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Positome: A method for improving protein-protein interaction quality and prediction accuracy
- Source :
- CIBCB
- Publication Year :
- 2017
- Publisher :
- IEEE, 2017.
-
Abstract
- The progressive elucidation of positive protein-protein interactions (PPIs) as wet-lab techniques continue to improve in both throughput and precision has increased the number and quality of known PPIs across the spectrum of life. Creating high quality datasets of positive PPIs is critical for training PPI prediction algorithms and for assessing the performance of PPI detection efforts. We present the Positome, a web service to acquire sets of positive PPIs based on user-defined criteria pertaining to data provenance including interaction type, throughput level, and detection method selection in addition to filtration by multiple lines of evidence (i.e. PPIs reported by independent research groups). The Positome provides a tunable interface to obtain a specified subset of interacting PPIs from the BioGRlD database. Both intra- and inter-species PPIs are supported. Using a number of model organisms, we demonstrate the trade-off between data quality and quantity, and the benefit of higher data quality on PPI prediction precision and recall. A web interface and REST web service are available at http://bioinf.sce.carleton.ca/POSITOME/.
- Subjects :
- 0301 basic medicine
Computer science
media_common.quotation_subject
Interface (computing)
computer.software_genre
03 medical and health sciences
030104 developmental biology
Data quality
Quality (business)
Protein–protein interaction prediction
Data mining
User interface
Web service
Precision and recall
Throughput (business)
computer
media_common
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
- Accession number :
- edsair.doi...........1ca2ef7700244a34e1a00d4b8f78d8c4
- Full Text :
- https://doi.org/10.1109/cibcb.2017.8058545