Nothing matched

[luisenriqueramos1977]

HI,

I run the tool, and uploaded two different owl ontology, and nothing happens. Then, I uploaded two times the same ontologies, and nothing happens as well.

What should I be doing wrong?

Luis

[cpesquita]

Dear Luis,

After loading the ontologies you need to select the option to run the alignment job. If this does not solve your issue, please let us know which ontologies you are trying to align so we can replicate the issue.

Thank you for using AML.

[samsontu]

I ran AML using the GUI and found that, after specifying the source and target ontologies and clicking the "Open" button, the app hangs with the Console showing "Loading source ontology". Then I tried using the command line. The app appears to work, but no output file is generated. Appended below is the log of the CLI interaction. I am using an M1 MacBook Pro with Sonoma OS and running OpenJDK Runtime Environment (build 20.0.2+9-78).

(base) samsons02114mbp:AML_v3.2 tu$ java -jar AgreementMakerLight.jar -s $dir/ontologies/ICD10-label.owl -t $dir/ontologies/ICD11-label.owl -o ICD10-11AML.rdf -a Loading source ontology http://purl.bioontology.org/ontology/ICD10 loaded in 1 seconds Classes: 12318 Individuals: 0 Properties: 0 Loading target ontology file:/Users/tu/Documents/Dropbox/Ontologies/ICD11.owl loaded in 3 seconds Classes: 77036 Individuals: 0 Properties: 0 Direct Relationships: 99981 Running transitive closure on RelationshipMap Transitive closure finished in 2 seconds Extended Relationships: 704651 Disjoints: 0 Reading config.ini file Finished! Running Lexical Matcher Finished in 1 seconds Loading mediating ontology doid.owl http://purl.obolibrary.org/obo/doid.owl loaded in 0 seconds Running Mediating Cross-Reference Matcher using http://purl.obolibrary.org/obo/doid.owl Finished in 0 seconds doid.owl selected as a mediator Loading mediating ontology uberon.owl http://purl.obolibrary.org/obo/uberon.owl loaded in 2 seconds Running Mediating Cross-Reference Matcher using http://purl.obolibrary.org/obo/uberon.owl Finished in 0 seconds uberon.owl discarded Extending Alignment with String Matcher Matching Children & Parents Matching Siblings Finished in 3 seconds Running Obsoletion Filter Finished in 0 seconds Computing High-Level Structure Overlap Finished in 0 seconds Computing Neighbor Similarity Finished in 0 seconds Performing Selection Finished in 0 seconds Building Repair Map Nothing to repair! Alignment is coherent (base) samsons02114mbp:AML_v3.2 tu$

[samsontu]

I was able to receive output after I added the following in my java call: java --add-opens java.base/java.lang=ALL-UNNAMED -Xms2G -Xmx6G -DentityExpansionLimit=100000000 -jar AgreementMakerLight.jar ... Thanks.

[cpesquita]

Happy to see you have it working now!