Open bgyori opened 8 years ago
@bgyori: we know "associated with" is ambiguous, but we're not sure how to disambiguate it. Any simple ideas?
I have some ideas:
A associates with B
as likely to refer to a physical interaction between two molecular entities and A is/was associated with B
as unlikely to refer to a physical interaction. A
and B
are recognized as molecular entities (that is, proteins, protein families, complexes, chemicals) then extracting the complex formation event is warranted, otherwise the event should not be extracted.3 is a very good catch! We should do this! @myedibleenso @marcovzla: can you please make sure that Binding rules operate only proteins, families, or chemicals?
@myedibleenso, @marcovzla: if the above idea doesn't work, let's go brute force and simply remove "associate" from the list of triggers. It seems too noisy.
Another weird example for "associated with": Yields a binding event between TGF-beta and PAK2, even though the sentence doesn't support that::
[Evidence(reach, PMID22880011, {'cell_type': [u'cl:CL:0008019'], 'organ': None, 'tissue': None, 'location': None, 'cell_line': None, 'species': [u'taxonomy:4932']}, Pak2 is specifically activated by TGF-beta only in mesenchymal cells, as the result of phosphatidylinositol 3-kinase (PI3K) activation and may be associated with TGF-beta activation of Ras XREF_BIBR, XREF_BIBR, XREF_BIBR.)]
@MihaiSurdeanu will try to clean binding_17 next.
The binding_17 rule extracts complex formation events for
A is associated with B
sentences. However,is associated with
seems to be usually used to draw an observational, statistical link between "distant" molecular players or higher level processes - things likeSmoking is associated with lung cancer
. Theassociated with
pattern accounts for a lot of the extractions from binding_17 (~50%) and it turns out that these sentences overwhelmingly talk about associations that are not related to complex formation based on the samples we looked at.Here are some examples of failure modes:
Finally, an example where
associated with
actually means complex formation (at least as far as I understand):