This page includes examples of the usage of the web service for the evaluation of metrics.

Case study 1: structural ontology metrics

Description: 19 metrics measuring structural aspects of bio-ontologies have been analysed on two different corpora of ontologies: OBO Foundry and AgroPortal.

Sample input data:

• 80 OBO Foundry ontologies
• 119 OBO Foundry ontologies
• 78 AgroPortal ontologies

Source of data: Franco M, Vivo JM, Quesada-Martínez M, Duque-Ramos A, Fernández-Breis JT. Evaluation of structural ontology metrics based on public repository data. Briefings in Bioinformatics, submitted

Case study 2: RNA quality metrics for the assessment of gene expression differences

Description: 2 quality metrics from 16 aliquots of a unique batch of RNA Samples. The metrics are Degradation Factor (DegFact) and RNA Integrity Number (RIN).

Sample input data: Case study 2 dataset

Source of data:  Imbeaud, Sandrine, et al. "Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces." Nucleic acids research 33.6 (2005): e56-e56.

Case study 3: metrics for biological pathways

Description: 2 metrics that quantitative characterizations of the importance of regulation in biochemical pathway systems, including systems designed for applications in synthetic biology or metabolic engineering. The metrics are reachability and efficiency.

Sample input data: Case study 3 dataset

Source of data: Davis, J. D., & Voit, E. O. (2018). Metrics for Regulated Biochemical Pathway Systems. Bioinformatics.

Case study 4: Metrics from the Journal Citation Report

Description: Data from the 2016 Journal Citation Report. We are using the impact factor, immediacy index and the total number of citations of more than 11,000 journals.

Sample input data: Case study 4 dataset

Source of data: Manually curated data from JCR inCites information.