TY - JOUR
T1 - Datanator
T2 - An integrated database of molecular data for quantitatively modeling cellular behavior
AU - Roth, Yosef D.
AU - Lian, Zhouyang
AU - Pochiraju, Saahith
AU - Shaikh, Bilal
AU - Karr, Jonathan R.
N1 - Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
PY - 2021/1/8
Y1 - 2021/1/8
N2 - Integrative research about multiple biochemical subsystems has significant potential to help advance biology, bioengineering and medicine. However, it is difficult to obtain the diverse data needed for integrative research. To facilitate biochemical research, we developed Datanator (https://datanator.info), an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, as well as data about chemically-similar molecules and reactions in phylogenetically-similar organisms in similar environments. Currently, Datanator includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants about a broad range of organisms. Going forward, we aim to launch a community initiative to curate additional data. Datanator also provides tools for filtering, visualizing and exporting these data clouds. We believe that Datanator can facilitate a wide range of research from integrative mechanistic models, such as whole-cell models, to comparative data-driven analyses of multiple organisms.
AB - Integrative research about multiple biochemical subsystems has significant potential to help advance biology, bioengineering and medicine. However, it is difficult to obtain the diverse data needed for integrative research. To facilitate biochemical research, we developed Datanator (https://datanator.info), an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, as well as data about chemically-similar molecules and reactions in phylogenetically-similar organisms in similar environments. Currently, Datanator includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants about a broad range of organisms. Going forward, we aim to launch a community initiative to curate additional data. Datanator also provides tools for filtering, visualizing and exporting these data clouds. We believe that Datanator can facilitate a wide range of research from integrative mechanistic models, such as whole-cell models, to comparative data-driven analyses of multiple organisms.
UR - https://www.scopus.com/pages/publications/85099428438
U2 - 10.1093/nar/gkaa1008
DO - 10.1093/nar/gkaa1008
M3 - Article
C2 - 33174603
AN - SCOPUS:85099428438
SN - 0305-1048
VL - 49
SP - D516-D522
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -