merge turbomam's 2024-11-11 am branches into a new branch and test

[turbomam]

new and isolated summary statistics

• new and isolated summary statistics #139

remove "compare to 2024-06-26 " targets

• remove "compare to 2024-06-26 " targets #137

all-extras-all target includes bridge owl

• all-extras-all target includes bridge owl #135

---

git merge 129-add-bridge-owl-generation-to-makefile 

git merge 136-remove-compare-to-2024-06-26-targets 

git merge 138-isolate-oaidb-related-targets 

may need to approve merge messages in-between

---

git merge 142-remove-srcontologycomponentsprocessing

[turbomam]

after merging in all three branches and resolving a merge conflict (in aio.Makefile (bad ordering of merges?)

from src/ontology

./run.sh make all-extras-all

---

@caufieldjh

then would we run these next? or does there have to be a commit and push inbetween?

./run.sh make prepare_release
./run.sh make public_release

[turbomam]

then, four our own paper-writing purposes:

make aio-root-statistics-transposed-filtered.tsv
```

[turbomam]

aio.Makefile with conflicts resolved:

## Customize Makefile settings for artificial-intelligence-ontology
## 
## If you need to customize your Makefile, make
## changes here rather than in the main Makefile


.PHONY: clean all all-extras-all all-extras-clean all-extras-build

all-extras-all: all-extras-clean all-extras-build

all-extras-clean: clean clean-extras remove-old-input

all-extras-build: components-from-new-input all bridge/aio-bridge-to-upper.owl

# Source of truth for AIO.
# This is a ROBOT template.
SRC_URL = 'https://docs.google.com/spreadsheets/d/1LVubUGg56YDGJ0VUdJDMNBPY8iFfissRfy4eM56bUFg/export?exportFormat=csv'
SRC_CSV_FILE = aio-src.csv

RELEASE_ASSETS = \
  $(MAIN_FILES) \
  $(SUBSET_FILES) \
  $(REPORT_FILES) \
  $(SRC_CSV_FILE)

# TODO: ensure this gets checked in to the repo
aio-src.csv:
	curl -L -s $(SRC_URL) > $@

components/aio-component.owl: aio-src.csv
	# the prefix AIO is used in the Google Sheet so we provide an expansion here
	# but aio-edit.owl asserts the same expansion for aio, so that becomes authoritative downstream
	robot template \
	  --add-prefix 'AIO: https://w3id.org/aio/' \
	  --add-prefix 'oio: http://www.geneontology.org/formats/oboInOwl#' \
	  -t $< \
	  annotate --annotation-file aio-annotations.ttl \
	  -o $@

components/%.owl: components/%.csv
	robot template \
	  --add-prefix 'AIO: https://w3id.org/aio/' \
	  --add-prefix 'oio: http://www.geneontology.org/formats/oboInOwl#' \
	  -t $< \
	  annotate --annotation-file aio-annotations.ttl \
	  -o $@

clean-extras:
	rm -rf aio.db aio-root-statistics* bridge/aio-bridge-to-upper.owl aio-2024-06-26.owl current-vs-2024-06-26-diff* aio-relation-graph.tsv.gz

remove-old-input:
	rm -rf aio-src.csv
	rm -rf components/aio-component.owl

components-from-new-input: remove-old-input
	make aio-src.csv
	make components/aio-component.owl

include stats-with-semsql.Makefile