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clulab / reach

Reach Biomedical Information Extraction
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Mention filter for issue #605 #619

Closed maxaalexeeva closed 5 years ago

maxaalexeeva commented 5 years ago

The filter removes (some of) the mentions that incorrectly grab arguments from other mentions E.g., in "Insulin stimulated tyrosine phosphorylation of IRS-1, PI 3-kinase activity, and Akt phosphorylation.", the filter eliminates the following incorrect relations: phosphorylation1-Akt and phosphorylation2-IRS1

@MihaiSurdeanu, before opening a pull request, I merged master into my branch. There was one conflict, but I think I resolved it correctly--- the conflict was in ReachSystem.scala around line 140, where I am calling the new filter (filterOverlappingMentions). Is the protocol normally to open a pull request first and then resolve conflicts or merge master into your branch before opening a pull request? Thanks!

MihaiSurdeanu commented 5 years ago

@maxaalexeeva: you did the right thing. You should merge master in your branch before a PR.

maxaalexeeva commented 5 years ago

We should ScalaDoc/JavaDoc for the headers of methods. That is, use the: /* *// comments for method headers. Ping me if you don't know what this is. But this fine as is.

Ah, yes, I know what you mean. Thanks!