The field of protein function prediction as viewed by different domain scientists

Experimental biologists, biocurators, and computational biologists all play a role in characterizing a protein’s function. The discovery of protein function in the laboratory by experimental scientists is the foundation of our knowledge about proteins. Experimental findings are compiled in knowledge-bases by biocurators to provide standardized, readily accessible, and computationally amenable information. Computational biologists train their methods using these data to predict protein function and guide subsequent experiments. To understand the state of affairs in this ecosystem, centered here around protein function prediction, we surveyed scientists from these three constituent communities. Our objective was to understand their views on this research area, including the importance of the problem, the usefulness of the methods, the bottlenecks in the field, and the level of interaction between the communities. We show that the three core communities have common but also idiosyncratic perspectives on the field. Most strikingly, experimentalists rarely use modern prediction software, but when presented with predictions, report many to be surprising and useful. Ontologies appear to be highly valued by biocurators, less so by experimentalists and computational biologists, yet controlled vocabularies bridge the communities and simplify the prediction task. Additionally, many software tools are not readily accessible and the predictions presented to the users can be broad and uninformative. To meet both the social and technical challenges in the field, a more productive and meaningful interaction between members of the core communities is necessary.