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neuroelectro / neuroelectro_org

The NeuroElectro Project: Compiling information on neuron electrophysiology through literature text-mining.
neuroelectro.org
GNU General Public License v2.0
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how much extra effort to extract common compounds blocking synapses? #330

Closed stripathy closed 8 years ago

stripathy commented 8 years ago

inhibitory blockers: bicuculline, picrotoxin, gabazine excitatory blockers: CNQX, NBQX, (D-APV or DAP5)

dtebaykin commented 8 years ago

Need the regex's for them, after that it takes 5 minutes to add them into the extraction pipeline and test whether it is working as intended.

rgerkin commented 8 years ago

Add DNQX, MK-801, and kyurenic acid (kyurenate) to the excitatory list

stripathy commented 8 years ago

Thanks for the suggestions! I also noticed CPP too. Let us know if you think of any others

On Sat, Aug 27, 2016, 9:42 AM Richard C Gerkin notifications@github.com wrote:

Add DNQX, MK-801, and kyurenic acid (kyurenate) to the excitatory list

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/neuroelectro/neuroelectro_org/issues/330#issuecomment-242927544, or mute the thread https://github.com/notifications/unsubscribe-auth/ACWEWVl_61p_T73qwZEqeKHQ6FGKiGkwks5qkGkPgaJpZM4JuG2a .

Shreejoy Tripathy Post-Doctoral Researcher Department of Psychiatry University of British Columbia

dtebaykin commented 8 years ago

Added the following synaptic compounds:

cnqx_extract_re = re.compile(ur'CNQX', flags=re.UNICODE|re.IGNORECASE) dnqx_extract_re = re.compile(ur'DNQX', flags=re.UNICODE|re.IGNORECASE) nbqx_extract_re = re.compile(ur'NBQX', flags=re.UNICODE|re.IGNORECASE) mk801_extract_re = re.compile(ur'MK-?\s?801', flags=re.UNICODE|re.IGNORECASE) dapv_extract_re = re.compile(ur'D?-?\s?AP(5|V)', flags=re.UNICODE|re.IGNORECASE) cpp_extract_re = re.compile(ur'CPP', flags=re.UNICODE|re.IGNORECASE) kynur_extract_re = re.compile(ur'kynurenic acid|kynurate', flags=re.UNICODE|re.IGNORECASE) bic_extract_re = re.compile(ur'bicucul?line', flags=re.UNICODE|re.IGNORECASE) picro_extract_re = re.compile(ur'picrotoxin', flags=re.UNICODE|re.IGNORECASE) gabazine_extract_re= re.compile(ur'gabazine', flags=re.UNICODE|re.IGNORECASE) cgp_extract_re = re.compile(ur'CGP', flags=re.UNICODE|re.IGNORECASE) strychnine_extract_re = re.compile(ur'strychnine', flags=re.UNICODE|re.IGNORECASE)