"damage" matched as entity

[herongrove]

There are a lot of damage-binding proteins and other entities with "damage" in their name, but I don't think "damage" should be matched as it is being, e.g. in "Two of these sites ( Ser966 and Ser957 in Smc1 ) have been shown to be phosphorylated by the ATM kinase in response to DNA damage."

[herongrove]

I've prepared an exhaustive list of words that overlap between capitalized protein names and English words. This isn't filtered for word frequency, so use with care -- aah is unlikely to appear in a biomedical text except as a protein name, but that might not be the case for cat, ape, chimp, etc.
overlap.txt

[MihaiSurdeanu]

Hi @danebell: I would like to add this list to bioresources and use it to filter out false positives in the rule-based NER. But, at this point, it seems too over-inclusive. Can you please do another pass over it, and keep just words that are likely to appear as non-proteins in bio texts? For example, I would remove the first 9 entries (they are likely to be only used as proteins), but keep ACT, ANT, etc.

[herongrove]

Yes, I can definitely do this, but there are over 1000 entries, so if it's okay, I will wait for at least a week to do so.

[MihaiSurdeanu]

Agreed, it can wait. I suspect that less than 10% of this are actually
relevant in this list (the rest are valid protein names that are unlikely
to be used otherwise in bio texts).

On Wed, Feb 24, 2016 at 11:03 AM, Dane Bell notifications@github.com
wrote:

Yes, I can definitely do this, but there are over 1000 entries, so if it's
okay, I will wait for at least a week to do so.

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Reply to this email directly or view it on GitHub
#25 (comment).

[MihaiSurdeanu]

closed by the addition of the NER stop list in bioresources 1.1.9.