Convert to full use of ODK for ontology development

[ramonawalls]

Things that need to be fixed after updating to ODK 1.3.0:

DOSDP patterns:

• So far, I can run sh run.sh make ../patterns/definitions.owl -B IMP=false, but sh run.sh make ../patterns/pattern.owl -B IMP=false throws the error below, which is not terribly helpful. However, definitions.owl is all I really need.

if [ true  = true ]; then dosdp-tools prototype --obo-prefixes true --template=../patterns/dosdp-patterns --outfile=../patterns/pattern.owl; fi
make: *** [Makefile:507: ../patterns/pattern.owl] Error 1

• Can I improve the way ACS5 patterns are managed with ODK?

Imports:

• Make sure ODK knows that chebi is a large file.
• Add import statements to srpdio-edit.owl manually, rather than through protege.
• Other?

Modules:

• They are already well handled in sdrpio.Makefile, but they need to be included as imports manually via srpdio-edit.owl for the release to work properly.
• There was a problem with the old version of ODK including patterns in with modules, but that has been fixed.

*Releases:** TBD. Maybe once I fix patterns and imports, it will work correctly. For now, I have to run make IMP=false PAT=false prepare_release for it to work correctly (but first make sure the imports and patterns are up to date).

[ramonawalls]

**DOSDP patterns:

• So far, I can run sh run.sh make ../patterns/definitions.owl -B IMP=false, but sh run.sh make ../patterns/pattern.owl -B IMP=false throws the error below, which is not terribly helpful. However, definitions.owl is all I really need.

if [ true  = true ]; then dosdp-tools prototype --obo-prefixes true --template=../patterns/dosdp-patterns --outfile=../patterns/pattern.owl; fi
make: *** [Makefile:507: ../patterns/pattern.owl] Error 1

• Can I improve the way ACS5 patterns are managed with ODK?

TODO:

• [x] What is patterns.owl and why can’t I make it? (It is an independent file with your patterns, sort of. It will make if you include the pattern IRIs in your YAML file. Working now.)
• [x] This section of OBOOK seems incomplete at the end. (I let Nico know about it.
• [ ] Improve the way ACS5 patterns are managed with ODK

[ramonawalls]

Imports: Make sure ODK knows that chebi is a large file. Add import statements to srpdio-edit.owl manually, rather than through protege. Other?

TODO:

• [x] Make sure ODK knows that chebi is a large file.
• [x] Add import statements to srpdio-edit.owl manually, rather than through protege. (Done via repo update)
• [ ] Why is chebi refresh failing?

if [ true = true ] && [ true = true ] && [ true = true ]; then curl -L http://purl.obolibrary.org/obo/chebi.owl.gz --create-dirs -o mirror/chebi.owl.gz --retry 4 --max-time 200 && robot --catalog catalog-v001.xml convert -i mirror/chebi.owl.gz -o mirror-chebi.tmp.owl && \
    robot --catalog catalog-v001.xml remove -i mirror-chebi.tmp.owl --base-iri http://purl.obolibrary.org/obo/CHEBI --axioms external --preserve-structure false --trim false -o mirror-chebi.tmp.owl && mv mirror-chebi.tmp.owl tmp/mirror-chebi.owl; fi
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   331  100   331    0     0   1808      0 --:--:-- --:--:-- --:--:--  1808
100 44.8M  100 44.8M    0     0   757k      0  0:01:00  0:01:00 --:--:--  758k
Killed
make[1]: *** [Makefile:316: mirror-chebi] Error 137

[ramonawalls]

Modules:

• They are already well handled in sdrpio.Makefile, but they need to be included as imports manually via srpdio-edit.owl for the release to work properly.
• There was a problem with the old version of ODK including patterns in with modules, but that has been fixed.

TODO:

• [ ] Add import statements to srpdio-edit.owl manually, rather than through protege, for robot modules.
• [ ] Can this be done with the make file, similar to modules?

[ramonawalls]

Releases:* TBD. Maybe once I fix patterns and imports, it will work correctly. For now, I have to run make IMP=false PAT=false prepare_release for it to work correctly (but first make sure the imports and patterns are up to date).

TODO