Issue 300 Creation of animal parts module

[kaiiam]

Cross reference to #300

Additional run information to be added to the documentation for the organism parts modules:

Test animal parts module:

bash run_organism_parts.sh MODE="test" MODULE="animal" TERM_CONTRIBUTOR_STR="https://orcid.org/0000-0002-3410-4655|https://orcid.org/0000-0002-3410-4655"

Run animal part module:

bash run_organism_parts.sh MODE="run" MODULE="animal" TERM_CONTRIBUTOR_STR="https://orcid.org/0000-0001-5275-8866|https://orcid.org/0000-0002-8844-9165|https://orcid.org/0000-0002-3410-4655|https://orcid.org/0000-0002-3410-4655"

Test plant parts module:

bash run_organism_parts.sh MODE="test" MODULE="plant" TERM_CONTRIBUTOR_STR="https://orcid.org/0000-0002-3410-4655|https://orcid.org/0000-0002-3410-4655"

Run plant parts module:

bash run_organism_parts.sh MODE="run" MODULE="plant" TERM_CONTRIBUTOR_STR="https://orcid.org/0000-0001-5275-8866|https://orcid.org/0000-0002-8844-9165|https://orcid.org/0000-0002-3410-4655|https://orcid.org/0000-0002-3410-4655"

[kaiiam]

To add to the docs the dependencies for running the modules: bash (I was using 3.2), python3 (I was using 3.11.4), robot (I was using 1.9.3).

[kaiiam]

Just added the demo SPARQL query script to get at the old APs from the terms in the values block. The query script is run with a command like

robot query --input foodon_merged.owl --query scripts/foodon_extras.sparql results/foodon_extras_metadata.csv

Not this is an example command not reflective of the FOODON directory structure.

[kaiiam]

Note that you need to be in foodon/src/ontology/scripts to run the commands. To add to the docs about this.

[kaiiam]

Note a user will also have to run make in order for the commands to work. Note that we probably don't want to commit the local changes to foodon-merged.ofn in the workflow we should clarify this in the docs.