classify command

[alePelus]

Hi!

I am having an issue with the classify tool (-classify)

So, as results of the clasification I am having 4 relationship (with active = 1) that are already inactivated in the last extension and it is re-activating these 4 relationship

It is possible that the classify tool is inferring the active=1 to the extension that I am classifying?

I would like to know what the classify tool do in the background in order to understand the process and try to find a solution for my problem...

so thank you in advance!

[kaicode]

Were the packages were already classified with these relationships inactive and after the stated relationship to axiom conversion process the relationships became active again during classification?

It's very hard to give advice on this without seeing the content. If you email the packages I could take a closer look at these 4 relationships. kke@snomed.org

[kaicode]

I get the same 4 relationship changes when classifying just the international and SNS packages. This indicates that either the SNS 20231201 package is not classified correctly or that it was classified against a different version of the International Edition when the release was created.

[kaicode]

Are you in touch with the maintainers of the SNS package? I would recommend that they use this SNOMED OWL Toolkit to classify their release package to pick up inferred relationship changes to include in the package for publication.

It's possible to verify that a package contains all intended inferred relationship changes by using the classify function (as you have). There should be no inferred relationship changes.

[alePelus]

Hi!

There have been some changes/updates in the current version for the classify command in the toolkit? because I just tried to classify an old extension and I don't get the same result.

Thank you in advance.

[kaicode]

Nothing has changed in the SNOMED OWL Toolkit that should affect these classification results. I think the issue may be memory starvation. When I classify the SNS package using toolkit version 3.0.6 I get the same 4 results.
Please ensure you give java at least 4g of memory rather than the 2g in your example. If the toolkit doesn't have enough memory the results may be incorrect and inconsistent.

[alePelus]

Hi,

I just discovered the issue, thank you for everything!

In addition, I had another question, there is some command to save the logs of the command in a file? because I was seeing the logs in the cmd, but I couldn't save them.

Thank you in advance.

[kaicode]

The toolkit is not able to write to a log file but depending on your operating system you may be able to capture the command output into a log file automatically. For example in Linux based systems like MacOS or Ubuntu the tee command can copy output to a log file while still streaming it to the terminal to see live.

java -Xms4g -jar snomed-owl-toolkit*executable.jar -classify -rf2-snapshot-archives SnomedCT_InternationalRF2.zip | tee output.txt

On Windows using PowerShell should also support this.