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

Klein A, Sarker A, Cai H, Weissenbacher D, Gonzalez G. Social Media Mining for Birth Defects Research: A Rule-Based, Bootstrapping Approach to Collecting Data for Rare Health-Related Events on Twitter. Journal of Biomedical Informatics. 2018 Nov; Vol. 87:68-78. doi: 10.1016/j.jbi.2018.10.001.

Magge A, Weissenbacher D, Sarker A, Scotch M, Gonzalez G. Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature. PSB-2019 (in press).

Sarker A, Belousov M, Friedrichs J, Hakala K, Kiritchenko S, Mehryary F, Han S, Tran T, Rios A, Kavuluru R, De Bruijn B, Ginter F, Mahata D, Mohammad S, Nenadic G, Gonzalez G. Data and Systems for Medication-related Text Classification and Concept Normalization from Twitter: Insights from the Social Media Mining for Health (SMM4H)-2017 Shared Task, Journal of the American Medical Informatics Association, ocy114. doi: 10.1093/jamia/ocy114.

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.