Using machine learning tools for protein database biocuration assistance
König, Caroline (Universitat Politècnica de Catalunya)
Shaim, Ilmira (Universitat Politècnica de Catalunya)
Vellido, Alfredo (Universitat Politècnica de Catalunya)
Romero, Enrique (Universitat Politècnica de Catalunya)
Alquézar, René (Universitat Politècnica de Catalunya)
Giraldo, Jesús (Universitat Autònoma de Barcelona. Departament de Pediatria, Obstetrícia i Ginecologia i Medicina Preventiva i Salut Pública)

Data:	2018
Resum:	Biocuration in the omics sciences has become paramount, as research in these fields rapidly evolves towards increasingly data-dependent models. As a result, the management of web-accessible publicly-available databases becomes a central task in biological knowledge dissemination. One relevant challenge for biocurators is the unambiguous identification of biological entities. In this study, we illustrate the adequacy of machine learning methods as biocuration assistance tools using a publicly available protein database as an example. This database contains information on G Protein-Coupled Receptors (GPCRs), which are part of eukaryotic cell membranes and relevant in cell communication as well as major drug targets in pharmacology. These receptors are characterized according to subtype labels. Previous analysis of this database provided evidence that some of the receptor sequences could be affected by a case of label noise, as they appeared to be too consistently misclassified by machine learning methods. Here, we extend our analysis to recent and quite substantially modified new versions of the database and reveal their now extremely accurate labeling using several machine learning models and different transformations of the unaligned sequences. These findings support the adequacy of our proposed method to identify problematic labeling cases as a tool for database biocuration.
Ajuts:	Ministerio de Economía y Competitividad SAF2014-58396-R
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Publicat a:	Scientific reports, Vol. 8 (july 2018) , ISSN 2045-2322

DOI: 10.1038/s41598-018-28330-z
PMID: 29977071

10 p, 1.1 MB

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