Generate reports

How to create a new SPARQL report¶

Go to https://yasgui.triply.cc/#
Find a blueprint from src/sparql/reports directory
Copy and paste into yasqui and edit as needed
Run query and ensure it works make sure you are using the end point: https://ubergraph.apps.renci.org/sparql
In Atom (text editor), go to src/sparql/reports directory
Right click on any file name and duplicate
Rename file appropriately
Paste contents of query into file
In Terminal run sh run.sh make report-query-disease-labeled-terms
The report will be in the src/sparql/reports folder

Tips¶

Tip 1: If you want to look a the report quickly, type in Terminal atom reports/report-disease-labeled-terms.tsv. This will open it in Atom.
Tip 2: In Terminal, open reports - this will open the file in Finder.

How to generate reports¶

Reports are generally created like this:

sh run.sh make report-query-%

For example, the following command...

sh run.sh make report-query-obsoletion-candidates

will run this:

robot --catalog catalog-v001.xml query --use-graphs true -i mondo-edit.obo -f tsv --query ../sparql/reports/obsoletion-candidates.sparql reports/report-obsoletion-candidates.tsv

Which will generate a TSV report here: reports/report-obsoletion-candidates.tsv.

The only requirement for a report is, that a suitable SPARQL query can be found in ../sparql/reports/, for example, ../sparql/reports/obsoletion-candidates.sparql.

Note: If you want to run a query using the "inferred" version of the ontology (e.g. harrisonview-termlist requires to check whether any parents (asserted and inferred) have the 'harrisonview' tag), use the following command: sh run.sh make report-reason-query-

If you want to create your very own report, you can:

tweak an existing command, for example using Ubergraph (https://api.triplydb.com/s/YfJCi9mrR)
Save the query as a .sparql query in ../sparql/reports/, for example, ../sparql/reports/my-query.sparql.
Run sh run.sh make report-query-my-query to generate the report as above.