No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects.

Autor: Danchin A; Integromics, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75013, Paris, France.; School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, Hong Kong., Ouzounis C; Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica, 57001, Greece., Tokuyasu T; Shenzhen Institutes of Advanced Technology, Institute of Synthetic Biology, Shenzhen University Town, 1068 Xueyuan Avenue, Shenzhen, China., Zucker JD; Integromics, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75013, Paris, France.
Jazyk: angličtina
Zdroj: Microbial biotechnology [Microb Biotechnol] 2018 Jul; Vol. 11 (4), pp. 588-605. Date of Electronic Publication: 2018 May 28.
DOI: 10.1111/1751-7915.13284
Abstrakt: Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from 'the sequence tells the structure tells the function' fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.
(© 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
Databáze: MEDLINE
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