paxtools is an application used for the Data Exchange Format for Biological Pathway Information.
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.
Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data.
By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently.
In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge.
The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
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This tool is used to download and modify BioPAX (
It uses a lightweight HTTP client and can be use with any IPC mechanism including shell scripts and command line programs.
The software has been tested on Unix/Linux and Windows platforms with Common Lisp implementations.
It is available under an ISC license as a product download from SourceForge.
paxtools Description:
This tool is used to download and modify BioPAX (
It uses a lightweight HTTP client and can be use with any IPC mechanism including shell scripts and command line programs.
The software has been tested on Unix/Linux and Windows platforms with Common Lisp implementations.
It is available under an ISC license as a product download from SourceForge.
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.
Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data.
By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently.
In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge.
The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
paxtools Description:
This tool is used to download and modify BioPAX (
It uses a lightweight HTTP client and can be use with any IPC mechanism including shell scripts and command line programs.
The software has been tested on Unix/Linux and Windows platforms with Common Lisp implementations.
It is available under an ISC license as a product download from SourceForge.S. Guruswamy
S. Guruswamy, S. N. Guruswamy or S. N. Guruswamy (, born 1953) is an Indian film director, screenwriter, producer, artist and entrepreneur. He is known for his work in Telugu cinema. He directed more than 50 films in Telugu cinema.
Career
Guruswamy was born in 1953 to Shri Bal
Paxtools
paxtools is a command line application that facilitates importing and exporting BioPAX pathway data.
It has a simple yet powerful toolset for parsing files and interacting with the BioPAX data repository.
Because of the flexibility of BioPAX, paxtools can be used as a generic command line application for many purposes.
The BioPAX Data Exchange Format
The BioPAX format is based on a Directory-like structure with a defined directory hierarchy.
The namespaces of the data types are defined and can be interpreted by the BioPAX engine.
Similar to the MS-DOS filesystem, the top level directories of the BioPAX structure act as ‘folders’ with the semantics of directories.
Each BioPAX structure has a namespace defined in an absolute path, starting with the ‘/’.
This path serves as the namespace for the whole hierarchy of definitions.
Upon parsing a file, a namespace is created for the structure, which contains all the sub-structures available in the file.
It is therefore possible to access the data in a file by specifying the namespace and if necessary, traverse the hierarchy to gather the data in a specified location.
The BioPAX standards are developed in close cooperation with many scientists and require the participation of many parties to ensure the format is well defined.
Therefore, paxtools implements strict syntax conventions, provenance information, and offline validation routines.
paxtools is able to make semantic decisions (such as inferring the intended meaning of a BioPAX node) using the context it has been provided with.
For example, the names of the Gene/Proteins, Complex, Entity and Reaction keys in BioPAX are inferred from the names of the corresponding components in the KEGG database.
Since paxtools can parse structures from different sources, it is important to make these names consistent.
paxtools provides flexibility for files of various data types and formats.
paxtools supports:
– Binary Files
– Comma Separated Files
– Tab Separated Files
– XML Files
– RDF Files
– MS-TXT Files
– MS-CSV Files
– MS-PST Files
– MS-TSV Files
– MS-DGV Files
– MS-EXC Files
– DSN Files
– Biomart Files
– Accession File Format
– FASTA Files
– FASTA Files + Accession File Format
– F
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paxtools is a tool for assessing and improving the quality of BioPAX.
paxtools can be used for analyzing pathways, for assessing the quality of pathways in the BioPAX format, and also for converting BioPAX into other formats.
paxtools reads BioPAX-compliant files and produces metrics for each pathway, which can be reviewed and analyzed.
BioPAX-compliant files are XML files of the BioPAX format.
paxtools can be used to assess the quality of the input BioPAX by a number of metrics.
BioPAX, however, is based on a semantics-driven approach to data representation and paxtools allows the quality of BioPAX to be assessed by considering only the model elements.
paxtools makes use of the following data types:
Standard Metrics Metrics are reviewed and may include those that are specific to BioPAX or may be used for representation of other standards.
Note: A typical run for a BioPAX file takes approximately 10 seconds (on current server hardware) and a run for an XML file will take approximately 5 seconds for the same processor.
It takes approximately 3 hours to test a BioPAX file for all possible BioPAX elements
A typical BioPAX file is approximately 3 MB and may take 2-3 minutes to read.
Multiple runs are automatically produced.
Note: paxtools does not examine the content of the file, only the pathway model elements and the way that they are implemented.
paxtools can be used as a standalone application or integrated into a code base
Input BioPAX File Examples:
Input BioPAX file examples can be found at the BioPAX test page
View BioPAX files for which metrics have been generated
Input Example BioPAX File
Input example BioPAX file.
This file has been generated by paxtools using the BioPAX standard elements.
This file is a network with all the core standard elements applied.
The following files are included:
paxtools Output Files:
paxtools produces a number of output files.
The following files are created for a BioPAX file:
paxtools reads the input file, generates a parse graph of the BioPAX file, and applies a series of checks to the model in order to produce metrics for the model.
paxtools generates a series of log files as the model is processed
What’s New in the?
paxtools is the software for generating BioPAX files from other
file formats and compresses them. It also can validate a BioPAX
file and convert BioPAX to other formats. The paxtools library is based on the psort plugin, a data exchange toolkit for the PSI Pathomics project.
paxtools is a GPL compatible software.
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paxtools is an application used for the Data Exchange Format for Biological Pathway Information.
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.
Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data.
By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently.
In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge.
The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
paxtools Description:
paxtools is the software for generating BioPAX files from other
file formats and compresses them. It also can validate a BioPAX
file and convert BioPAX to other formats. The paxtools library is based on the psort plugin, a data exchange toolkit for the PSI Pathomics project.
paxtools is a GPL compatible software.Archive for October, 2009
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