Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers
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 betwe...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2017-11-01
|
| Series: | Data |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2306-5729/2/4/38 |
| _version_ | 1811303614872813568 |
|---|---|
| author | Sandeep Subramanian Madhavi K. Ganapathiraju |
| author_facet | Sandeep Subramanian Madhavi K. Ganapathiraju |
| author_sort | Sandeep Subramanian |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T07:51:02Z |
| format | Article |
| id | doaj.art-3c509040eaf6466aa24c0ef250108dfb |
| institution | Directory Open Access Journal |
| issn | 2306-5729 |
| language | English |
| last_indexed | 2024-04-13T07:51:02Z |
| publishDate | 2017-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Data |
| spelling | doaj.art-3c509040eaf6466aa24c0ef250108dfb2022-12-22T02:55:32ZengMDPI AGData2306-57292017-11-01243810.3390/data2040038data2040038Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and SeekersSandeep Subramanian0Madhavi K. Ganapathiraju1Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USALanguage Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USABio-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.https://www.mdpi.com/2306-5729/2/4/38data exchangeresource donationstext mining |
| spellingShingle | Sandeep Subramanian Madhavi K. Ganapathiraju Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers Data data exchange resource donations text mining |
| title | Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers |
| title_full | Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers |
| title_fullStr | Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers |
| title_full_unstemmed | Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers |
| title_short | Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers |
| title_sort | antibody exchange information extraction of biological antibody donation and a web portal to find donors and seekers |
| topic | data exchange resource donations text mining |
| url | https://www.mdpi.com/2306-5729/2/4/38 |
| work_keys_str_mv | AT sandeepsubramanian antibodyexchangeinformationextractionofbiologicalantibodydonationandawebportaltofinddonorsandseekers AT madhavikganapathiraju antibodyexchangeinformationextractionofbiologicalantibodydonationandawebportaltofinddonorsandseekers |