4. (if updating the annotations)
   1. A ROBOT template is created, including the annotations replacing the one removed.
   2. the ROBOT template is merged using the regular "Merging a ROBOT template" process

Removing annotations in bulk:

1. Create a ROBOT template for annotations to remove.
   1. create a Google sheet including: Mondo term ID, Annotations to be removed Note: the column names for the annotations to remove follow the regular ROBOT template semantics
   2. Publish the spreadsheet on the web, in .tsv format
      1. Click File->Share->Publish to the Web
      2. Publish the specific sheet as TSV
      3. Copy the link to the TSV
2. Create the .owl version of the spreadsheet
   1. In Terminal, run : sh run.sh make TMP_TEMPLATE_URL="xxx" temporary_template -B
   2. where xxx is the link to the ROBOT template tsv_ (see example below)
   3. Note: this file will be in the temp folder (~/ontology/tmp/temporary.owl), and will not be seen in GitHub diff.
3. Unmerge the .owl file from the ontology
   1. In Terminal, run: sh run.sh make UNMERGE_FILE=tmp/temporary.owl unmerge -B
4. Check the GitHub diff: you should see that the annotations from the ROBOT template have been removed (note that the term IDs, though required in the ROBOT template, will not be removed)

Updating annotations in bulk:

1. Remove the annotations to be updated as explained above, in removing annotations in bulk
2. Create a ROBOT template with the updated annotations.
   1. For annotations replacement, the ROBOT template would essentially be the same as the one used for removing annotations (ie same fields), but with the new annotations.
3. Merge this ROBOT template following the regular process (explained here)
   1. Run: sh run.sh make TEMPLATE_URL="yyy" merge_template -B where yyy = the ROBOT template link
4. The end result is essentially an update of existing annotations.

Important note:

This workflow does NOT work in cases when one of many annotation needs to be updated. For example, updating the 'MONDO:equivalentTo' to 'MONDO:equivalentObsolete' for the OMIM x-ref in the example below could not be done using this workflow as this x-ref has other annotations

Examples:

Remove 'obsoletion-candidate' tag, and 'date of obsoletion'

This might be done when terms were removed from the obsoletion candidate list. 1. Robot template:

id	label	Obsoletion candidate subset	obsoletion date
ID		AI oboInOwl:inSubset	A IAO:0006012
MONDO:0008856	immunodeficiency 27A	http://purl.obolibrary.org/obo/mondo#obsoletion_candidate	2022-05-01
MONDO:0020248	vitreoretinal degeneration	http://purl.obolibrary.org/obo/mondo#obsoletion_candidate	2022-05-01
MONDO:0020094	obsolete autosomal dominant disease with diffuse palmoplantar keratoderma as a major feature	http://purl.obolibrary.org/obo/mondo#obsoletion_candidate
MONDO:0017671	obsolete autosomal recessive disease with diffuse palmoplantar keratoderma as a major feature	http://purl.obolibrary.org/obo/mondo#obsoletion_candidate

1. Create the .owl version of the spreadsheet: Run: sh run.sh make TMP_TEMPLATE_URL="https://docs.google.com/spreadsheets/d/e/2PACX-1vSEgalBcvuURhnd2pGGYU4r4cxpkOEMQN1Rzcb2rOem-foKrFc-svrOmqteBdadmHnSly8JEG1n_1mq/pub?gid=1507538904&single=true&output=tsv" temporary_template -B
2. Unmerge the .owl file from the ontology: Run: sh run.sh make UNMERGE_FILE=tmp/temporary.owl unmerge -B
3. Results:
4. 'obsoletion candidate' tag is removed for all the terms
5. 'obsoletion date' will be removed for the terms which has that information in the template, ie, in this example: MONDO:0008856, MONDO:0020248

Update 'exclusion code'

We might need to do this when we review the exclusion code usage and/or we create a new exclusion code to replace an existing one. 1. Robot template with annotations to remove:

termid	?label	has obsolescence	reason	?source
ID		A IAO:0000231	>A oboInOwl:source
MONDO:0000601	obsolete autoimmune disorder of urogenital tract	out of scope	MONDO:excludeGroupingClass
MONDO:0001424	obsolete sarcoid meningitis	out of scope	MONDO:excludeFinding
MONDO:0002336	obsolete inflammatory and toxic neuropathy	out of scope	MONDO:excludeConditionsCausedByExternalForce

1. Create the .owl version of the spreadsheet: Run: sh run.sh make TMP_TEMPLATE_URL="https://docs.google.com/spreadsheets/d/e/2PACX-1vQ8cszVqBNOeClD6uFif3QRHn0Ud_Cyt_gylyTTFJ-RoJaOwNWS7Qv3c516bJoTBaKT1WLagSQ7CQqS/pub?gid=0&single=true&output=tsv" temporary_template -B
2. Unmerge the .owl file from the ontology: Run:sh run.sh make UNMERGE_FILE=tmp/temporary.owl unmerge -B
3. GitHub diff: the exclusion code +source are removed for all the terms.
4. Create ROBOT template with the updated annotations:

termid	?label	has obsolescence	reason	new exclusion code
ID		A IAO:0000231	>A oboInOwl:source
MONDO:0000601	obsolete autoimmune disorder of urogenital tract	out of scope	MONDO:excludeGroupingMorpho
MONDO:0001424	obsolete sarcoid meningitis	out of scope	MONDO:excludePhenotype
MONDO:0002336	obsolete inflammatory and toxic neuropathy	out of scope	MONDO:excludeGrouping

1. Merge the new ROBOT template: Run: sh run.sh make TEMPLATE_URL="https://docs.google.com/spreadsheets/d/e/2PACX-1vQ8cszVqBNOeClD6uFif3QRHn0Ud_Cyt_gylyTTFJ-RoJaOwNWS7Qv3c516bJoTBaKT1WLagSQ7CQqS/pub?gid=365804501&single=true&output=tsv" merge_template -B
2. Results: the Mondo terms have an updated source associated to the "out of scope" exclusion reasons.