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MathIOmica: An Integrative Platform for Dynamic Omics

View Article: PubMed Central - PubMed

ABSTRACT

Multiple omics data are rapidly becoming available, necessitating the use of new methods to integrate different technologies and interpret the results arising from multimodal assaying. The MathIOmica package for Mathematica provides one of the first extensive introductions to the use of the Wolfram Language to tackle such problems in bioinformatics. The package particularly addresses the necessity to integrate multiple omics information arising from dynamic profiling in a personalized medicine approach. It provides multiple tools to facilitate bioinformatics analysis, including importing data, annotating datasets, tracking missing values, normalizing data, clustering and visualizing the classification of data, carrying out annotation and enumeration of ontology memberships and pathway analysis. We anticipate MathIOmica to not only help in the creation of new bioinformatics tools, but also in promoting interdisciplinary investigations, particularly from researchers in mathematical, physical science and engineering fields transitioning into genomics, bioinformatics and omics data integration.

No MeSH data available.


MathIOmica OmicsObject Format.The MathIOmica v.1 input format was redesigned to implement the 10.3+ Wolfram Language improvements to use associations (cf. dictionaries in Python). The data format is termed an OmicsObject, and is an association of associations with common identifiers as inner association keys across multiple samples. It addresses rapid sample identification, measurement and metadata all maintained for user accessibility and additionally accommodates missing values. In addition to the user having control of all aspects of the input data via Query commands on the OmicsObject representing the data, MathIOmica includes specialized functions designed specifically for creating and manipulating an OmicsObject.
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f2: MathIOmica OmicsObject Format.The MathIOmica v.1 input format was redesigned to implement the 10.3+ Wolfram Language improvements to use associations (cf. dictionaries in Python). The data format is termed an OmicsObject, and is an association of associations with common identifiers as inner association keys across multiple samples. It addresses rapid sample identification, measurement and metadata all maintained for user accessibility and additionally accommodates missing values. In addition to the user having control of all aspects of the input data via Query commands on the OmicsObject representing the data, MathIOmica includes specialized functions designed specifically for creating and manipulating an OmicsObject.

Mentions: We have been developing an integrative framework, MathIOmica, with multiple modules for omics downstream statistical analysis now completed. MathIOmica has multiple functions, Fig. 1, utilizes a flexible data format, Fig. 2, can implement multi-omics analyses, as shown in the example workflow in Fig. 3, and provides various graphical interfaces and result visualizations, Fig. 4. MathIOmica integrates multiple omics information starting from mapped experimental omics data - typically RNA-Sequencing expression levels, mapped protein intensities, and small molecules intensities. Using this framework we can analyze different omics data (genome, transcriptome and proteome) individually, based on each technology’s requirements, perform quality control (accounting for experimental and technical limitations) and set all the different technologies on common ground (statistical transformations). MathIOmica provides classification methods to identify patterns in the data, as well as annotation capabilities as discussed briefly below. Finally, extensive documentation is provided for every function and its option set.


MathIOmica: An Integrative Platform for Dynamic Omics
MathIOmica OmicsObject Format.The MathIOmica v.1 input format was redesigned to implement the 10.3+ Wolfram Language improvements to use associations (cf. dictionaries in Python). The data format is termed an OmicsObject, and is an association of associations with common identifiers as inner association keys across multiple samples. It addresses rapid sample identification, measurement and metadata all maintained for user accessibility and additionally accommodates missing values. In addition to the user having control of all aspects of the input data via Query commands on the OmicsObject representing the data, MathIOmica includes specialized functions designed specifically for creating and manipulating an OmicsObject.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121649&req=5

f2: MathIOmica OmicsObject Format.The MathIOmica v.1 input format was redesigned to implement the 10.3+ Wolfram Language improvements to use associations (cf. dictionaries in Python). The data format is termed an OmicsObject, and is an association of associations with common identifiers as inner association keys across multiple samples. It addresses rapid sample identification, measurement and metadata all maintained for user accessibility and additionally accommodates missing values. In addition to the user having control of all aspects of the input data via Query commands on the OmicsObject representing the data, MathIOmica includes specialized functions designed specifically for creating and manipulating an OmicsObject.
Mentions: We have been developing an integrative framework, MathIOmica, with multiple modules for omics downstream statistical analysis now completed. MathIOmica has multiple functions, Fig. 1, utilizes a flexible data format, Fig. 2, can implement multi-omics analyses, as shown in the example workflow in Fig. 3, and provides various graphical interfaces and result visualizations, Fig. 4. MathIOmica integrates multiple omics information starting from mapped experimental omics data - typically RNA-Sequencing expression levels, mapped protein intensities, and small molecules intensities. Using this framework we can analyze different omics data (genome, transcriptome and proteome) individually, based on each technology’s requirements, perform quality control (accounting for experimental and technical limitations) and set all the different technologies on common ground (statistical transformations). MathIOmica provides classification methods to identify patterns in the data, as well as annotation capabilities as discussed briefly below. Finally, extensive documentation is provided for every function and its option set.

View Article: PubMed Central - PubMed

ABSTRACT

Multiple omics data are rapidly becoming available, necessitating the use of new methods to integrate different technologies and interpret the results arising from multimodal assaying. The MathIOmica package for Mathematica provides one of the first extensive introductions to the use of the Wolfram Language to tackle such problems in bioinformatics. The package particularly addresses the necessity to integrate multiple omics information arising from dynamic profiling in a personalized medicine approach. It provides multiple tools to facilitate bioinformatics analysis, including importing data, annotating datasets, tracking missing values, normalizing data, clustering and visualizing the classification of data, carrying out annotation and enumeration of ontology memberships and pathway analysis. We anticipate MathIOmica to not only help in the creation of new bioinformatics tools, but also in promoting interdisciplinary investigations, particularly from researchers in mathematical, physical science and engineering fields transitioning into genomics, bioinformatics and omics data integration.

No MeSH data available.