Updates Ubergraph instructions for Fall 2023

data/README.md

@@ -12,25 +12,37 @@
 
 ### Graph (Ontology relation graph)
 
-The [Ubergraph project](https://github.com/INCATools/ubergraph) within the [INCA Tools effort](https://reporter.nih.gov/search/Ah2TPoNbR0i36EpF0YKQbw/project-details/9545836) is integrating numerous bio-ontologies and transforming them into a simplified graph model (for example, existential property restrictions on classes are simplified to direct relations between nodes that represent classses).
+The [Ubergraph project](https://github.com/INCATools/ubergraph) within the [INCA Tools effort](https://reporter.nih.gov/search/Ah2TPoNbR0i36EpF0YKQbw/project-details/9545836) is integrating numerous bio-ontologies and [transforming them into a simplified graph model](https://github.com/INCATools/ubergraph#graph-organization) (for example, existential property restrictions on classes are simplified to direct relations between nodes that represent classes).
 
 > Balhoff, J., Bayindir, U., Caron, A. R., Matentzoglu, N., Osumi-Sutherland, D., & Mungall, C. J. (2022). [Ubergraph: integrating OBO ontologies into a unified semantic graph](https://doi.org/10.5281/zenodo.7249759). In ICBO-2022: International Conference on Biomedical Ontology (Vol. 1613, p. 73). Ann Arbor, Michigan.
 
-We will use one of their downloads: <https://ubergraph.apps.renci.org/downloads/current/nonredundant-graph-table-labeled.tgz>
+We will use one of their [downloads](https://github.com/INCATools/ubergraph#downloads). More specifically, because the downloads currenly maintained by RENCI's Ubergraph database don't include the node (class) and edge (property) labels anymore, we will use a [legacy download obtained in Nov 2022](https://huggingface.co/datasets/hlapp/ubergraph).
 
 -   Download the file (using `curl` or other means), and unpack its contents. For example (on macOS/Unix command line):
 
-        curl -LO https://ubergraph.apps.renci.org/downloads/current/nonredundant-graph-table-labeled.tgz
-        tar zxf nonredundant-graph-table-labeled.tgz
+    ```
+    curl -LO https://huggingface.co/datasets/hlapp/ubergraph/resolve/main/nonredundant-graph-table-labeled.tgz?download=true
+    tar zxf nonredundant-graph-table-labeled.tgz
+    ```
 
 -   Change into the directory where the unpacked files are:
 
-          cd nonredundant-graph-table-labeled
+    ```
+    cd nonredundant-graph-table-labeled
+    ```
 
 -   Open SQLite3 on a new database file:
 
-          sqlite3 obo-graph.db
+    ```
+    sqlite3 obo-graph.db
+    ```
 
 -   In the SQLite shell, execute the commands in [`obo-graph-transform.sql`](obo-graph-transform.sql).
 
-    -   The commands create temporary tables and persistent tables. The temporary tables will disappear once you exit the SQLite shell (or close the SQLite database connection), but the persistent ones (`Node` and `Edge`) will remain, and will be there next time you open the database in SQLite.
+    - You can do this using copy&paste, but you can also run the whole file at once if you downloaded it, using the `.read` SQLite shell command:
+
+        ```
+        sqlite> .read path/to/obo-graph-transform.sql
+        ```
+
+    - The commands create temporary tables and persistent tables. The temporary tables will disappear once you exit the SQLite shell (or close the SQLite database connection), but the persistent ones (`Node` and `Edge`) will remain, and will be there next time you open the database in SQLite.