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This is something I've run across before, but never really addressed it. In some dialects (like North Junín), the root yaćha- can mean "to reside" or it can mean "to know". But in other dialects, "to reside" is a separate root (like "tiya-") and "to know" is a separate root (yaćha-). I thought that if I made two senses to the lexical entry for yaćha- in North Junín, one for "to reside" and another for "to know", then the parse would give me an ambiguity between the two for me to choose. However, that is not the case. The parser just gives me the first sense.

So that tells me that for dialects like North Junín, I need to have two lexical entries for yaćha-, one for "to reside" and a separate one for "to know". Then the parser will generate the ambiguity and I can choose between the two, so that FLExTrans will then know which of the two "senses" it should work with.

Is this correct? If so, then what is the purpose of the 1.1, 1.2, 2.1, etc. in FLExTrans?
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You have the right idea of how to handle two senses of a word in your first paragraph. We just need to help FLEx a bit so that it shows us the ambiguous parses.

When you are using the FLEx parser, you will just see the first sense shown for the parses. (Unless the two senses have different grammatical categories.) This is by design, I think, to reduce how many parses you see. You see this behavior in Try a Word and if you are parsing a word in a text. But, if you have that word in a text and you choose the 2nd sense of the word (by clicking the arrow beside the root) and accept that parse, FLEx now remembers two parses for the word. Now if that word shows up in a new text, the word will show with the normal yellow color to indicate there is more than one parse. Unfortunately, you have to do this for all the inflections you may have.

So the key is to manually select the 2nd sense one time and approve it.

There is no need to separate the senses into two separate lexical entries if you use this method.

The implications for FLExTrans by having two senses, is that you can link each sense separately to the target sense that it should go with. In your example, yacha1.1 would link to tiya1.1 (in the target lexicon) and yacha1.2 would link to yacha1.1.
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