A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions

J Integr Bioinform. 2018 Dec 21;16(1):20180068. doi: 10.1515/jib-2018-0068.


Metabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism.

Keywords: Genome-scale metabolic models; database integration; human metabolism; omics databases.

MeSH terms

  • Computational Biology / methods*
  • Databases, Factual
  • Genome, Human*
  • Humans
  • Metabolic Networks and Pathways*
  • Models, Statistical*
  • Molecular Sequence Annotation
  • Transcription, Genetic