Consolidate property maps

- There have been 2 property map TSV files used by robot rename. However, we are now utilizing the --allow-duplicates flag, which allows us to consolidate them into 1 file.
- Delete: one of the property map files
- Rename: the other of the files
- Update: components goals to utilize the new/updated file
- Update: Docs regarding this aspect of adding a new source

docs/developer/add-new-source.md

@@ -55,12 +55,11 @@ When `mondo-ingest-odk.yaml` is edited and `update_repo` is run, a new `componen
 `src/ontology/Makefile`. This essentially downloads a copy of the source. But, for it to be used in `mondo-ingest`, it 
 needs to be modified. This is done by creating a `$(COMPONENTSDIR)/omim.owl` goal in `mondo-ingest.Makefile` which runs 
 a composite `robot` command. Here are some sections you'll likely want to add that command:  
-- `rename --mappings config/SOURCE-property-map.sssom.tsv`: You'll notice that there are two other lines on most goals 
-for `property-map.sssom.tsv` and `property-map-2.sssom.tsv`. These handle some common renamings. However, 
-if your source has any properties that need to be renamed which are specific to that source, then you should create a 
-new file for that. While doing this, it might be useful to check any other `SOURCE-property-map.sssom.tsv` files to see 
-if they share any of the same property renamings. If so, it might be a good idea to move them to 
-`property-map.sssom.tsv` instead.
+- `rename --mappings config/SOURCE-property-map.sssom.tsv`: You'll notice that all components goals have a such a line 
+using `property-map.sssom.tsv`. This is for some common property renamings. However, if your source has any properties 
+that need to be renamed which are specific to that source, then you should create a new file for that. While doing this,
+ it might be useful to check any other `SOURCE-property-map.sssom.tsv` files to see if they share any of the same  
+property renamings. If so, it might be a good idea to move them to `property-map.sssom.tsv` instead.
 - `query --update ../sparql/SPARQL.ru`: There may be more complex modifications that need to be made to the ontology. If
  so, this can be done by 1 or more SPARQL queries.
 - `remove -T config/properties.txt --select complement --select properties --trim true`: `properties.txt` contains a 
@@ -78,4 +77,4 @@ all of the steps, but with modifications so that you're only running it for the
 For example, instead of `make slurp-all` you'd run `make slurp-*`.
 
 There are a few other files that will probably need to be added as well, such as `src/ontology/config/*_exclusions.tsv`.
-A full list of such things should be found in [this issue](https://github.com/monarch-initiative/mondo-ingest/issues/2).
+A full list of such things should be found in [this issue](https://github.com/monarch-initiative/mondo-ingest/issues/2).

src/ontology/config/property-map-2.sssom.tsv → src/ontology/config/property-map.sssom.tsv

@@ -1,4 +1,7 @@
 subject_id	object_id
+http://purl.org/dc/elements/1.1/source	oboInOwl:source
+http://www.w3.org/2004/02/skos/core#prefLabel	http://www.w3.org/2000/01/rdf-schema#label
+http://www.w3.org/2004/02/skos/core#altLabel	oboInOwl:hasExactSynonym
 http://www.ebi.ac.uk/efo/definition	http://purl.obolibrary.org/obo/IAO_0000115
 http://www.ebi.ac.uk/efo/reason_for_obsolescence	rdfs:comment
 http://www.ebi.ac.uk/efo/alternative_term	oboInOwl:hasExactSynonym

src/ontology/mondo-ingest.Makefile

@@ -63,8 +63,7 @@ $(TMPDIR)/ordo_relevant_signature.txt: component-download-ordo.owl | $(TMPDIR)
 #  - #60 needs to be fixed at source, but a workaround can probably be implemented in this goal
 $(COMPONENTSDIR)/omim.owl: $(TMPDIR)/omim_relevant_signature.txt | component-download-omim.owl
 	if [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-omim.owl.owl --select imports \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
-		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		remove -T $(TMPDIR)/omim_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		remove -T config/remove.txt --axioms equivalent \
 		query \
@@ -77,8 +76,7 @@ $(COMPONENTSDIR)/omim.owl: $(TMPDIR)/omim_relevant_signature.txt | component-dow
 $(COMPONENTSDIR)/ordo.owl: $(TMPDIR)/ordo_relevant_signature.txt config/properties.txt | component-download-ordo.owl
 	if [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-ordo.owl.owl --select imports \
 		merge \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
-		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		query \
 			--update ../sparql/fix_partof.ru \
 			--update ../sparql/fix_deprecated.ru \
@@ -95,8 +93,7 @@ $(COMPONENTSDIR)/ordo.owl: $(TMPDIR)/ordo_relevant_signature.txt config/properti
 
 $(COMPONENTSDIR)/ncit.owl: $(TMPDIR)/ncit_relevant_signature.txt | component-download-ncit.owl
 	if [ $(SKIP_HUGE) = false ] && [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-ncit.owl.owl --select imports \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
-		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		query --update ../sparql/rm_xref_by_prefix.ru \
 		remove -T $(TMPDIR)/ncit_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		remove -T config/properties.txt --select complement --select properties --trim true \
@@ -106,8 +103,7 @@ $(COMPONENTSDIR)/ncit.owl: $(TMPDIR)/ncit_relevant_signature.txt | component-dow
 # todo: See #1 at top of file
 $(COMPONENTSDIR)/doid.owl: $(TMPDIR)/doid_relevant_signature.txt | component-download-doid.owl
 	if [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-doid.owl.owl --select imports \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
-		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		remove -T $(TMPDIR)/doid_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		query \
 			--update ../sparql/fix_omimps.ru \
@@ -132,8 +128,7 @@ component-download-icd10cm.owl: | $(TMPDIR)
 # todo: See #1 at top of file
 $(COMPONENTSDIR)/icd10cm.owl: $(TMPDIR)/icd10cm_relevant_signature.txt | component-download-icd10cm.owl
 	if [ $(COMP) = true ]; then $(ROBOT) merge -i $(TMPDIR)/component-download-icd10cm.owl.owl \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
-		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		remove -T $(TMPDIR)/icd10cm_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		remove -T $(TMPDIR)/icd10cm_relevant_signature.txt --select individuals \
 		query \
@@ -145,8 +140,7 @@ $(COMPONENTSDIR)/icd10cm.owl: $(TMPDIR)/icd10cm_relevant_signature.txt | compone
 # todo: See #1 at top of file
 $(COMPONENTSDIR)/icd10who.owl: $(TMPDIR)/icd10who_relevant_signature.txt | component-download-icd10who.owl
 	if [ $(COMP) = true ] ; then $(ROBOT) remove -i $(TMPDIR)/component-download-icd10who.owl.owl --select imports \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
-		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		remove -T $(TMPDIR)/icd10who_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		remove -T $(TMPDIR)/icd10who_relevant_signature.txt --select individuals \
 		query \
@@ -157,7 +151,7 @@ $(COMPONENTSDIR)/icd10who.owl: $(TMPDIR)/icd10who_relevant_signature.txt | compo
 
 $(COMPONENTSDIR)/icd11foundation.owl: $(TMPDIR)/icd11foundation_relevant_signature.txt | component-download-icd11foundation.owl
 	if [ $(COMP) = true ] ; then $(ROBOT) remove -i $(TMPDIR)/component-download-icd11foundation.owl.owl --select imports \
-		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
+		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
 		rename --mappings config/icd11foundation-property-map.sssom.tsv \
 		remove -T $(TMPDIR)/icd11foundation_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		remove -T $(TMPDIR)/icd11foundation_relevant_signature.txt --select individuals \