Software and downloads

We are constantly releasing data and software with our publications. The following is a list of recent publications and associated resources.

Our page on bitbucket: https://bitbucket.org/pennhlp/

Publication Resources

Sarker A, Chandrashekar P, Magge A, Cai H, Klein AZ, Gonzalez G. Discovering Cohorts of Pregnant Women from Social Media for Safety Surveillance and Analysis. J Med Internet Res. 2017 Oct 30;19(10):e361. doi: 10.2196/jmir.8164.

Klein AZ, Sarker A, Rouhizadeh M, O’Connor K, Gonzalez, G. Detecting Personal Medication Intake in Twitter: An Annotated Corpus and Baseline Classification System. BIONLP-2017. Vancouver, BC, Canada. pages 136-142.

Sarker A, Gonzalez G. A corpus for mining drug-related knowledge from Twitter chatter: Language models and their utilities, Data in Brief Journal. dx.doi.org/10.1016/j.dib.2016.11.056

Tahsin, T., Weissenbacher, D., Rivera, R., Beard, R., Firago, M., Wallstrom, G., Scotch, M., & Gonzalez, G.; A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. Journal of the American Medical Informatics Association, 2016 Sep; 23(5):934-941. doi: 10.1093/jamia/ocv172.
Sarker A, O’Connor K, Ginn R, Scotch M, Smith K, Malone D, Gonzalez G.; Social media mining for toxicovigilance: automatic monitoring of prescription medication abuse from Twitter, Drug Safety, 2016 Mar;39(3):231-40. doi: 10.1007/s40264-015-0379-4.
Nikfarjam A, Sarker A, O’Connor K, Ginn R, Gonzalez G.; Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features, Journal of the American Medical Informatics Association, 2015 Mar 9. pii: ocu041. doi: 10.1093/jamia/ocu041.
Sarker A, Nikfarjam A, O’Connor K, Ginn R, Upadhaya T, Jayaraman S, Smith K, Gonzalez G; Utilizing social media data for pharmacovigilance: A review, Journal of Biomedical Informatics 2015 Feb 23. pii: S1532-0464(15)00036-2. doi: 10.1016/j.jbi.2015.02.004.
Sarker A, Gonzalez G; Portable Automatic Text Classification for Adverse Drug Reaction Detection via Multi-corpus Training, Journal of Biomedical Informatics, 2015 Feb;53:196-207. doi: 10.1016/j.jbi.2014.11.002. Epub 2014 Nov 8.
Pimpalkhute P, Patki A, Nikfarjam A, Gonzalez G; Phonetic spelling filter for keyword selection in drug mention mining from social media. AMIA Summits Transl Sci Proc. 2014 Apr 7;2014:90-5. eCollection 2014.