Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers
AbstractBio-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
- Supplementary File 1:
Supplementary (ZIP, 14 KB)
Externally hosted supplementary file 1
Description: Annotated acknowledgements sections. Annotations contain information about donors, affiliations, antibody names, and other such donated resources.
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
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.
Subramanian S, Ganapathiraju MK. Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers. Data. 2017; 2(4):38.Chicago/Turabian Style
Subramanian, Sandeep; Ganapathiraju, Madhavi K. 2017. "Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers." Data 2, no. 4: 38.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.