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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.
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
.
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:
- Open
src/patterns/data/default/abnormalBiologicalProcessInLocation.tsv
and delete the row forMP:0000001
. - 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.
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
.