Capitalization of detected symbols in "Alternative title(s)" and "Included title(s)" may be incorrect

[joeflack4]

Overview

Some of the synonym capitalizations for "alternative" & "included" titles may be incorrect.

Breakdown

Context: In working on #128, #126 , and #125, I also noticed a problem with how synonym capitalization is being done for the Alternative Title(s); symbol(s) and Included Title(s); symbols we are getting from mimTitles.txt

We have this block of code:

        for exact_label in exact_labels:
            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(exact_label, abbrev))))
        for label in other_labels:
            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(label, abbrev))))
        for included_label in cleaned_inc_labels:
            graph.add((omim_uri, URIRef(INCLUDED_URI), Literal(label_cleaner.clean(included_label, abbrev))))

It uses .clean(), which uses various rules to determine the appropriate capitalization of "alternative titles" and "included titles". It takes a second, optional param: abbrev above. I believe that the important part here is that it is trying to look for symbols that are also contained within titles, and make sure that those are capitalized.

The potential issue I see is that the abbrev being used are the one(s) from Preferred Title; symbol only. It does not consider the "alternative symbols" or "included symbols". I think this is a bug, and that we also want to capitalize these too.

Suggestion

I believe that all of the symbols from all of the titles (preferred, alternative, included) should be passed into .clean() so that if any of those symbols appear within the text of any of those labels, they will be capitalized. I believe that this was the original intention.