Add a note on merge before extract, fixes
@@ -71,6 +71,8 @@ The reuse of ontology terms creates links between data, making the ontology and
--term-file uberon_module.txt \
--output results/uberon_module.owl
+NOTE: The `extract` command works on the input ontology, not its imports. To extract from imports you should first `merge`.
+
The `--method` options fall into two groups: Minimal Information for Reuse of External Ontology Term (MIREOT) and Syntactic Locality Module Extractor (SLME).
- MIREOT: extract a simple hierarchy of terms
