SOP: Changing an existing EQ definition

Patternised logical definitions must be edited only using the tsvs located in src/patterns/data/*/*.tsv e.g. src/patterns/data/abnormalAnatomicalEntity.tsv. There are two rough scenarios of interest: (1) changing a definitions' variables (for example from when GO process to another) and (2) moving an EQ to a different pattern. Note that scenario (2) should happen only very, very rarely, and if it does, usually as a consequence to discussions in the Phenotype Ontology Reconciliation Effort.

Examples:

Scenario 1: Changing a definitions' variables.

Assume we have this definition in src/patterns/data/default/abnormalBiologicalProcessInLocation.tsv.

defined_class	biological_process	biological_process_label	location	location_label
MP:0000001	GOX:0000001	fictional process	UBERX:0000001	fictional anatomical entity

We determine that the affected process GOX:0000001 is wrong or imprecise for some reason, and needs to be replaced by GOX:0000009. To that end, we open the tsv file above either Excel or a regular text editor, and then change GOX:0000001 to GOX:0000009.

Scenario 2: Moving an EQ to a different pattern.

Assume we have this definition in src/patterns/data/default/abnormalBiologicalProcessInLocation.tsv.

defined_class	biological_process	biological_process_label	location	location_label
MP:0000001	GOX:0000001	fictional process	UBERX:0000001	fictional anatomical entity

We determine that the logical definition (EQ) of MP:0000001 is better served by the abnormalBiologicalProcess pattern because the location turns out to be redundant and is now asserted in the fictional process ontology GOX. To move MP:0000001 to abnormalBiologicalProcess, we follow the following steps:

1. Open src/patterns/data/default/abnormalBiologicalProcessInLocation.tsv and delete the row for MP:0000001.
2. Open src/patterns/data/default/abnormalBiologicalProcess.tsv and add a new row:

defined_class	biological_process	biological_process_label
MP:0000001	GOX:0000001	fictional process

If src/patterns/data/default/abnormalBiologicalProcess.tsv does not exist, follow these instructions.

The important thing here is to make sure that different patterns have differently named, and ordered, columns. So it is very important that you make sure that all the values of the moved definition are in the right columns.

Re-building src/patterns/definitions.owl

If it is vital to update the definitions immediately, you move on to rebuild definitions:

cd src/ontology
sh run.sh make ../patterns/definitions.owl

or, if no new terms were introduced:

cd src/ontology
sh run.sh make IMP=false ../patterns/definitions.owl

Note that the usual release command:

cd src/ontology
sh run.sh make prepare_release

Will also rebuild definitions.owl.