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An expanded evaluation of protein function prediction methods shows an improvement in accuracy
(2016)
Background
A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.
Results
We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.
Conclusions
The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.
The boreal winter 2019/2020 was very irregular in Europe. While there was very little snow in Central Europe, the opposite was the case in northern Fenno-Scandia, particularly in the Arctic. The snow cover was more persistent here and its rapid melting led to flooding in many places. Since the last severe spring floods occurred in the region in 2018, this raises the question of whether more frequent occurrences can be expected in the future. To assess the variability of snowmelt related flooding we used snow cover maps (derived from the DLR's Global SnowPack MODIS snow product) and freely available data on runoff, precipitation, and air temperature in eight unregulated river catchment areas. A trend analysis (Mann-Kendall test) was carried out to assess the development of the parameters, and the interdependencies of the parameters were examined with a correlation analysis. Finally, a simple snowmelt runoff model was tested for its applicability to this region. We noticed an extraordinary variability in the duration of snow cover. If this extends well into spring, rapid air temperature increases leads to enhanced thawing. According to the last flood years 2005, 2010, 2018, and 2020, we were able to differentiate between four synoptic flood types based on their special hydrometeorological and snow situation and simulate them with the snowmelt runoff model (SRM).