apache / apache/ctakes

[Feature]: intro and contributing to ctakes-ytex

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Java
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Description

### What problem does this solve?

I have been able to update the ctakes-ytex build process to now run with
modern versions of MySQL (using Ubuntu 23.10 and MySQL version 8.0.35)
which I would like to contribute back to the project. In addition, I
have found some computational "bugs" in a couple of the kernel metrics
in the ctakes-ytex package which I have now been able to correct and
match the outputs generated from the old Perl UMLS::Similarity package.
In addition, I've added a couple of metrics provided by the Perl module
which were not in the ctakes-ytex code (such as Resnik and Faith
algorithms).

### Describe the solution you'd like

I was going to propose submitting as 3 separate pull requests:

PR-1 : update build process to support modern MySQL database

Q's - is it appopriate to update the supplied MRCONSO.RRF and MRSTY.RRF
files from UMLS with current versions? How about me updating the
pre-built concept graphs as binary .gz files?

To support the MySQL connection, there are XML templates which parse the
DB connection and I don't have an elegant way to pass through the & vs
& so I had created two separate DB properties (one for direct JDBC
connections in the ctake-ytex code that can't work with the &
escaped version and another for the XML templates to parse)

PR-2 : submit corrections to the metrics which are broken

PR-3 : submit new metrics

Please let me know if this makes sense, and how best to work with your
team. Should I fork the github repo into my own or create a new branch
and submit the PRs from there? What are the preferred ways of working
and contributing to the cTakes project?

### Alternative solutions you've considered

_No response_

### Priority

None

### Contact Details

_No response_

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