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Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers

1
Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
2
Department of Biomedical Informatics, and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA 15260, USA
*
Author to whom correspondence should be addressed.
Received: 18 October 2017 / Revised: 16 November 2017 / Accepted: 17 November 2017 / Published: 21 November 2017
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Abstract

Bio-molecular reagents, like antibodies that are required in experimental biology are expensive and their effectiveness, among other things, is critical to the success of the experiment. Although such resources are sometimes donated by one investigator to another through personal communication between the two, there is no previous study to our knowledge on the extent of such donations, nor a central platform that directs resource seekers to donors. In this paper, we describe, to our knowledge, a first attempt at building a web-portal titled Antibody Exchange (or more general ‘Bio-Resource Exchange’) that attempts to bridge this gap between resource seekers and donors in the domain of experimental biology. Users on this portal can request for or donate antibodies, cell-lines, and DNA Constructs. This resource could also serve as a crowd-sourced database of resources for experimental biology. Further, we also studied the extent of antibody donations by mining the acknowledgement sections of scientific articles. Specifically, we extracted the name of the donor, his/her affiliation, and the name of the antibody for every donation by parsing the acknowledgements sections of articles. To extract annotations at this level, we adopted two approaches—a rule based algorithm and a bootstrapped pattern learning algorithm. The algorithms extracted donor names, affiliations, and antibody names with average accuracies of 57% and 62%, respectively. We also created a dataset of 50 expert-annotated acknowledgements sections that will serve as a gold standard dataset to evaluate extraction algorithms in the future. View Full-Text
Keywords: data exchange; resource donations; text mining data exchange; resource donations; text mining
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Subramanian, S.; Ganapathiraju, M.K. Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers. Data 2017, 2, 38.

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