Simplify the ingest process and make source of monarch mp-hp-etc mappings more transparent

[cmungall]

Currently we have this Makefile process:

monarch-mapping-commons/monarch_mapping_commons.Makefile

Lines 61 to 69 in e8dc36f

	$(TMP_DIR)/upheno/%:
	mkdir -p $(TMP_DIR)/upheno/
	wget -q https://bbop-ontologies.s3.amazonaws.com/upheno/current/upheno-release/all/$* -O $@
	$(MAPPING_DIR)/upheno_custom.sssom.tsv: $(patsubst %, $(TMP_DIR)/upheno/%, upheno_species_lexical.csv upheno_mapping_logical.csv upheno_all_with_relations.owl)
	mkdir -p $(MAPPING_DIR) $(TMP_DIR)
	$(RUN) phenio-toolkit lexical-mapping --species-lexical $(TMP_DIR)/upheno/upheno_species_lexical.csv -m $(TMP_DIR)/upheno/upheno_mapping_logical.csv -o $(TMP_DIR)
	$(RUN) sssom parse $(TMP_DIR)/upheno_custom_mapping.sssom.tsv --metadata $(METADATA_DIR)/upheno_custom_mapping.sssom.yml -C merged -o $@

This is not documented, but it seems to grab a CSV of unknown provenance from https://bbop-ontologies.s3.amazonaws.com/upheno/current/upheno-release/all/upheno_species_lexical.csv and run a bespoke mapping process.

This file doesn't seem to have been updated since 2022:

curl -I  https://bbop-ontologies.s3.amazonaws.com/upheno/current/upheno-release/all/upheno_species_lexical.csv

HTTP/1.1 200 OK
x-amz-id-2: JvpiirNXlumH4JRMltKcm8FrdDzmON8hMwyFsBofTV0QpujZHle2RH9gz31PuHSex/DjRtGq0C6aG4WPEc4qCQ==
x-amz-request-id: DXVS5HMZHFRAK1BA
Date: Fri, 06 Sep 2024 22:24:27 GMT
Last-Modified: Sun, 19 Jun 2022 18:33:20 GMT
ETag: "8433a4c273d87bd4f5d268989dd5d264-4"
Accept-Ranges: bytes
Content-Type: text/csv
Server: AmazonS3
Content-Length: 29130561

Same for
https://bbop-ontologies.s3.amazonaws.com/upheno/current/upheno-release/all/upheno_mapping_logical.csv

After this a bespoke mapping process using https://github.com/souzadevinicius/phenio-toolkit is used to make the sssom file used in monarch (see also obophenotype/upheno-dev#53)

See also obophenotype/upheno#962

[matentzn]

Before things become easier I documented the entire complexity here:

obophenotype/upheno#963

Working on simplifying HP MP mappings there.

[matentzn]

I have addressed the complexity of the pipeline in #63, but this does not automatically increase HP-MP mapping transparency!

[matentzn]

pipeline is simplified, but will leave a bit open until my big refactoting is finished #63