Synthetic Biology Data

Leveraging Existing Biological Data and Making Sense of it

Abstract

Objectives

• Show

  • The value of Open and standardised data

  • How to generate and find these data

  • How to access and use them

  • Some examples

Content

• Introduction
• No data, no fun
• Objectives / material
• Open science
• FAIR data
• Ontologies
• Data sources - databases
• Working with these databases - GUI/API
• Sharing data
• Graphs/Networks
• Knowledge Graphs
• Use case
• Tools
• GraphML
• QA

References

• A parasite's perspective on data sharing YoSon Park; Casey S Greene Gigascience

• Network biology: understanding the cell's functional organization Albert-László Barabási; Zoltán N. Oltvai Nat. Reviews Genetics

• Data-Driven Synthetic Cell Factories Development for Industrial Biomanufacturing Zhenkun Shi; Pi Liu; Xiaoping Liao; Zhitao Mao; Jianqi Zhang; Qinhong Wang; Jibin Sun; Hongwu Ma; Yanhe Ma BioDesign Research

• Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories João G. R. Cardoso; Kristian Jensen; Christian Lieven; Anne Sofie Lærke Hansen; Svetlana Galkina; Moritz Beber; Emre Özdemir; Markus J. Herrgård; Henning Redestig; Nikolaus Sonnenschein ACS Synthetic Biology

• Automating the design-build-test-learn cycle towards next-generation bacterial cell factories Nicolás Gurdo; Daniel C. Volke; Douglas McCloskey; Pablo Iván Nikel New Biotechnology

• Nine quick tips for analyzing network data Vincent Miele; Catherine Matias; Stéphane Robin; Stéphane Dray PLOS Computational Biology

• Sharing biological data: why, when, and how Samantha L. Wilson; Gregory P. Way; Wout Bittremieux; Jean-Paul Armache; Melissa A. Haendel; Michael M. Hoffman FEBS Letters

• The role of ontologies in biological and biomedical research: a functional perspective Robert Hoehndorf; Paul N. Schofield; Georgios V. Gkoutos Briefings in Bioinformatics

• The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; ...; Richard H Scheuermann, Nigam Shah, Patricia L Whetzel & Suzanna Lewis Nature Biotechnology