Merge pull request #496 from monarch-initiative/docs-add-new-source-u…

…pdates

Update `add-new-source.md`

docs/developer/add-new-source.md

@@ -5,10 +5,10 @@ In several of the filename patterns below, `*` represents the ontology name/id.
 ### 1.1. Add source info
 Add a new filename and URL to the `products` > `components` section in [src/ontology/mondo-ingest-odk.yaml](https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/mondo-ingest-odk.yaml).
 
-### 1.2. `update_repo`
+### 1.2. Run `update_repo`
 From `src/ontology`, run `sh run.sh make update_repo`.
 
-What this does: This will update several files, including the addition of components goals to src/ontology/Makefile.
+What this does: This will update several files, including the addition of components goals to `src/ontology/Makefile`.
 
 It is possible you may need to run this command twice. The first time will update the update process itself, and the 
 second time will run the update.
@@ -50,7 +50,24 @@ Run `sh run.sh make ../../docs/metrics/*.md` from `src/ontology`.
 ### 3.5. `docs/metrics.md`
 Add a link to your new `.md` file created in the last step.
 
-## 4. Everything else
+## 4. The `components/` goal
+When `mondo-ingest-odk.yaml` is edited and `update_repo` is run, a new `component-download-SOURCE.owl` goal is added to 
+`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.
+- `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 
+list of the only allowable properties for any component. If there are any properties in the source that are not in this 
+file that you wish to keep, they should be added.
+
+## 5. Everything else
 Steps 1-3 take care of the basic setup. Ideally, if everything is automated correctly and the nature of the ontology 
 being ingested is not significantly different than what has been ingested before, running `make build-mondo-ingest` 
 should include all of the output artefacts and remaining documentation for the new ontology.